5WFS

70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.

Fislage, M.Zhang, J.Brown, Z.P.Mandava, C.S.Sanyal, S.Ehrenberg, M.Frank, J.

(2018) Nucleic Acids Res 46: 5861-5874

  • DOI: https://doi.org/10.1093/nar/gky346
  • Primary Citation of Related Structures:  
    5WDT, 5WE4, 5WE6, 5WF0, 5WFK, 5WFS

  • PubMed Abstract: 

    The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2271Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3208Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4200Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5177Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6174Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9149Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11141Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13141Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14122Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15143Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16136Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17119Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18116Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19114Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20115Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21102Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22109Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2392Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24102Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2592Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2775Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2877Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2960Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3056Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth 0]55Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth 1]51Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 2]45Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth 3]64Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36 1EA [auth 4]38Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10FA [auth 5]131Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31GA [auth 6]66Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth b]218Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth c]206Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth d]205Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth e]157Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth f]100Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth g]151Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth h]129Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth i]127Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth j]98Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth k]116Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth l]121Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth m]115Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14UA [auth n]101Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth o]88Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth p]82Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth q]80Escherichia coliMutation(s): 0 
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Find proteins for P0AG63 (Escherichia coli (strain K12))
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UniProt GroupP0AG63
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth r]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7T7
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth s]79Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7U3
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth t]85Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7U7
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21BB [auth u]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68679
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu 2GB [auth z]393Escherichia coliMutation(s): 1 
UniProt
Find proteins for P0CE48 (Escherichia coli (strain K12))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CE48
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNA2,903Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNA120Escherichia coli
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Entity ID: 34
MoleculeChains LengthOrganismImage
16S rRNAHA [auth a]1,540Escherichia coli
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Entity ID: 55
MoleculeChains LengthOrganismImage
tRNA-fMetCB [auth v],
DB [auth w]
77Escherichia coli
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Entity ID: 56
MoleculeChains LengthOrganismImage
mRNAEB [auth x]12Escherichia coli
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Entity ID: 57
MoleculeChains LengthOrganismImage
Phe-tRNA-PheFB [auth y]76Escherichia coli
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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DGB [auth z]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
FME
Query on FME

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HB [auth A]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
PHE
Query on PHE

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CGB [auth z]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
K
Query on K

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COA [auth A]
DOA [auth A]
EOA [auth A]
FOA [auth A]
GOA [auth A]
COA [auth A],
DOA [auth A],
EOA [auth A],
FOA [auth A],
GOA [auth A],
HOA [auth A],
LFB [auth a]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AAA [auth A]
AAB [auth a]
ABA [auth A]
ABB [auth a]
AC [auth A]
AAA [auth A],
AAB [auth a],
ABA [auth A],
ABB [auth a],
AC [auth A],
ACA [auth A],
ACB [auth a],
AD [auth A],
ADA [auth A],
ADB [auth a],
AE [auth A],
AEA [auth A],
AEB [auth a],
AF [auth A],
AFA [auth A],
AFB [auth a],
AG [auth A],
AGA [auth A],
AGB [auth y],
AH [auth A],
AHA [auth A],
AI [auth A],
AIA [auth A],
AJ [auth A],
AJA [auth A],
AK [auth A],
AKA [auth A],
AL [auth A],
ALA [auth A],
AM [auth A],
AMA [auth A],
AN [auth A],
ANA [auth A],
AO [auth A],
AOA [auth A],
AP [auth A],
APA [auth B],
AQ [auth A],
AQA [auth M],
AR [auth A],
ARA [auth a],
AS [auth A],
ASA [auth a],
AT [auth A],
ATA [auth a],
AU [auth A],
AUA [auth a],
AV [auth A],
AVA [auth a],
AW [auth A],
AWA [auth a],
AX [auth A],
AXA [auth a],
AY [auth A],
AYA [auth a],
AZ [auth A],
AZA [auth a],
BAA [auth A],
BAB [auth a],
BBA [auth A],
BBB [auth a],
BC [auth A],
BCA [auth A],
BCB [auth a],
BD [auth A],
BDA [auth A],
BDB [auth a],
