4V4W

Structure of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements

Mitra, K.Schaffitzel, C.Fabiola, F.Chapman, M.S.Ban, N.Frank, J.

(2006) Mol Cell 22: 533-543

  • DOI: 10.1016/j.molcel.2006.05.003
  • Primary Citation of Related Structures:  
    4V4V, 4V4W

  • PubMed Abstract: 
  • In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron ...

    In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron microscopy reconstructions of a pretranslocational and SecM-stalled E. coli ribosome complex. A cascade of RNA rearrangements propagates from the exit tunnel throughout the large subunit, affecting intersubunit bridges and tRNA positions, which in turn reorient small subunit RNA elements. Elongation arrest could result from the inhibition of mRNA.(tRNAs) translocation, E site tRNA egress, and perhaps translation factor activation at the GTPase-associated center. Our study suggests that the specific secondary and tertiary arrangement of ribosomal RNA provides the basis for internal signal transduction within the ribosome. Thus, the ribosome may itself have the ability to regulate its progression through translation by modulating its structure and consequently its receptivity to activation by cofactors.


    Related Citations: 
    • Structure of the E. coli protein-conducting channel bound to a translating ribosome
      Mitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks III, C.L., Ban, N., Frank, J.
      (2005) Nature 438: 318
    • Locking and unlocking of ribosomal motions
      Valle, M., Zavialov, A.V., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J.
      (2003) Cell 114: 123
    • A model for co-translational translocation: ribosome-regulated nascent polypeptide translocation at the protein-conducting channel
      Mitra, K., Frank, J.
      (2006) FEBS Lett 580: 3353

    Organizational Affiliation

    Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, Empire State Plaza, Albany, New York 12201, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal subunit protein S2AB236Escherichia coliMutation(s): 0 
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Entity ID: 4
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30S ribosomal subunit protein S3AC206Escherichia coliMutation(s): 0 
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Entity ID: 5
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30S ribosomal subunit protein S4AD204Escherichia coliMutation(s): 0 
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Entity ID: 6
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30S ribosomal subunit protein S5AE148Escherichia coliMutation(s): 0 
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Entity ID: 7
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30S ribosomal subunit protein S6AF95Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S7AG137Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S8AH127Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S9AI126Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S10AJ96Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S11AK116Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S12AL101Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S13AM115Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S14AN61Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S15AO86Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S16AP78Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S17AQ79Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S18AR69Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S19AS87Escherichia coliMutation(s): 0 
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30S ribosomal subunit protein S20AT83Escherichia coliMutation(s): 0 
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50S ribosomal protein L1B2222Escherichia coliMutation(s): 0 
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50S ribosomal protein L7/L12B3B5119Escherichia coliMutation(s): 0 
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50S ribosomal protein L2BA227Escherichia coliMutation(s): 0 
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50S ribosomal protein L3BB209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4BC198Escherichia coliMutation(s): 0 
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50S ribosomal protein L5BD177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6BE167Escherichia coliMutation(s): 0 
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50S ribosomal protein L9BF149Escherichia coliMutation(s): 0 
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50S ribosomal protein L11BG139Escherichia coliMutation(s): 0 
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50S ribosomal protein L13BH142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14BI122Escherichia coliMutation(s): 0 
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50S ribosomal protein L15BJ140Escherichia coliMutation(s): 0 
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50S ribosomal protein L16BK131Escherichia coliMutation(s): 0 
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50S ribosomal protein L17BL114Escherichia coliMutation(s): 0 
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50S ribosomal protein L18BM113Escherichia coliMutation(s): 0 
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50S ribosomal protein L19BN114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20BO115Escherichia coliMutation(s): 0 
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50S ribosomal protein L22BQ106Escherichia coliMutation(s): 0 
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50S ribosomal protein L23BR92Escherichia coliMutation(s): 0 
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50S ribosomal protein L24BS99Escherichia coliMutation(s): 0 
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50S ribosomal protein L25BT94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27BU84Escherichia coliMutation(s): 0 
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50S ribosomal protein L29BW60Escherichia coliMutation(s): 0 
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50S ribosomal protein L30BX56Escherichia coliMutation(s): 0 
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50S ribosomal protein L32BZ29Escherichia coliMutation(s): 0 
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50S ribosomal protein L33B152Escherichia coliMutation(s): 0 
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Entity ID: 1
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16S ribosomal RNAAA1488Escherichia coli
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tRNAAU, AV, AW76Escherichia coli
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Entity ID: 22
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23S ribosomal RNAB02740Escherichia coli
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5S ribosomal RNAB9108Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-05-09 
  • Released Date: 2014-07-09 
  • Deposition Author(s): Mitra, K., Frank, J.
  • This entry supersedes: 2GYB, 2GYC

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-18
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Other