5AFI

2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 3.1 of the entry. See complete history


Literature

Structure of the E. coli ribosome-EF-Tu complex at <3 angstrom resolution by Cs-corrected cryo-EM.

Fischer, N.Neumann, P.Konevega, A.L.Bock, L.V.Ficner, R.Rodnina, M.V.Stark, H.

(2015) Nature 520: 567-570

  • DOI: https://doi.org/10.1038/nature14275
  • Primary Citation of Related Structures:  
    5AFI

  • PubMed Abstract: 

    Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes.


  • Organizational Affiliation

    3D Electron Cryomicroscopy Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]240Escherichia coliMutation(s): 0 
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Entity ID: 3
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30S ribosomal protein S3C [auth c]233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]135Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]179Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]130Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth j]103Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]129Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]124Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]118Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth n]102Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth o]89Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]82Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]84Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]75Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]92Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]87Escherichia coliMutation(s): 0 
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Entity ID: 21
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30S ribosomal protein S21U [auth u]71Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu 2Z [auth z]393Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2CA [auth C]273Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L3DA [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L4EA [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5FA [auth F]179Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6GA [auth G]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L9HA [auth H]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L11IA [auth I]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13JA [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 36
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50S ribosomal protein L14KA [auth K]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15LA [auth L]144Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16MA [auth M]136Escherichia coliMutation(s): 0 
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Entity ID: 39
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50S ribosomal protein L17NA [auth N]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18OA [auth O]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19PA [auth P]115Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20QA [auth Q]118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21RA [auth R]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22SA [auth S]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23TA [auth T]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24UA [auth U]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25VA [auth V]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27WA [auth W]85Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28XA [auth X]78Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29YA [auth Y]63Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30ZA [auth Z]59Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AB [auth 0]57Escherichia coliMutation(s): 0 
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UniProt GroupP0A7N4
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BB [auth 1]55Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CB [auth 2]46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DB [auth 3]65Escherichia coliMutation(s): 0 
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Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EB [auth 4]38Escherichia coliMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10FB [auth 5]165Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7J3 (Escherichia coli (strain K12))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31GB [auth 6]70Escherichia coliMutation(s): 0 
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Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth a]1,539Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-site fMet-tRNAfMetV [auth v],
W [auth w]
77Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
mRNAX [auth x]11Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
A/T-site Phe-tRNAPheY [auth y]77Escherichia coli
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Entity ID: 26
MoleculeChains LengthOrganismImage
23S ribosomal RNAAA [auth A]2,903Escherichia coli
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Entity ID: 27
MoleculeChains LengthOrganismImage
5S ribosomal RNABA [auth B]120Escherichia coli
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KIR
Query on KIR

Download Ideal Coordinates CCD File 
SE [auth z]KIRROMYCIN
C43 H60 N2 O12
HMSYAPGFKGSXAJ-PAHGNTJYSA-N
GDP
Query on GDP

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TE [auth z]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
FME
Query on FME

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RE [auth v]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
ZN
Query on ZN

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JO [auth 4],
KO [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