BE [auth A],
BEA [auth A],
BEB [auth a],
BF [auth A],
BFA [auth A],
BFB [auth a],
BG [auth A],
BGA [auth A],
BGB [auth y],
BH [auth A],
BHA [auth A],
BI [auth A],
BIA [auth A],
BJ [auth A],
BJA [auth A],
BK [auth A],
BKA [auth A],
BL [auth A],
BLA [auth A],
BM [auth A],
BMA [auth A],
BN [auth A],
BNA [auth A],
BO [auth A],
BOA [auth A],
BP [auth A],
BPA [auth B],
BQ [auth A],
BQA [auth M],
BR [auth A],
BRA [auth a],
BS [auth A],
BSA [auth a],
BT [auth A],
BTA [auth a],
BU [auth A],
BUA [auth a],
BV [auth A],
BVA [auth a],
BW [auth A],
BWA [auth a],
BX [auth A],
BXA [auth a],
BY [auth A],
BYA [auth a],
BZ [auth A],
BZA [auth a],
CAA [auth A],
CAB [auth a],
CBA [auth A],
CBB [auth a],
CC [auth A],
CCA [auth A],
CCB [auth a],
CD [auth A],
CDA [auth A],
CDB [auth a],
CE [auth A],
CEA [auth A],
CEB [auth a],
CF [auth A],
CFA [auth A],
CFB [auth a],
CG [auth A],
CGA [auth A],
CH [auth A],
CHA [auth A],
CI [auth A],
CIA [auth A],
CJ [auth A],
CJA [auth A],
CK [auth A],
CKA [auth A],
CL [auth A],
CLA [auth A],
CM [auth A],
CMA [auth A],
CN [auth A],
CNA [auth A],
CO [auth A],
CP [auth A],
CPA [auth B],
CQ [auth A],
CQA [auth N],
CR [auth A],
CRA [auth a],
CS [auth A],
CSA [auth a],
CT [auth A],
CTA [auth a],
CU [auth A],
CUA [auth a],
CV [auth A],
CVA [auth a],
CW [auth A],
CWA [auth a],
CX [auth A],
CXA [auth a],
CY [auth A],
CYA [auth a],
CZ [auth A],
CZA [auth a],
DAA [auth A],
DAB [auth a],
DBA [auth A],
DBB [auth a],
DC [auth A],
DCA [auth A],
DCB [auth a],
DD [auth A],
DDA [auth A],
DDB [auth a],
DE [auth A],
DEA [auth A],
DEB [auth a],
DF [auth A],
DFA [auth A],
DFB [auth a],
DG [auth A],
DGA [auth A],
DH [auth A],
DHA [auth A],
DI [auth A],
DIA [auth A],
DJ [auth A],
DJA [auth A],
DK [auth A],
DKA [auth A],
DL [auth A],
DLA [auth A],
DM [auth A],
DMA [auth A],
DN [auth A],
DNA [auth A],
DO [auth A],
DP [auth A],
DPA [auth B],
DQ [auth A],
DQA [auth Q],
DR [auth A],
DRA [auth a],
DS [auth A],
DSA [auth a],
DT [auth A],
DTA [auth a],
DU [auth A],
DUA [auth a],
DV [auth A],
DVA [auth a],
DW [auth A],
DWA [auth a],
DX [auth A],
DXA [auth a],
DY [auth A],
DYA [auth a],
DZ [auth A],
DZA [auth a],
EAA [auth A],
EAB [auth a],
EBA [auth A],
EBB [auth a],
EC [auth A],
ECA [auth A],
ECB [auth a],
ED [auth A],
EDA [auth A],
EDB [auth a],
EE [auth A],
EEA [auth A],
EEB [auth a],
EF [auth A],
EFA [auth A],
EFB [auth a],
EG [auth A],
EGA [auth A],
EGB [auth z],
EH [auth A],
EHA [auth A],
EI [auth A],
EIA [auth A],
EJ [auth A],
EJA [auth A],
EK [auth A],
EKA [auth A],
EL [auth A],
ELA [auth A],
EM [auth A],
EMA [auth A],
EN [auth A],
ENA [auth A],
EO [auth A],
EP [auth A],
EPA [auth B],
EQ [auth A],
EQA [auth T],
ER [auth A],
ERA [auth a],
ES [auth A],
ESA [auth a],
ET [auth A],
ETA [auth a],
EU [auth A],
EUA [auth a],
EV [auth A],
EVA [auth a],
EW [auth A],
EWA [auth a],
EX [auth A],
EXA [auth a],
EY [auth A],
EYA [auth a],
EZ [auth A],
EZA [auth a],
FAA [auth A],
FAB [auth a],
FBA [auth A],
FBB [auth a],
FC [auth A],
FCA [auth A],
FCB [auth a],
FD [auth A],
FDA [auth A],
FDB [auth a],
FE [auth A],
FEA [auth A],
FEB [auth a],
FF [auth A],
FFA [auth A],
FFB [auth a],
FG [auth A],
FGA [auth A],
FGB [auth z],
FH [auth A],
FHA [auth A],
FI [auth A],
FIA [auth A],
FJ [auth A],
FJA [auth A],
