5UYM

70S ribosome bound with cognate ternary complex base-paired to A site codon, closed 30S (Structure III)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Ensemble cryo-EM elucidates the mechanism of translation fidelity

Loveland, A.B.Demo, G.Grigorieff, N.Korostelev, A.A.

(2017) Nature 546: 113-117

  • DOI: https://doi.org/10.1038/nature22397
  • Primary Citation of Related Structures:  
    5UYK, 5UYL, 5UYM, 5UYN, 5UYP, 5UYQ

  • PubMed Abstract: 

    Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit. A transient conformation of decoding-centre nucleotide G530 stabilizes the cognate codon-anticodon helix, initiating step-wise 'latching' of the decoding centre. The resulting closure of the 30S subunit docks EF-Tu at the sarcin-ricin loop of the 50S subunit, activating EF-Tu for GTP hydrolysis and enabling accommodation of the aminoacyl-tRNA. By contrast, near-cognate complexes fail to induce the G530 latch, thus favouring open 30S pre-accommodation intermediates with inactive EF-Tu. This work reveals long-sought structural differences between the pre-accommodation of cognate and near-cognate tRNAs that elucidate the mechanism of accurate decoding.


  • Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2A [auth 04]271Escherichia coli K-12Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3B [auth 05]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth 06]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5D [auth 07]177Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6E [auth 08]176Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9F [auth 09]149Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10G [auth 10]131Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11H [auth 11]141Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth 12]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth 13]122Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth 14]143Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth 15]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth 16]120Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18N [auth 17]116Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth 18]114Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth 19]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth 20]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth 21]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth 22]93Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth 23]102Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth 24]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth 25]75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth 26]77Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth 27]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth 28]58Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31Z [auth 29]66Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth 30]56Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth 31]50Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 32]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth 33]64Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth 34]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2FA [auth B]218Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3GA [auth C]206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4HA [auth D]205Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5IA [auth E]157Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6JA [auth F]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7KA [auth G]151Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8LA [auth H]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9MA [auth I]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10NA [auth J]98Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11OA [auth K]116Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12PA [auth L]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13QA [auth M]114Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14RA [auth N]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15SA [auth O]88Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16TA [auth P]82Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17UA [auth Q]80Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18VA [auth R]65Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19WA [auth S]79Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20XA [auth T]85Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21YA [auth U]65Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1ZA [auth 03]223Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu 2HB [auth Z]392Escherichia coli K-12Mutation(s): 0 
Gene Names: tufAb3339JW3301
UniProt
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Entity ID: 53
MoleculeChains LengthOrganismImage
16S ribosomal RNAAB [auth A]1,539Escherichia coli K-12
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Entity ID: 54
MoleculeChains LengthOrganismImage
23S ribosomal RNABB [auth 01]2,903Escherichia coli K-12
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Entity ID: 55
MoleculeChains LengthOrganismImage
5S ribosomal RNACB [auth 02]120Escherichia coli K-12
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Entity ID: 56
MoleculeChains LengthOrganismImage
tRNAfMetDB [auth X],
FB [auth W]
77Escherichia coli K-12
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Entity ID: 57
MoleculeChains LengthOrganismImage
mRNAEB [auth V]18Escherichia coli K-12
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Entity ID: 58
MoleculeChains LengthOrganismImage
Phe-tRNAPheGB [auth Y]76Escherichia coli K-12
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
FQ [auth Z]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
FME
Query on FME

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BQ [auth W]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
PHE
Query on PHE

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DQ [auth Y]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
ZN
Query on ZN

