4Q5S Transcription Dna Rna date Apr 17, 2014
title Thermus Thermophilus Rna Polymerase Initially Transcribing C Containing 6-Mer Rna
authors K.S.Murakami
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Strain: Hb8

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852
Strain: Hb8

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Siga, Ttha0532
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Cpcptpgpcpaptpcpcpgptpgpapgptpgpcpapgp 3');
Chain: G
Engineered: Yes
Other_details: Template Dna

Synthetic: Yes

Molecule: Dna (5'- D(Tpaptpapaptpgpgpgpapgpcptpgptpcpapcpgp Gpcpapgpg)-3');
Chain: H
Engineered: Yes
Other_details: Non-Template Dna

Synthetic: Yes

Molecule: Rna (5'-R(Pcpupcpapc)-3')
Chain: I
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.269 R_Free 0.294
crystal
cell
length a length b length c angle alpha angle beta angle gamma
187.089 102.075 297.263 90.00 98.14 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand ATP, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


  • Primary referenceStructural Basis of Transcription Initiation by Bacterial RNA Polymerase holoenzyme., Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D, Fernandez-Tornero C, Kulbachinskiy A, Murakami KS, J Biol Chem. 2014 Jun 27. pii: jbc.M114.584037. PMID:24973216
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1229 Kb) [Save to disk]
  • Biological Unit Coordinates (4q5s.pdb1.gz) 1216 Kb
  • LPC: Ligand-Protein Contacts for 4Q5S
  • CSU: Contacts of Structural Units for 4Q5S
  • Structure Factors (1642 Kb)
  • Retrieve 4Q5S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Q5S from S2C, [Save to disk]
  • Re-refined 4q5s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q5S 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 4Q5S
  • 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 4Q5S, from MSDmotif at EBI
  • Fold representative 4q5s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q5s_E] [4q5s_A] [4q5s] [4q5s_B] [4q5s_F] [4q5s_I] [4q5s_C] [4q5s_G] [4q5s_H] [4q5s_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4Q5S: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4Q5S
  • Community annotation for 4Q5S at PDBWiki (http://pdbwiki.org)

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