4WQS Transferase Dna Rna date Oct 22, 2014
title Thermus Thermophilus Rna Polymerase Backtracked Complex
authors Y.Murayama, S.Sekine, S.Yokoyama
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, K, L
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, M
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, N
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E, O
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: Dna (28-Mer)
Chain: G, X
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

Molecule: Rna (5'- R(Pcpcpapgpcpcpgpgpcpgpcpupcpgpcpa)-3');
Chain: H, Y
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

Molecule: Dna (5'- D(Pgptpapgpcptptpgptpgpgptpapgptpgpapcpg 3');
Chain: I, Z
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644
symmetry Space Group: P 41
R_factor 0.281 R_Free 0.311
crystal
cell
length a length b length c angle alpha angle beta angle gamma
155.983 155.983 495.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.31 Å
ligand ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


M, C


N, D


O, E


Primary referenceThe ratcheted and ratchetable structural States of RNA polymerase underlie multiple transcriptional functions., Sekine S, Murayama Y, Svetlov V, Nudler E, Yokoyama S, Mol Cell. 2015 Feb 5;57(3):408-21. doi: 10.1016/j.molcel.2014.12.014. Epub 2015, Jan 15. PMID:25601758
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (938 Kb) [Save to disk]
  • Biological Unit Coordinates (4wqs.pdb1.gz) 461 Kb
  • Biological Unit Coordinates (4wqs.pdb2.gz) 479 Kb
  • LPC: Ligand-Protein Contacts for 4WQS
  • CSU: Contacts of Structural Units for 4WQS
  • Structure Factors (1470 Kb)
  • Retrieve 4WQS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4WQS from S2C, [Save to disk]
  • Re-refined 4wqs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4WQS 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 4WQS
  • 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 4WQS, from MSDmotif at EBI
  • Fold representative 4wqs from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4wqs_Z] [4wqs_X] [4wqs_N] [4wqs_L] [4wqs_C] [4wqs_D] [4wqs_G] [4wqs_H] [4wqs_Y] [4wqs_M] [4wqs_E] [4wqs_I] [4wqs_K] [4wqs_A] [4wqs_B] [4wqs] [4wqs_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4WQS: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4WQS
  • Community annotation for 4WQS at PDBWiki (http://pdbwiki.org)

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