7M5D

Cryo-EM structure of a non-rotated E.coli 70S ribosome in complex with RF3-GTP, RF1 and P-tRNA (state I)

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-03-23 Released: 2022-10-19 
  • Deposition Author(s): Zhang, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Cryo-EM structure of a non-rotated E.coli 70S ribosome in complex with RF3-GTP, RF1 and P-tRNA (state I)

Zhang, J.

To be published.

Macromolecules

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2F [auth B]271Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3G [auth C]209Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4H [auth D]201Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5I [auth E]177Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6J [auth F]175Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9K [auth G]149Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13L [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14M [auth K]123Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15N [auth L]144Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16O [auth M]136Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17P [auth N]119Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18Q [auth O]116Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19R [auth P]114Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20S [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21T [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22U [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23V [auth T]94Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24W [auth U]103Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25X [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Y [auth W]76Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Z [auth X]77Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29AA [auth Y]62Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30BA [auth Z]58Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31CA [auth a]66Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DA [auth b]56Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33EA [auth c]52Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34FA [auth d]46Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35GA [auth e]64Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36HA [auth f]38Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth g]225Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth h]208Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth i]205Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth j]156Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth k]104Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth l]151Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth m]129Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth n]127Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth o]99Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth p]117Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth q]123Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth r]116Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14UA [auth s]100Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth t]88Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth u]82Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth v]80Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth w]66Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth x]83Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth y]86Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21BB [auth z]70Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 3CB [auth 7]525Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7I4 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11DB [auth I]141Escherichia coliMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EB [auth H]131Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 1FB [auth A]360Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
FME-PHE-PHEGB [auth 6]3Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 1]2,903Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
16S ribosomal RNAB [auth 2]1,534Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth 3]120Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
mRNAD [auth 4]15Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
P-tRNAE [auth 5]76Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
HB [auth a]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
0TD
Query on 0TD		SA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
FME
Query on FME		GB [auth 6]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-10-19 
    • Deposition Author(s): Zhang, J.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release