4V5H

E.Coli 70s Ribosome Stalled During Translation Of Tnac Leader Peptide.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

Structural insight into nascent polypeptide chain-mediated translational stalling.

Seidelt, B.Innis, C.A.Wilson, D.N.Gartmann, M.Armache, J.P.Villa, E.Trabuco, L.G.Becker, T.Mielke, T.Schulten, K.Steitz, T.A.Beckmann, R.

(2009) Science 326: 1412-1415

  • DOI: https://doi.org/10.1126/science.1177662
  • Primary Citation of Related Structures:  
    4V5H

  • PubMed Abstract: 

    Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a 5.8 angstrom-resolution cryo-electron microscopy and single-particle reconstruction of a ribosome stalled during translation of the tnaC leader gene. The nascent chain was extended within the exit tunnel, making contacts with ribosomal components at distinct sites. Upon stalling, two conserved residues within the peptidyltransferase center adopted conformations that preclude binding of release factors. We propose a model whereby interactions within the tunnel are relayed to the peptidyltransferase center to inhibit translation. Moreover, we show that nascent chains adopt distinct conformations within the ribosomal exit tunnel.


  • Organizational Affiliation

    Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department for Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B [auth AB]218Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C [auth AC]206Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D [auth AD]205Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E [auth AE]150Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F [auth AF]100Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G [auth AG]150Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H [auth AH]129Escherichia coliMutation(s): 0 
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Entity ID: 9
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30S RIBOSOMAL PROTEIN S9I [auth AI]127Escherichia coliMutation(s): 0 
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S10J [auth AJ]98Escherichia coliMutation(s): 0 
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S11K [auth AK]117Escherichia coliMutation(s): 0 
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S12L [auth AL]123Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M [auth AM]113Escherichia coliMutation(s): 0 
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S14N [auth AN]96Escherichia coliMutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S15O [auth AO]88Escherichia coliMutation(s): 0 
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Entity ID: 16
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30S RIBOSOMAL PROTEIN S16P [auth AP]80Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q [auth AQ]80Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R [auth AR]55Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S [auth AS]79Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20T [auth AT]85Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S21U [auth AU]51Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
POLY-ALA NASCENT CHAINX [auth AZ]20Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28Y [auth B0]77Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29Z [auth B1]63Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30AA [auth B2]58Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32BA [auth B3]56Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33CA [auth B4]50Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1DA [auth B5]234Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34EA [auth B6]46Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35FA [auth B7]64Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S RIBOSOMAL PROTEIN L36GA [auth B8]38Escherichia coliMutation(s): 0 
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Entity ID: 36
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50S RIBOSOMAL PROTEIN L2JA [auth BC]271Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3KA [auth BD]209Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L4LA [auth BE]201Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L5MA [auth BF]178Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L6NA [auth BG]176Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L9OA [auth BH]149Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L11PA [auth BI]141Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L13QA [auth BJ]142Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L14RA [auth BK]121Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L15SA [auth BL]143Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L16TA [auth BM]136Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L17UA [auth BN]120Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L18VA [auth BO]116Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L19WA [auth BP]114Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20XA [auth BQ]117Escherichia coliMutation(s): 0 
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UniProt GroupP0A7L3
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21YA [auth BR]103Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
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UniProt GroupP0AG48
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22ZA [auth BS]110Escherichia coliMutation(s): 0 
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23AB [auth BT]93Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24BB [auth BU]102Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25CB [auth BW]94Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27DB [auth BY]79Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNAA [auth AA]1,530Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-SITE TRNAV [auth AV]77Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
MRNAW [auth AX]11synthetic construct
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Entity ID: 34
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAHA [auth BA]117Escherichia coli
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Entity ID: 35
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAIA [auth BB]2,903Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

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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: 2015-02-04
    Changes: Other
  • Version 1.3: 2015-03-18
    Changes: Other
  • Version 1.4: 2017-07-26
    Changes: Data collection, Derived calculations
  • Version 1.5: 2018-04-18
    Changes: Data collection, Database references, Other, Source and taxonomy
  • Version 1.6: 2019-12-11
    Changes: Derived calculations, Other
  • Version 1.7: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description