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KB [auth 29],
LB [auth 34]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth 01]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth 01],
AH [auth 01],
AI [auth 01],
AJ [auth 01],
AK [auth 01],
AL [auth 01],
AM [auth 01],
AN [auth 01],
AO [auth 01],
AP [auth 01],
AQ [auth V],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth 01],
BH [auth 01],
BI [auth 01],
BJ [auth 01],
BK [auth 01],
BL [auth 01],
BM [auth 01],
BN [auth 01],
BO [auth 01],
BP [auth 01],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth 01],
CH [auth 01],
CI [auth 01],
CJ [auth 01],
CK [auth 01],
CL [auth 01],
CM [auth 01],
CN [auth 01],
CO [auth 01],
CP [auth 01],
CQ [auth W],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth 01],
DH [auth 01],
DI [auth 01],
DJ [auth 01],
DK [auth 01],
DL [auth 01],
DM [auth 01],
DN [auth 01],
DO [auth 01],
DP [auth 01],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth 01],
EH [auth 01],
EI [auth 01],
EJ [auth 01],
EK [auth 01],
EL [auth 01],
EM [auth 01],
EN [auth 01],
EO [auth 01],
EP [auth 01],
EQ [auth Z],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth 01],
FH [auth 01],
FI [auth 01],
FJ [auth 01],
FK [auth 01],
FL [auth 01],
FM [auth 01],
FN [auth 01],
FO [auth 01],
FP [auth 01],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth 01],
GH [auth 01],
GI [auth 01],
GJ [auth 01],
GK [auth 01],
GL [auth 01],
GM [auth 01],
GN [auth 01],
GO [auth 01],
GP [auth 01],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth 01],
HH [auth 01],
HI [auth 01],
HJ [auth 01],
HK [auth 01],
HL [auth 01],
HM [auth 01],
HN [auth 01],
HO [auth 01],
HP [auth 01],
IB [auth 12],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth 01],
IH [auth 01],
II [auth 01],
IJ [auth 01],
IK [auth 01],
IL [auth 01],
IM [auth 01],
IN [auth 01],
IO [auth 01],
IP [auth 01],
JB [auth 25],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth 01],
JH [auth 01],
JI [auth 01],
JJ [auth 01],
JK [auth 01],
JL [auth 01],
JM [auth 01],
JN [auth 01],
JO [auth 01],
JP [auth 01],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth 01],
KH [auth 01],
KI [auth 01],
KJ [auth 01],
KK [auth 01],
KL [auth 01],
KM [auth 01],
KN [auth 01],
KO [auth 01],
KP [auth 01],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth 01],
LH [auth 01],
LI [auth 01],
LJ [auth 01],
LK [auth 01],
LL [auth 01],
LM [auth 01],
LN [auth 01],
LO [auth 01],
LP [auth 01],
MB [auth N],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth 01],
MH [auth 01],
MI [auth 01],
MJ [auth 01],
MK [auth 01],
ML [auth 01],
MM [auth 01],
MN [auth 01],
MO [auth 01],
MP [auth 01],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth 01],
NH [auth 01],
NI [auth 01],
NJ [auth 01],
NK [auth 01],
NL [auth 01],
NM [auth 01],
NN [auth 01],
NO [auth 01],
NP [auth 01],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth 01],
OH [auth 01],
OI [auth 01],
OJ [auth 01],
OK [auth 01],
OL [auth 01],
OM [auth 01],
ON [auth 01],
OO [auth 01],
OP [auth 01],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth 01],
PH [auth 01],
PI [auth 01],
PJ [auth 01],
PK [auth 01],
PL [auth 01],
PM [auth 01],
PN [auth 01],
PO [auth 01],
PP [auth 01],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth 01],
QG [auth 01],
QH [auth 01],
QI [auth 01],
QJ [auth 01],
QK [auth 01],
QL [auth 01],
QM [auth 01],
QN [auth 01],
QO [auth 01],
QP [auth 01],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth 01],
RG [auth 01],
RH [auth 01],
RI [auth 01],
RJ [auth 01],
RK [auth 01],
RL [auth 01],
RM [auth 01],
RN [auth 01],
RO [auth 01],
RP [auth 01],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth 01],
SG [auth 01],
SH [auth 01],
SI [auth 01],
SJ [auth 01],
SK [auth 01],
SL [auth 01],
SM [auth 01],
SN [auth 01],
SO [auth 01],
SP [auth 01],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth 01],
TG [auth 01],
TH [auth 01],
TI [auth 01],
TJ [auth 01],
TK [auth 01],
TL [auth 01],
TM [auth 01],
TN [auth 01],
TO [auth 01],
TP [auth 02],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth 01],
UG [auth 01],
UH [auth 01],
UI [auth 01],
UJ [auth 01],
UK [auth 01],
UL [auth 01],
UM [auth 01],
UN [auth 01],
UO [auth 01],
UP [auth 02],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth 01],
VG [auth 01],
VH [auth 01],
VI [auth 01],
VJ [auth 01],
VK [auth 01],
VL [auth 01],
VM [auth 01],
VN [auth 01],
VO [auth 01],
VP [auth 02],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth 01],
WG [auth 01],
WH [auth 01],
WI [auth 01],
WJ [auth 01],
WK [auth 01],
WL [auth 01],
WM [auth 01],
WN [auth 01],
WO [auth 01],
WP [auth 02],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth 01],
XG [auth 01],
XH [auth 01],
XI [auth 01],
XJ [auth 01],
XK [auth 01],
XL [auth 01],
XM [auth 01],
XN [auth 01],
XO [auth 01],
XP [auth 02],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth 01],
YG [auth 01],
YH [auth 01],
YI [auth 01],
YJ [auth 01],
YK [auth 01],
YL [auth 01],
YM [auth 01],
YN [auth 01],
YO [auth 01],
YP [auth 02],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth 01],
ZG [auth 01],
ZH [auth 01],
ZI [auth 01],
ZJ [auth 01],
ZK [auth 01],
ZL [auth 01],
ZM [auth 01],
ZN [auth 01],
ZO [auth 01],
ZP [auth V]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRSRef1.1
MODEL REFINEMENTCNS1.3
MODEL REFINEMENTPHENIX1.11
RECONSTRUCTIONFREALIGN9.11

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM106105
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM107465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01 GM62580
Howard Hughes Medical Institute (HHMI)United StatesHoward Hughes Medical Institute Post-Doctoral Fellow of the Helen Hay Whitney Foundation

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations