486D Ribosome date Sep 09, 1999
title X-Ray Crystal Structures Of 70s Ribosome Functional Complexe
authors J.H.Cate, M.M.Yusupov, G.Zh.Yusupova, T.N.Earnest, H.F.Noller
compound source
Molecule: P-Site Trna Of 70s Ribosome
Chain: A
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: P-Site Codon Of 70s Ribosome
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Sequence From T. Thermophilus

Molecule: A-Site Trna Of 70s Ribosome
Chain: C

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: A-Site Codon Of 70s Ribosome
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Sequence From T. Thermophilus

Molecule: E-Site Trna Of 70s Ribosome
Chain: E

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Penultimate Stem Of 16s Rrna In The 70s Ribosome
Chain: F

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 900 Stem-Loop Of 16s Rrna In The 70s Ribosome
Chain: G

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: I 4 2 2
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
508.020 508.020 802.790 90.00 90.00 90.00
method X-Ray Diffractionresolution 7.50 Å
ligand 1MA, 1MG, 2MG, 5MC, 5MU, 7MG, H2U, IR, M2G, OMC, PSU, YYG enzyme
Primary referenceX-ray crystal structures of 70S ribosome functional complexes., Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, Noller HF, Science 1999 Sep 24;285(5436):2095-104. PMID:10497122
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (486d.pdb1.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 486D
  • CSU: Contacts of Structural Units for 486D
  • Likely Quarternary Molecular Structure file(s) for 486D
  • Retrieve 486D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 486D from S2C, [Save to disk]
  • View 486D in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 486D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 486D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d486da_, region A [Jmol] [rasmolscript] [script source]
        - Domain d486db_, region B [Jmol] [rasmolscript] [script source]
        - Domain d486dc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d486dd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d486de_, region E [Jmol] [rasmolscript] [script source]
        - Domain d486df_, region F [Jmol] [rasmolscript] [script source]
        - Domain d486dg_, region G [Jmol] [rasmolscript] [script source]
  • Fold representative 486d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [486d_C] [486d_A] [486d] [486d_F] [486d_D] [486d_E] [486d_B] [486d_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 486D
  • Community annotation for 486D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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