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ED [auth a],
PK [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AC [auth a]
AD [auth a]
AE [auth a]
AF [auth A]
AG [auth A]
AC [auth a],
AD [auth a],
AE [auth a],
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth A],
AJ [auth A],
AK [auth A],
AL [auth A],
AM [auth A],
AN [auth A],
AO [auth B],
BC [auth a],
BD [auth a],
BE [auth a],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth A],
BM [auth A],
BN [auth A],
BO [auth B],
CC [auth a],
CD [auth a],
CE [auth a],
CF [auth A],
CG [auth A],
CH [auth A],
CI [auth A],
CJ [auth A],
CK [auth A],
CL [auth A],
CM [auth A],
CN [auth A],
CO [auth B],
DC [auth a],
DD [auth a],
DE [auth a],
DF [auth A],
DG [auth A],
DH [auth A],
DI [auth A],
DJ [auth A],
DK [auth A],
DL [auth A],
DM [auth A],
DN [auth A],
DO [auth B],
EC [auth a],
EE [auth a],
EF [auth A],
EG [auth A],
EH [auth A],
EI [auth A],
EJ [auth A],
EK [auth A],
EL [auth A],
EM [auth A],
EN [auth A],
FC [auth a],
FD [auth a],
FE [auth a],
FF [auth A],
FG [auth A],
FH [auth A],
FI [auth A],
FJ [auth A],
FK [auth A],
FL [auth A],
FM [auth A],
FN [auth A],
FO [auth N],
GC [auth a],
GD [auth a],
GE [auth a],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth A],
GJ [auth A],
GK [auth A],
GL [auth A],
GM [auth A],
GN [auth A],
GO [auth N],
HB [auth a],
HC [auth a],
HD [auth a],
HE [auth a],
HF [auth A],
HG [auth A],
HH [auth A],
HI [auth A],
HJ [auth A],
HK [auth A],
HL [auth A],
HM [auth A],
HN [auth A],
HO [auth 0],
IB [auth a],
IC [auth a],
ID [auth a],
IE [auth a],
IF [auth A],
IG [auth A],
IH [auth A],
II [auth A],
IJ [auth A],
IK [auth A],
IL [auth A],
IM [auth A],
IN [auth A],
IO [auth 4],
JB [auth a],
JC [auth a],
JD [auth a],
JE [auth a],
JF [auth A],
JG [auth A],
JH [auth A],
JI [auth A],
JJ [auth A],
JK [auth A],
JL [auth A],
JM [auth A],
JN [auth A],
KB [auth a],
KC [auth a],
KD [auth a],
KE [auth a],
KF [auth A],
KG [auth A],
KH [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
KL [auth A],
KM [auth A],
KN [auth A],
LB [auth a],
LC [auth a],
LD [auth a],
LE [auth a],
LF [auth A],
LG [auth A],
LH [auth A],
LI [auth A],
LJ [auth A],
LK [auth A],
LL [auth A],
LM [auth A],
LN [auth A],
MB [auth a],
MC [auth a],
MD [auth a],
ME [auth a],
MF [auth A],
MG [auth A],
MH [auth A],
MI [auth A],
MJ [auth A],
MK [auth A],
ML [auth A],
MM [auth A],
MN [auth A],
NB [auth a],
NC [auth a],
ND [auth a],
NE [auth v],
NF [auth A],
NG [auth A],
NH [auth A],
NI [auth A],
NJ [auth A],
NK [auth A],
NL [auth A],
NM [auth A],
NN [auth A],
OB [auth a],
OC [auth a],
OD [auth a],
OE [auth v],
OF [auth A],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth A],
OK [auth A],
OL [auth A],
OM [auth A],
ON [auth A],
PB [auth a],
PC [auth a],
PD [auth a],
PE [auth v],
PF [auth A],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth A],
PL [auth A],
PM [auth A],
PN [auth A],
QB [auth a],
QC [auth a],
QD [auth a],
QE [auth v],
QF [auth A],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth A],
QK [auth A],
QL [auth A],
QM [auth A],
QN [auth A],
RB [auth a],
RC [auth a],
RD [auth a],
RF [auth A],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth A],
RK [auth A],
RL [auth A],
RM [auth A],
RN [auth A],
SB [auth a],
SC [auth a],
SD [auth a],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth A],
SL [auth A],
SM [auth A],
SN [auth A],
TB [auth a],
TC [auth a],
TD [auth a],
TF [auth A],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth A],
TK [auth A],
TL [auth A],
TM [auth A],
TN [auth A],
UB [auth a],
UC [auth a],
UD [auth a],
UE [auth z],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth A],
UL [auth A],
UM [auth A],
UN [auth A],
VB [auth a],
VC [auth a],
VD [auth a],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth A],
VK [auth A],
VL [auth A],
VM [auth A],
WB [auth a],
WC [auth a],
WD [auth a],
WE [auth A],
WF [auth A],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth A],
WK [auth A],
WL [auth A],
WM [auth A],
WN [auth A],
XB [auth a],
XC [auth a],
XD [auth a],
XE [auth A],
XF [auth A],
XG [auth A],
XH [auth A],
XI [auth A],
XJ [auth A],
XK [auth A],
XL [auth A],
XM [auth A],
XN [auth B],
YB [auth a],
YC [auth a],
YD [auth a],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth A],
YI [auth A],
YJ [auth A],
YK [auth A],
YL [auth A],
YM [auth A],
YN [auth B],
ZB [auth a],
ZC [auth a],
ZD [auth a],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth A],
ZI [auth A],
ZJ [auth A],
ZK [auth A],
ZL [auth A],
ZM [auth A],
ZN [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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EO [auth B],
VN [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONCustom
RECONSTRUCTIONIMAGIC5
RECONSTRUCTIONRELION1.2

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Atomic model, Derived calculations
  • Version 1.2: 2017-08-02
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2017-08-09
    Changes: Structure summary
  • Version 2.0: 2019-02-20
    Changes: Data collection, Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2019-06-26
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 3.1: 2019-12-18
    Changes: Other