4V6N

Structural characterization of mRNA-tRNA translocation intermediates (50S ribosome of class2 of the six classes)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.1 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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1AC234Sulfolobus acidocaldariusMutation(s): 0 
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Entity ID: 4
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50S ribosomal protein L2AD272Escherichia coliMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L3AE209Escherichia coliMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L4AF201Escherichia coliMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L5AG178Escherichia coliMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L6AH176Escherichia coliMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L9AI149Escherichia coliMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L10AJ164Sulfolobus acidocaldariusMutation(s): 0 
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50S ribosomal protein L11AK141Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L13AL142Escherichia coliMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L14AM123Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L15AN144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16AO136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17AP127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18AQ117Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L19AR114Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L20AS117Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L21AT103Escherichia coliMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L22AU110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23AV100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24AW103Escherichia coliMutation(s): 0 
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50S ribosomal protein L25AX94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27AY84Escherichia coliMutation(s): 0 
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50S ribosomal protein L28AZ77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29A063Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L30A158Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L31A270Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L32A356Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L33A454Escherichia coliMutation(s): 0 
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50S ribosomal protein L34A546Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L35A664Escherichia coliMutation(s): 0 
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Entity ID: 34
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50S ribosomal protein L36A738Escherichia coliMutation(s): 0 
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Entity ID: 39
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30S ribosomal protein S2BE240Escherichia coliMutation(s): 0 
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Entity ID: 40
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30S ribosomal protein S3BF232Escherichia coliMutation(s): 0 
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Entity ID: 41
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30S ribosomal protein S4BG205Escherichia coliMutation(s): 0 
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Entity ID: 42
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30S ribosomal protein S5BH166Escherichia coliMutation(s): 0 
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Entity ID: 43
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30S ribosomal protein S6BI135Escherichia coliMutation(s): 0 
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30S ribosomal protein S7BJ178Escherichia coliMutation(s): 0 
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30S ribosomal protein S8BK129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9BL129Escherichia coliMutation(s): 0 
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30S ribosomal protein S10BM103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11BN128Escherichia coliMutation(s): 0 
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30S ribosomal protein S12BO123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13BP117Escherichia coliMutation(s): 0 
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Entity ID: 51
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30S ribosomal protein S14BQ100Escherichia coliMutation(s): 0 
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Entity ID: 52
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30S ribosomal protein S15BR88Escherichia coliMutation(s): 0 
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Entity ID: 53
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30S ribosomal protein S16BS82Escherichia coliMutation(s): 0 
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Entity ID: 54
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30S ribosomal protein S17BT83Escherichia coliMutation(s): 0 
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Entity ID: 55
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30S ribosomal protein S18BU74Escherichia coliMutation(s): 0 
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Entity ID: 56
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30S ribosomal protein S19BV91Escherichia coliMutation(s): 0 
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Entity ID: 57
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30S ribosomal protein S20BW86Escherichia coliMutation(s): 0 
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Entity ID: 58
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30S ribosomal protein S21BX70Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5S ribosomal RNAAA120Escherichia coli
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Entity ID: 2
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23S ribosomal RNAAB2904Escherichia coli
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Entity ID: 35
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16S ribosomal RNABA1542Escherichia coli
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A site tRNABB76Escherichia coli
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Entity ID: 37
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mRNABC47Escherichia coli
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Entity ID: 38
MoleculeChainsLengthOrganismImage
P site tRNABD77Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.1 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