4V6P

Structural characterization of mRNA-tRNA translocation intermediates (class 4b of the six classes)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.3 of the entry. See complete history. 


Literature

Structural characterization of mRNA-tRNA translocation intermediates.

Agirrezabala, X., Liao, H.Y., Schreiner, E., Fu, J., Ortiz-Meoz, R.F., Schulten, K., Green, R., Frank, J.

(2012) Proc Natl Acad Sci U S A 109: 6094-6099

  • DOI: https://doi.org/10.1073/pnas.1201288109
  • Primary Citation of Related Structures:  
    4V6N, 4V6O, 4V6P, 4V6Q, 4V6R, 4V6S

  • PubMed Abstract: 

    Cryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of translocation, characterized by intermediate intersubunit rotations, L1 stalk positions, and tRNA configurations. Furthermore, we describe the domain rearrangements in quantitative terms, which has allowed us to characterize the processivity and coordination of the conformational reorganization of the ribosome, along with the associated changes in tRNA ribosome-binding configuration. The results are consistent with the view of the ribosome as a molecular machine employing Brownian motion to reach a functionally productive state via a series of substates with incremental changes in conformation.

    • Organizational Affiliation: 

    Structural Biology Unit, CIC-bioGUNE, Bizkaia Technology Park, Derio 48160, Basque Country, Spain.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2E [auth AE]240Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3F [auth AF]232Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4G [auth AG]205Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5H [auth AH]166Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6I [auth AI]135Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7J [auth AJ]178Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8K [auth AK]129Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9L [auth AL]129Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10M [auth AM]103Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11N [auth AN]128Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12O [auth AO]123Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13P [auth AP]117Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14Q [auth AQ]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15R [auth AR]88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16S [auth AS]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17T [auth AT]83Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18U [auth AU]74Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19V [auth AV]91Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20W [auth AW]86Escherichia coliMutation(s): 0 
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Entity ID: 24
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30S ribosomal protein S21X [auth AX]70Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1AA [auth BC]234Sulfolobus acidocaldariusMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L2BA [auth BD]272Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3CA [auth BE]209Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L4DA [auth BF]201Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L5EA [auth BG]178Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth BH]176Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9GA [auth BI]149Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10HA [auth BJ]164Sulfolobus acidocaldariusMutation(s): 0 
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50S ribosomal protein L11IA [auth BK]141Escherichia coliMutation(s): 0 
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50S ribosomal protein L13JA [auth BL]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14KA [auth BM]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15LA [auth BN]144Escherichia coliMutation(s): 0 
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Entity ID: 39
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50S ribosomal protein L16MA [auth BO]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17NA [auth BP]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18OA [auth BQ]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19PA [auth BR]114Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20QA [auth BS]117Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21RA [auth BT]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22SA [auth BU]110Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23TA [auth BV]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24UA [auth BW]103Escherichia coliMutation(s): 0 
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Entity ID: 48
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50S ribosomal protein L25VA [auth BX]94Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27WA [auth BY]84Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28XA [auth BZ]77Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29YA [auth B0]63Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30ZA [auth B1]58Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31AB [auth B2]70Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BB [auth B3]56Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CB [auth B4]54Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DB [auth B5]46Escherichia coliMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EB [auth B6]64Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FB [auth B7]38Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA]1,542Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
A site tRNAB [auth AB]76Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
mRNAC [auth AC]47Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
P site tRNAD [auth AD]77Escherichia coli
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Entity ID: 25
MoleculeChains LengthOrganismImage
5S ribosomal RNAY [auth BA]120Escherichia coli
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Entity ID: 26
MoleculeChains LengthOrganismImage
23S ribosomal RNAZ [auth BB]2,904Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER
RECONSTRUCTIONXmipp

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-01
    Changes: Other
  • Version 2.0: 2018-07-18
    Changes: Data collection, Database references, Polymer sequence
  • Version 3.0: 2019-07-03
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2019-12-18
    Changes: Other
  • Version 3.2: 2023-02-08
    Changes: Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.3: 2024-05-15
    Changes: Data collection, Refinement description