FK [auth A],
FKA [auth A],
FL [auth A],
FLA [auth A],
FM [auth A],
FMA [auth A],
FN [auth A],
FNA [auth A],
FO [auth A],
FP [auth A],
FPA [auth B],
FQ [auth A],
FQA [auth W],
FR [auth A],
FRA [auth a],
FS [auth A],
FSA [auth a],
FT [auth A],
FTA [auth a],
FU [auth A],
FUA [auth a],
FV [auth A],
FVA [auth a],
FW [auth A],
FWA [auth a],
FX [auth A],
FXA [auth a],
FY [auth A],
FYA [auth a],
FZ [auth A],
FZA [auth a],
GAA [auth A],
GAB [auth a],
GBA [auth A],
GBB [auth a],
GC [auth A],
GCA [auth A],
GCB [auth a],
GD [auth A],
GDA [auth A],
GDB [auth a],
GE [auth A],
GEA [auth A],
GEB [auth a],
GF [auth A],
GFA [auth A],
GFB [auth a],
GG [auth A],
GGA [auth A],
GH [auth A],
GHA [auth A],
GI [auth A],
GIA [auth A],
GJ [auth A],
GJA [auth A],
GK [auth A],
GKA [auth A],
GL [auth A],
GLA [auth A],
GM [auth A],
GMA [auth A],
GN [auth A],
GNA [auth A],
GO [auth A],
GP [auth A],
GPA [auth B],
GQ [auth A],
GQA [auth 0],
GR [auth A],
GRA [auth a],
GS [auth A],
GSA [auth a],
GT [auth A],
GTA [auth a],
GU [auth A],
GUA [auth a],
GV [auth A],
GVA [auth a],
GW [auth A],
GWA [auth a],
GX [auth A],
GXA [auth a],
GY [auth A],
GYA [auth a],
GZ [auth A],
GZA [auth a],
HAA [auth A],
HAB [auth a],
HBA [auth A],
HBB [auth a],
HC [auth A],
HCA [auth A],
HCB [auth a],
HD [auth A],
HDA [auth A],
HDB [auth a],
HE [auth A],
HEA [auth A],
HEB [auth a],
HF [auth A],
HFA [auth A],
HFB [auth a],
HG [auth A],
HGA [auth A],
HH [auth A],
HHA [auth A],
HI [auth A],
HIA [auth A],
HJ [auth A],
HJA [auth A],
HK [auth A],
HKA [auth A],
HL [auth A],
HLA [auth A],
HM [auth A],
HMA [auth A],
HN [auth A],
HNA [auth A],
HO [auth A],
HP [auth A],
HPA [auth B],
HQ [auth A],
HQA [auth 0],
HR [auth A],
HRA [auth a],
HS [auth A],
HSA [auth a],
HT [auth A],
HTA [auth a],
HU [auth A],
HUA [auth a],
HV [auth A],
HVA [auth a],
HW [auth A],
HWA [auth a],
HX [auth A],
HXA [auth a],
HY [auth A],
HYA [auth a],
HZ [auth A],
HZA [auth a],
IAA [auth A],
IAB [auth a],
IB [auth A],
IBA [auth A],
IBB [auth a],
IC [auth A],
ICA [auth A],
ICB [auth a],
ID [auth A],
IDA [auth A],
IDB [auth a],
IE [auth A],
IEA [auth A],
IEB [auth a],
IF [auth A],
IFA [auth A],
IFB [auth a],
IG [auth A],
IGA [auth A],
IH [auth A],
IHA [auth A],
II [auth A],
IIA [auth A],
IJ [auth A],
IJA [auth A],
IK [auth A],
IKA [auth A],
IL [auth A],
ILA [auth A],
IM [auth A],
IMA [auth A],
IN [auth A],
INA [auth A],
IO [auth A],
IOA [auth A],
IP [auth A],
IPA [auth B],
IQ [auth A],
IQA [auth 0],
IR [auth A],
IRA [auth a],
IS [auth A],
ISA [auth a],
IT [auth A],
ITA [auth a],
IU [auth A],
IUA [auth a],
IV [auth A],
IVA [auth a],
IW [auth A],
IWA [auth a],
IX [auth A],
IXA [auth a],
IY [auth A],
IYA [auth a],
IZ [auth A],
IZA [auth a],
JAA [auth A],
JAB [auth a],
JB [auth A],
JBA [auth A],
JBB [auth a],
JC [auth A],
JCA [auth A],
JCB [auth a],
JD [auth A],
JDA [auth A],
JDB [auth a],
JE [auth A],
JEA [auth A],
JEB [auth a],
JF [auth A],
JFA [auth A],
JFB [auth a],
JG [auth A],
JGA [auth A],
JH [auth A],
JHA [auth A],
JI [auth A],
JIA [auth A],
JJ [auth A],
JJA [auth A],
JK [auth A],
JKA [auth A],
JL [auth A],
JLA [auth A],
JM [auth A],
JMA [auth A],
JN [auth A],
JNA [auth A],
JO [auth A],
JOA [auth A],
JP [auth A],
JPA [auth B],
JQ [auth A],
JQA [auth 2],
JR [auth A],
JRA [auth a],
