5VO8 Transcription Dna Rna date May 02, 2017
title X-Ray Crystal Structure Of A Bacterial Reiterative Transcrip Complex Of Pyrg Promoter
authors K.S.Murakami, Y.Shin, C.L.Turnbough Jr, V.Molodtsov
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
 Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna (5'- D(Pgpgptpgpcpaptpcpapgpapgpcpcpcpapapapa
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423

Molecule: Dna (5'- D(Tpaptpapaptpgpgpgpcptpgpaptpgpcpapcpc)
Chain: H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423

Molecule: Rna (5'-D((Gtp))-R(Pgpgpgpgpgpgpg)-3')
Chain: I
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: C 1 2 1
R_factor 0.185 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
186.537 101.984 296.113 90.00 98.56 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand GTP, MG, POP, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


    • Primary referenceX-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway., Murakami KS, Shin Y, Turnbough CL Jr, Molodtsov V, Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8211-8216. doi:, 10.1073/pnas.1702741114. Epub 2017 Jun 26. PMID:28652344
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1231 Kb) [Save to disk]
  • Biological Unit Coordinates (5vo8.pdb1.gz) 1218 Kb
  • LPC: Ligand-Protein Contacts for 5VO8
  • CSU: Contacts of Structural Units for 5VO8
  • Structure Factors (2065 Kb)
  • Retrieve 5VO8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VO8 from S2C, [Save to disk]
  • Re-refined 5vo8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VO8 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 5VO8
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vo8_E] [5vo8_I] [5vo8_F] [5vo8_B] [5vo8_A] [5vo8_G] [5vo8] [5vo8_C] [5vo8_H] [5vo8_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VO8
  • Community annotation for 5VO8 at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science