4V47

Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the EF-G.GTP state of E. coli 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.3 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

Study of the structural dynamics of the E. coli 70S ribosome using real space refinement

Gao, H.Sengupta, J.Valle, M.Korostelev, A.Eswar, N.Stagg, S.M.Van Roey, P.Agrawal, R.K.Harvey, S.T.Sali, A.Chapman, M.S.Frank, J.

(2003) Cell 113: 789-801

  • DOI: 10.1016/s0092-8674(03)00427-6
  • Primary Citation of Related Structures:  
    4V47, 4V48

  • PubMed Abstract: 
  • Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from ...

    Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from a compact structure to a looser one, coupled with the rearrangement of many of the proteins. Furthermore, in contrast to the unchanged inter-subunit bridges formed wholly by RNA, the bridges involving proteins undergo large conformational changes following the ratchet-like motion, suggesting an important role of ribosomal proteins in facilitating the dynamics of translation.


    Related Citations: 
    • Solution structure of the E. coli 70S ribosome at 11.5 A resolution
      Gabashvili, I.S., Agrawal, R.K., Spahn, C.M.T., Grassucci, R., Svergun, D.I., Frank, J., Penczek, P.
      (2000) Cell 100: 537
    • A ratchet-like inter-subunit reorganization of the ribosome during translocation
      Frank, J., Agrawal, R.K.
      (2000) Nature 406: 318

    Organizational Affiliation

    Howard Hughes Medical Institute, Health Research, Inc, Empire State Plaza, Albany, NY 12201, USA.



Macromolecules

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Entity ID: 3
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50S ribosomal protein L2AA272Escherichia coliMutation(s): 0 
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50S ribosomal protein L3AB209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4AC201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5AD178Escherichia coliMutation(s): 0 
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50S ribosomal protein L6AE176Escherichia coliMutation(s): 0 
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50S ribosomal protein L9AF149Escherichia coliMutation(s): 0 
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50S ribosomal protein L11AG141Escherichia coliMutation(s): 0 
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50S ribosomal protein L13AH142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14AI123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15AJ144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16AK136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17AL127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18AM117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19AN114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20AO117Escherichia coliMutation(s): 0 
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50S ribosomal protein L22AQ110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23AR100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24AS103Escherichia coliMutation(s): 0 
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50S ribosomal protein L25AT94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27AU84Escherichia coliMutation(s): 0 
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50S ribosomal protein L29AW63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30AX58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32AZ56Escherichia coliMutation(s): 0 
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50S ribosomal protein L33A154Escherichia coliMutation(s): 0 
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50S ribosomal protein L36A438Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S3BC232Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S4BD205Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S5BE166Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S6BF135Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S7BG178Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S8BH129Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S9BI129Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S10BJ103Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S11BK128Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S12BL123Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S13BM117Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S14BN100Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S15BO88Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S16BP82Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S17BQ83Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S18BR74Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S19BS91Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S20BT86Escherichia coliMutation(s): 0 
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23S ribosomal RNAA02904Escherichia coli
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5S ribosomal RNAA9120Escherichia coli
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16S RIBOSOMAL RNABA1542Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.3 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: 2015-03-18
    Changes: Other
  • Version 1.3: 2018-01-24
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2019-12-18
    Changes: Other