4V6R

Structural characterization of mRNA-tRNA translocation intermediates (class 6 of the six classes)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.1 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: 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 intersub ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2AE240Escherichia coliMutation(s): 0 
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Entity ID: 6
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30S ribosomal protein S3AF232Escherichia coliMutation(s): 0 
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Entity ID: 7
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30S ribosomal protein S4AG205Escherichia coliMutation(s): 0 
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Entity ID: 8
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30S ribosomal protein S5AH166Escherichia coliMutation(s): 0 
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Entity ID: 9
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30S ribosomal protein S6AI135Escherichia coliMutation(s): 0 
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30S ribosomal protein S7AJ178Escherichia coliMutation(s): 0 
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Entity ID: 11
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30S ribosomal protein S8AK129Escherichia coliMutation(s): 0 
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Entity ID: 12
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30S ribosomal protein S9AL129Escherichia coliMutation(s): 0 
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30S ribosomal protein S10AM103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11AN128Escherichia coliMutation(s): 0 
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Entity ID: 15
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30S ribosomal protein S12AO123Escherichia coliMutation(s): 0 
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Entity ID: 16
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30S ribosomal protein S13AP117Escherichia coliMutation(s): 0 
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Entity ID: 17
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30S ribosomal protein S14AQ100Escherichia coliMutation(s): 0 
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Entity ID: 18
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30S ribosomal protein S15AR88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16AS82Escherichia coliMutation(s): 0 
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Entity ID: 20
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30S ribosomal protein S17AT83Escherichia coliMutation(s): 0 
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30S ribosomal protein S18AU74Escherichia coliMutation(s): 0 
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30S ribosomal protein S19AV91Escherichia coliMutation(s): 0 
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Entity ID: 23
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30S ribosomal protein S20AW86Escherichia coliMutation(s): 0 
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30S ribosomal protein S21AX70Escherichia coliMutation(s): 0 
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50S ribosomal protein L1BC234Sulfolobus acidocaldariusMutation(s): 0 
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50S ribosomal protein L2BD272Escherichia coliMutation(s): 0 
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50S ribosomal protein L3BE209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4BF201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5BG178Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L6BH176Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L9BI149Escherichia coliMutation(s): 0 
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Entity ID: 34
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50S ribosomal protein L10BJ164Sulfolobus acidocaldariusMutation(s): 0 
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50S ribosomal protein L11BK141Escherichia coliMutation(s): 0 
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Entity ID: 36
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50S ribosomal protein L13BL142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14BM123Escherichia coliMutation(s): 0 
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Entity ID: 38
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50S ribosomal protein L15BN144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16BO136Escherichia coliMutation(s): 0 
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Entity ID: 40
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50S ribosomal protein L17BP127Escherichia coliMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L18BQ117Escherichia coliMutation(s): 0 
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Entity ID: 42
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50S ribosomal protein L19BR114Escherichia coliMutation(s): 0 
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Entity ID: 43
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50S ribosomal protein L20BS117Escherichia coliMutation(s): 0 
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Entity ID: 44
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50S ribosomal protein L21BT103Escherichia coliMutation(s): 0 
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Entity ID: 45
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50S ribosomal protein L22BU110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23BV100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24BW103Escherichia coliMutation(s): 0 
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50S ribosomal protein L25BX94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27BY84Escherichia coliMutation(s): 0 
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50S ribosomal protein L28BZ77Escherichia coliMutation(s): 0 
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Entity ID: 51
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50S ribosomal protein L29B063Escherichia coliMutation(s): 0 
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Entity ID: 52
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50S ribosomal protein L30B158Escherichia coliMutation(s): 0 
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Entity ID: 53
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50S ribosomal protein L31B270Escherichia coliMutation(s): 0 
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Entity ID: 54
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50S ribosomal protein L32B356Escherichia coliMutation(s): 0 
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Entity ID: 55
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50S ribosomal protein L33B454Escherichia coliMutation(s): 0 
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Entity ID: 56
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50S ribosomal protein L34B546Escherichia coliMutation(s): 0 
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Entity ID: 57
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50S ribosomal protein L35B664Escherichia coliMutation(s): 0 
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Entity ID: 58
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50S ribosomal protein L36B738Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAAA1542Escherichia coli
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Entity ID: 2
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A site tRNAAB76Escherichia coli
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mRNAAC47Escherichia coli
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P site tRNAAD77Escherichia coli
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Entity ID: 25
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5S ribomosomal RNABA120Escherichia coli
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Entity ID: 26
MoleculeChainsLengthOrganismImage
23S ribomosomal RNABB2904Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download CCD File 
AB
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
FME
Query on FME

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BB
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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