JS [auth A],
JSA [auth a],
JT [auth A],
JTA [auth a],
JU [auth A],
JUA [auth a],
JV [auth A],
JVA [auth a],
JW [auth A],
JWA [auth a],
JX [auth A],
JXA [auth a],
JY [auth A],
JYA [auth a],
JZ [auth A],
JZA [auth a],
KAA [auth A],
KAB [auth a],
KB [auth A],
KBA [auth A],
KBB [auth a],
KC [auth A],
KCA [auth A],
KCB [auth a],
KD [auth A],
KDA [auth A],
KDB [auth a],
KE [auth A],
KEA [auth A],
KEB [auth a],
KF [auth A],
KFA [auth A],
KFB [auth a],
KG [auth A],
KGA [auth A],
KH [auth A],
KHA [auth A],
KI [auth A],
KIA [auth A],
KJ [auth A],
KJA [auth A],
KK [auth A],
KKA [auth A],
KL [auth A],
KLA [auth A],
KM [auth A],
KMA [auth A],
KN [auth A],
KNA [auth A],
KO [auth A],
KOA [auth A],
KP [auth A],
KPA [auth B],
KQ [auth A],
KQA [auth a],
KR [auth A],
KRA [auth a],
KS [auth A],
KSA [auth a],
KT [auth A],
KTA [auth a],
KU [auth A],
KUA [auth a],
KV [auth A],
KVA [auth a],
KW [auth A],
KWA [auth a],
KX [auth A],
KXA [auth a],
KY [auth A],
KYA [auth a],
KZ [auth A],
KZA [auth a],
LAA [auth A],
LAB [auth a],
LB [auth A],
LBA [auth A],
LBB [auth a],
LC [auth A],
LCA [auth A],
LCB [auth a],
LD [auth A],
LDA [auth A],
LDB [auth a],
LE [auth A],
LEA [auth A],
LEB [auth a],
LF [auth A],
LFA [auth A],
LG [auth A],
LGA [auth A],
LH [auth A],
LHA [auth A],
LI [auth A],
LIA [auth A],
LJ [auth A],
LJA [auth A],
LK [auth A],
LKA [auth A],
LL [auth A],
LLA [auth A],
LM [auth A],
LMA [auth A],
LN [auth A],
LNA [auth A],
LO [auth A],
LOA [auth B],
LP [auth A],
LPA [auth B],
LQ [auth A],
LQA [auth a],
LR [auth A],
LRA [auth a],
LS [auth A],
LSA [auth a],
LT [auth A],
LTA [auth a],
LU [auth A],
LUA [auth a],
LV [auth A],
LVA [auth a],
LW [auth A],
LWA [auth a],
LX [auth A],
LXA [auth a],
LY [auth A],
LYA [auth a],
LZ [auth A],
LZA [auth a],
MAA [auth A],
MAB [auth a],
MB [auth A],
MBA [auth A],
MBB [auth a],
MC [auth A],
MCA [auth A],
MCB [auth a],
MD [auth A],
MDA [auth A],
MDB [auth a],
ME [auth A],
MEA [auth A],
MEB [auth a],
MF [auth A],
MFA [auth A],
MFB [auth a],
MG [auth A],
MGA [auth A],
MH [auth A],
MHA [auth A],
MI [auth A],
MIA [auth A],
MJ [auth A],
MJA [auth A],
MK [auth A],
MKA [auth A],
ML [auth A],
MLA [auth A],
MM [auth A],
MMA [auth A],
MN [auth A],
MNA [auth A],
MO [auth A],
MOA [auth B],
MP [auth A],
MPA [auth B],
MQ [auth A],
MQA [auth a],
MR [auth A],
MRA [auth a],
MS [auth A],
MSA [auth a],
MT [auth A],
MTA [auth a],
MU [auth A],
MUA [auth a],
MV [auth A],
MVA [auth a],
MW [auth A],
MWA [auth a],
MX [auth A],
MXA [auth a],
MY [auth A],
MYA [auth a],
MZ [auth A],
MZA [auth a],
NAA [auth A],
NAB [auth a],
NB [auth A],
NBA [auth A],
NBB [auth a],
NC [auth A],
NCA [auth A],
NCB [auth a],
ND [auth A],
NDA [auth A],
NDB [auth a],
NE [auth A],
NEA [auth A],
NEB [auth a],
NF [auth A],
NFA [auth A],
NFB [auth d],
NG [auth A],
NGA [auth A],
NH [auth A],
NHA [auth A],
NI [auth A],
NIA [auth A],
NJ [auth A],
NJA [auth A],
NK [auth A],
NKA [auth A],
NL [auth A],
NLA [auth A],
NM [auth A],
NMA [auth A],
NN [auth A],
NNA [auth A],
NO [auth A],
NOA [auth B],
NP [auth A],
NPA [auth B],
NQ [auth A],
NQA [auth a],
NR [auth A],
NRA [auth a],
NS [auth A],
NSA [auth a],
NT [auth A],
NTA [auth a],
NU [auth A],
NUA [auth a],
NV [auth A],
NVA [auth a],
NW [auth A],
NWA [auth a],
NX [auth A],
NXA [auth a],
