486D

X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.50 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray crystal structures of 70S ribosome functional complexes.

Cate, J.H.Yusupov, M.M.Yusupova, G.Z.Earnest, T.N.Noller, H.F.

(1999) Science 285: 2095-2104

  • DOI: 10.1126/science.285.5436.2095
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Structures of 70S ribosome complexes containing messenger RNA and transfer RNA (tRNA), or tRNA analogs, have been solved by x-ray crystallography at up to 7.8 angstrom resolution. Many details of the interactions between tRNA and the ribosome, and of ...

    Structures of 70S ribosome complexes containing messenger RNA and transfer RNA (tRNA), or tRNA analogs, have been solved by x-ray crystallography at up to 7.8 angstrom resolution. Many details of the interactions between tRNA and the ribosome, and of the packing arrangements of ribosomal RNA (rRNA) helices in and between the ribosomal subunits, can be seen. Numerous contacts are made between the 30S subunit and the P-tRNA anticodon stem-loop; in contrast, the anticodon region of A-tRNA is much more exposed. A complex network of molecular interactions suggestive of a functional relay is centered around the long penultimate stem of 16S rRNA at the subunit interface, including interactions involving the "switch" helix and decoding site of 16S rRNA, and RNA bridges from the 50S subunit.


    Related Citations: 
    • Identification of an RNA-Protein Bridge Spanning the Ribosomal Subunit Interface
      Culver, G.M., Cate, J.H., Yusupova, G.Z., Yusupov, M.M., Noller, H.F.
      (1999) Science 285: 2133

    Organizational Affiliation

    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA. cate@wi.mit.edu



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
P-SITE TRNA OF 70S RIBOSOMEA74Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganism
P-SITE CODON OF 70S RIBOSOMEB3N/A

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Entity ID: 3
MoleculeChainsLengthOrganism
A-SITE TRNA OF 70S RIBOSOMEC72Saccharomyces cerevisiae
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Entity ID: 4
MoleculeChainsLengthOrganism
A-SITE CODON OF 70S RIBOSOMED3N/A

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Entity ID: 5
MoleculeChainsLengthOrganism
E-SITE TRNA OF 70S RIBOSOMEE72Thermus thermophilus

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Entity ID: 6
MoleculeChainsLengthOrganism
PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOMEF85Thermus thermophilus

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Entity ID: 7
MoleculeChainsLengthOrganism
900 STEM-LOOP OF 16S RRNA IN THE 70S RIBOSOMEG33Thermus thermophilus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IR
Query on IR

Download CCD File 
F
IRIDIUM ION
Ir
MOHYGSBMXIJZBJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.50 Å
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 508.02α = 90
b = 508.02β = 90
c = 802.79γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
Omodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance