2VQE Ribosome date Mar 13, 2008
title Modified Uridines With C5-Methylene Substituents At The Firs Of The Trna Anticodon Stabilize U-G Wobble Pairing During D
authors S.Kurata, A.Weixlbaumer, T.Ohtsuki, T.Shimazaki, T.Wada, Y.Kirino K.Watanabe, V.Ramakrishnan, T.Suzuki
compound source
Molecule: 16s Rrna
Chain: A
Other_details: Chain A (16s Rna) Has E.Coli Numbering, Base Structural Alignment With The Corresponding E.Coli Structur
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S2
Chain: B
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S3
Chain: C
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S4
Chain: D
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S5
Chain: E
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Ts9
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S7
Chain: G
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S8
Chain: H
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S9
Chain: I
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S10
Chain: J
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S11
Chain: K
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S12
Chain: L
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S13
Chain: M
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S14 Type Z
Chain: N
Synonym: 30s Ribosomal Protein S14
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S15
Chain: O
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S17
Chain: Q
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S18
Chain: R
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S19
Chain: S
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S20
Chain: T
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein Thx
Chain: U
Synonym: S31
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 5'-R(Upupapapapap)-3'
Chain: X
Synonym: Rna
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 5'-R(Gpcpapupgpcpuptm2papapap Apcpapupgpcp)-3';
Chain: Y
Synonym: Rna
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 41 21 2
R_factor 0.257 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
401.998 401.998 175.648 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand K, MG, PAR, TM2, ZN enzyme
note 2VQE is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


Primary referenceModified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding., Kurata S, Weixlbaumer A, Ohtsuki T, Shimazaki T, Wada T, Kirino Y, Takai K, Watanabe K, Ramakrishnan V, Suzuki T, J Biol Chem. 2008 Jul 4;283(27):18801-11. Epub 2008 May 2. PMID:18456657
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1045 Kb) [Save to disk]
  • Biological Unit Coordinates (2vqe.pdb1.gz) 1024 Kb
  • LPC: Ligand-Protein Contacts for 2VQE
  • CSU: Contacts of Structural Units for 2VQE
  • Likely Quarternary Molecular Structure file(s) for 2VQE
  • Structure Factors (4882 Kb)
  • Retrieve 2VQE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VQE from S2C, [Save to disk]
  • Re-refined 2vqe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VQE 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 2VQE
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2VQE, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vqe_G] [2vqe_D] [2vqe_T] [2vqe_E] [2vqe_M] [2vqe_I] [2vqe_S] [2vqe_X] [2vqe_B] [2vqe_O] [2vqe_L] [2vqe_K] [2vqe_J] [2vqe_Q] [2vqe_P] [2vqe_Y] [2vqe_N] [2vqe] [2vqe_H] [2vqe_F] [2vqe_A] [2vqe_C] [2vqe_U] [2vqe_R]
  • SWISS-PROT database: [Q5SHN7] [P80376] [Q5SHN3] [P80377] [Q5SHQ1] [Q5SJ76] [Q5SJH3] [P24321] [P80382] [Q5SHP2] [P62661] [P80371] [P80372] [P80373] [Q5SHQ5] [Q5SLP8] [P17291] [Q5SHQ2] [P62669] [Q5SIH3]
  • Domain organization of [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THETH] [RS18_THETH] [RS19_THET8] [RS20_THET2] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET2] [RSHX_THET8] by SWISSPFAM
  • Domains found in 2VQE: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 2VQE
  • Community annotation for 2VQE 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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