NY [auth A],
NYA [auth a],
NZ [auth A],
NZA [auth a],
OAA [auth A],
OAB [auth a],
OB [auth A],
OBA [auth A],
OBB [auth a],
OC [auth A],
OCA [auth A],
OCB [auth a],
OD [auth A],
ODA [auth A],
ODB [auth a],
OE [auth A],
OEA [auth A],
OEB [auth a],
OF [auth A],
OFA [auth A],
OFB [auth e],
OG [auth A],
OGA [auth A],
OH [auth A],
OHA [auth A],
OI [auth A],
OIA [auth A],
OJ [auth A],
OJA [auth A],
OK [auth A],
OKA [auth A],
OL [auth A],
OLA [auth A],
OM [auth A],
OMA [auth A],
ON [auth A],
ONA [auth A],
OO [auth A],
OOA [auth B],
OP [auth A],
OPA [auth B],
OQ [auth A],
OQA [auth a],
OR [auth A],
ORA [auth a],
OS [auth A],
OSA [auth a],
OT [auth A],
OTA [auth a],
OU [auth A],
OUA [auth a],
OV [auth A],
OVA [auth a],
OW [auth A],
OWA [auth a],
OX [auth A],
OXA [auth a],
OY [auth A],
OYA [auth a],
OZ [auth A],
OZA [auth a],
PAA [auth A],
PAB [auth a],
PB [auth A],
PBA [auth A],
PBB [auth a],
PC [auth A],
PCA [auth A],
PCB [auth a],
PD [auth A],
PDA [auth A],
PDB [auth a],
PE [auth A],
PEA [auth A],
PEB [auth a],
PF [auth A],
PFA [auth A],
PFB [auth i],
PG [auth A],
PGA [auth A],
PH [auth A],
PHA [auth A],
PI [auth A],
PIA [auth A],
PJ [auth A],
PJA [auth A],
PK [auth A],
PKA [auth A],
PL [auth A],
PLA [auth A],
PM [auth A],
PMA [auth A],
PN [auth A],
PNA [auth A],
PO [auth A],
POA [auth B],
PP [auth A],
PPA [auth B],
PQ [auth A],
PQA [auth a],
PR [auth A],
PRA [auth a],
PS [auth A],
PSA [auth a],
PT [auth A],
PTA [auth a],
PU [auth A],
PUA [auth a],
PV [auth A],
PVA [auth a],
PW [auth A],
PWA [auth a],
PX [auth A],
PXA [auth a],
PY [auth A],
PYA [auth a],
PZ [auth A],
PZA [auth a],
QAA [auth A],
QAB [auth a],
QB [auth A],
QBA [auth A],
QBB [auth a],
QC [auth A],
QCA [auth A],
QCB [auth a],
QD [auth A],
QDA [auth A],
QDB [auth a],
QE [auth A],
QEA [auth A],
QEB [auth a],
QF [auth A],
QFA [auth A],
QFB [auth u],
QG [auth A],
QGA [auth A],
QH [auth A],
QHA [auth A],
QI [auth A],
QIA [auth A],
QJ [auth A],
QJA [auth A],
QK [auth A],
QKA [auth A],
QL [auth A],
QLA [auth A],
QM [auth A],
QMA [auth A],
QN [auth A],
QNA [auth A],
QO [auth A],
QOA [auth B],
QP [auth A],
QPA [auth B],
QQ [auth A],
QQA [auth a],
QR [auth A],
QRA [auth a],
QS [auth A],
QSA [auth a],
QT [auth A],
QTA [auth a],
QU [auth A],
QUA [auth a],
QV [auth A],
QVA [auth a],
QW [auth A],
QWA [auth a],
QX [auth A],
QXA [auth a],
QY [auth A],
QYA [auth a],
QZ [auth A],
QZA [auth a],
RAA [auth A],
RAB [auth a],
RB [auth A],
RBA [auth A],
RBB [auth a],
RC [auth A],
RCA [auth A],
RCB [auth a],
RD [auth A],
RDA [auth A],
RDB [auth a],
RE [auth A],
REA [auth A],
REB [auth a],
RF [auth A],
RFA [auth A],
RFB [auth v],
RG [auth A],
RGA [auth A],
RH [auth A],
RHA [auth A],
RI [auth A],
RIA [auth A],
RJ [auth A],
RJA [auth A],
RK [auth A],
RKA [auth A],
RL [auth A],
RLA [auth A],
RM [auth A],
RMA [auth A],
RN [auth A],
RNA [auth A],
RO [auth A],
ROA [auth B],
RP [auth A],
RPA [auth B],
RQ [auth A],
RQA [auth a],
RR [auth A],
RRA [auth a],
RS [auth A],
RSA [auth a],
RT [auth A],
RTA [auth a],
RU [auth A],
RUA [auth a],
RV [auth A],
RVA [auth a],
RW [auth A],
RWA [auth a],
RX [auth A],
RXA [auth a],
RY [auth A],
RYA [auth a],
RZ [auth A],
RZA [auth a],
SAA [auth A],
SAB [auth a],
SB [auth A],
SBA [auth A],
SBB [auth a],
SC [auth A],
SCA [auth A],
