2VQF Ribosome date Mar 14, 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(Upupgpapapap)-3'
Chain: X
Synonym: Rna
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 5'-R(Gpcpapupgpcputm2papapap Apcpap 3';
Chain: Y
Synonym: Rna
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 41 21 2
R_factor 0.223 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
402.481 402.481 175.969 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand K, MG, PAR, TM2, ZN enzyme
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] (1047 Kb) [Save to disk]
  • Biological Unit Coordinates (2vqf.pdb1.gz) 1025 Kb
  • LPC: Ligand-Protein Contacts for 2VQF
  • CSU: Contacts of Structural Units for 2VQF
  • Likely Quarternary Molecular Structure file(s) for 2VQF
  • Structure Factors (2871 Kb)
  • Retrieve 2VQF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VQF from S2C, [Save to disk]
  • Re-refined 2vqf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VQF 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 2VQF
  • 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 2VQF, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vqf_M] [2vqf_O] [2vqf_K] [2vqf_T] [2vqf_R] [2vqf_U] [2vqf_L] [2vqf_N] [2vqf_J] [2vqf_H] [2vqf_A] [2vqf_S] [2vqf_F] [2vqf_D] [2vqf] [2vqf_Y] [2vqf_E] [2vqf_Q] [2vqf_G] [2vqf_C] [2vqf_I] [2vqf_X] [2vqf_P] [2vqf_B]
  • 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 2VQF: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 2VQF
  • Community annotation for 2VQF 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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