486D

X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.5 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


  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
P-SITE TRNA OF 70S RIBOSOMEA74Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
P-SITE CODON OF 70S RIBOSOMEB3N/A
Entity ID: 3
MoleculeChainsLengthOrganism
A-SITE TRNA OF 70S RIBOSOMEC72Saccharomyces cerevisiae
Entity ID: 4
MoleculeChainsLengthOrganism
A-SITE CODON OF 70S RIBOSOMED3N/A
Entity ID: 5
MoleculeChainsLengthOrganism
E-SITE TRNA OF 70S RIBOSOMEE72Thermus thermophilus
Entity ID: 6
MoleculeChainsLengthOrganism
PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOMEF85Thermus thermophilus
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 SDF File 
Download CCD File 
F
IRIDIUM ION
Ir
MOHYGSBMXIJZBJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A, C, E
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A, C, E
RNA LINKINGC10 H16 N3 O8 PC
1MG
Query on 1MG
C, E
RNA LINKINGC11 H16 N5 O8 PG
M2G
Query on M2G
A, C
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
C
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
A
RNA LINKINGC10 H16 N3 O8 PC
YYG
Query on YYG
A
RNA LINKINGC21 H29 N6 O12 PG
2MG
Query on 2MG
C
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
C
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
A, C, E
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
A, C, E
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.5 Å
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 508.020α = 90.00
b = 508.020β = 90.00
c = 802.790γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
Omodel building
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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