SCB [auth a],
SD [auth A],
SDA [auth A],
SDB [auth a],
SE [auth A],
SEA [auth A],
SEB [auth a],
SF [auth A],
SFA [auth A],
SFB [auth v],
SG [auth A],
SGA [auth A],
SH [auth A],
SHA [auth A],
SI [auth A],
SIA [auth A],
SJ [auth A],
SJA [auth A],
SK [auth A],
SKA [auth A],
SL [auth A],
SLA [auth A],
SM [auth A],
SMA [auth A],
SN [auth A],
SNA [auth A],
SO [auth A],
SOA [auth B],
SP [auth A],
SPA [auth B],
SQ [auth A],
SQA [auth a],
SR [auth A],
SRA [auth a],
SS [auth A],
SSA [auth a],
ST [auth A],
STA [auth a],
SU [auth A],
SUA [auth a],
SV [auth A],
SVA [auth a],
SW [auth A],
SWA [auth a],
SX [auth A],
SXA [auth a],
SY [auth A],
SYA [auth a],
SZ [auth A],
SZA [auth a],
TAA [auth A],
TAB [auth a],
TB [auth A],
TBA [auth A],
TBB [auth a],
TC [auth A],
TCA [auth A],
TCB [auth a],
TD [auth A],
TDA [auth A],
TDB [auth a],
TE [auth A],
TEA [auth A],
TEB [auth a],
TF [auth A],
TFA [auth A],
TFB [auth v],
TG [auth A],
TGA [auth A],
TH [auth A],
THA [auth A],
TI [auth A],
TIA [auth A],
TJ [auth A],
TJA [auth A],
TK [auth A],
TKA [auth A],
TL [auth A],
TLA [auth A],
TM [auth A],
TMA [auth A],
TN [auth A],
TNA [auth A],
TO [auth A],
TOA [auth B],
TP [auth A],
TPA [auth B],
TQ [auth A],
TQA [auth a],
TR [auth A],
TRA [auth a],
TS [auth A],
TSA [auth a],
TT [auth A],
TTA [auth a],
TU [auth A],
TUA [auth a],
TV [auth A],
TVA [auth a],
TW [auth A],
TWA [auth a],
TX [auth A],
TXA [auth a],
TY [auth A],
TYA [auth a],
TZ [auth A],
TZA [auth a],
UAA [auth A],
UAB [auth a],
UB [auth A],
UBA [auth A],
UBB [auth a],
UC [auth A],
UCA [auth A],
UCB [auth a],
UD [auth A],
UDA [auth A],
UDB [auth a],
UE [auth A],
UEA [auth A],
UEB [auth a],
UF [auth A],
UFA [auth A],
UFB [auth v],
UG [auth A],
UGA [auth A],
UH [auth A],
UHA [auth A],
UI [auth A],
UIA [auth A],
UJ [auth A],
UJA [auth A],
UK [auth A],
UKA [auth A],
UL [auth A],
ULA [auth A],
UM [auth A],
UMA [auth A],
UN [auth A],
UNA [auth A],
UO [auth A],
UOA [auth B],
UP [auth A],
UPA [auth B],
UQ [auth A],
UQA [auth a],
UR [auth A],
URA [auth a],
US [auth A],
USA [auth a],
UT [auth A],
UTA [auth a],
UU [auth A],
UUA [auth a],
UV [auth A],
UVA [auth a],
UW [auth A],
UWA [auth a],
UX [auth A],
UXA [auth a],
UY [auth A],
UYA [auth a],
UZ [auth A],
UZA [auth a],
VAA [auth A],
VAB [auth a],
VB [auth A],
VBA [auth A],
VBB [auth a],
VC [auth A],
VCA [auth A],
VCB [auth a],
VD [auth A],
VDA [auth A],
VDB [auth a],
VE [auth A],
VEA [auth A],
VEB [auth a],
VF [auth A],
VFA [auth A],
VFB [auth v],
VG [auth A],
VGA [auth A],
VH [auth A],
VHA [auth A],
VI [auth A],
VIA [auth A],
VJ [auth A],
VJA [auth A],
VK [auth A],
VKA [auth A],
VL [auth A],
VLA [auth A],
VM [auth A],
VMA [auth A],
VN [auth A],
VNA [auth A],
VO [auth A],
VOA [auth B],
VP [auth A],
VPA [auth B],
VQ [auth A],
VQA [auth a],
VR [auth A],
VRA [auth a],
VS [auth A],
VSA [auth a],
VT [auth A],
VTA [auth a],
VU [auth A],
VUA [auth a],
VV [auth A],
VVA [auth a],
VW [auth A],
VWA [auth a],
VX [auth A],
VXA [auth a],
VY [auth A],
VYA [auth a],
VZ [auth A],
VZA [auth a],
WAA [auth A],
WAB [auth a],
WB [auth A],
WBA [auth A],
WBB [auth a],
WC [auth A],
WCA [auth A],
WCB [auth a],
WD [auth A],
WDA [auth A],
WDB [auth a],
WE [auth A],
WEA [auth A],
WEB [auth a],
WF [auth A],
WFA [auth A],
WFB [auth v],
WG [auth A],
WGA [auth A],
WH [auth A],
WHA [auth A],
WI [auth A],
WIA [auth A],
WJ [auth A],
WJA [auth A],
WK [auth A],
WKA [auth A],
WL [auth A],
WLA [auth A],
WM [auth A],
WMA [auth A],
WN [auth A],
WNA [auth A],
WO [auth A],
WOA [auth B],
WP [auth A],
WPA [auth C],
WQ [auth A],
WQA [auth a],
WR [auth A],
WRA [auth a],
WS [auth A],
WSA [auth a],
WT [auth A],
WTA [auth a],
WU [auth A],
WUA [auth a],
WV [auth A],
WVA [auth a],
WW [auth A],
WWA [auth a],
WX [auth A],
WXA [auth a],
WY [auth A],
WYA [auth a],
WZ [auth A],
WZA [auth a],
XAA [auth A],
XAB [auth a],
XB [auth A],
XBA [auth A],
XBB [auth a],
XC [auth A],
XCA [auth A],
XCB [auth a],
XD [auth A],
XDA [auth A],
XDB [auth a],
XE [auth A],
XEA [auth A],
XEB [auth a],
XF [auth A],
XFA [auth A],
XFB [auth w],
XG [auth A],
XGA [auth A],
XH [auth A],
XHA [auth A],
XI [auth A],
XIA [auth A],
XJ [auth A],
XJA [auth A],
XK [auth A],
XKA [auth A],
XL [auth A],
XLA [auth A],
XM [auth A],
XMA [auth A],
XN [auth A],
XNA [auth A],
XO [auth A],
XOA [auth B],
XP [auth A],
XPA [auth D],
XQ [auth A],
XQA [auth a],
XR [auth A],
XRA [auth a],
XS [auth A],
XSA [auth a],
XT [auth A],
XTA [auth a],
XU [auth A],
XUA [auth a],
XV [auth A],
XVA [auth a],
XW [auth A],
XWA [auth a],
XX [auth A],
XXA [auth a],
XY [auth A],
XYA [auth a],
XZ [auth A],
XZA [auth a],
YAA [auth A],
YAB [auth a],
YB [auth A],
YBA [auth A],
YBB [auth a],
YC [auth A],
YCA [auth A],
YCB [auth a],
YD [auth A],
YDA [auth A],
YDB [auth a],
YE [auth A],
YEA [auth A],
YEB [auth a],
YF [auth A],
YFA [auth A],
YFB [auth w],
YG [auth A],
YGA [auth A],
YH [auth A],
YHA [auth A],
YI [auth A],
YIA [auth A],
YJ [auth A],
YJA [auth A],
YK [auth A],
YKA [auth A],
YL [auth A],
YLA [auth A],
YM [auth A],
YMA [auth A],
YN [auth A],
YNA [auth A],
YO [auth A],
YOA [auth B],
YP [auth A],
YPA [auth D],
YQ [auth A],
YQA [auth a],
YR [auth A],
YRA [auth a],
YS [auth A],
YSA [auth a],
YT [auth A],
YTA [auth a],
YU [auth A],
YUA [auth a],
YV [auth A],
YVA [auth a],
YW [auth A],
YWA [auth a],
YX [auth A],
YXA [auth a],
YY [auth A],
YYA [auth a],
YZ [auth A],
YZA [auth a],
ZAA [auth A],
ZAB [auth a],
ZB [auth A],
ZBA [auth A],
ZBB [auth a],
ZC [auth A],
ZCA [auth A],
ZCB [auth a],
ZD [auth A],
ZDA [auth A],
ZDB [auth a],
ZE [auth A],
ZEA [auth A],
ZEB [auth a],
ZF [auth A],
ZFA [auth A],
ZFB [auth x],
ZG [auth A],
ZGA [auth A],
ZH [auth A],
ZHA [auth A],
ZI [auth A],
ZIA [auth A],
ZJ [auth A],
ZJA [auth A],
ZK [auth A],
ZKA [auth A],
ZL [auth A],
ZLA [auth A],
ZM [auth A],
ZMA [auth A],
ZN [auth A],
ZNA [auth A],
ZO [auth A],
ZOA [auth B],
ZP [auth A],
ZPA [auth E],
ZQ [auth A],
ZQA [auth a],
ZR [auth A],
ZRA [auth a],
ZS [auth A],
ZSA [auth a],
ZT [auth A],
ZTA [auth a],
ZU [auth A],
ZUA [auth a],
ZV [auth A],
ZVA [auth a],
ZW [auth A],
ZWA [auth a],
ZX [auth A],
ZXA [auth a],
ZY [auth A],
ZYA [auth a],
ZZ [auth A],
ZZA [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2
MODEL REFINEMENTREFMAC5.7

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM29169

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2019-07-03
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2019-11-20
    Changes: Author supporting evidence
  • Version 2.2: 2024-03-13
    Changes: Data collection, Database references