4Q4Z Transcription Dna date Apr 15, 2014
title Thermus Thermophilus Rna Polymerase De Novo Transcription In Complex
authors K.S.Murakami
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
Organism_taxid: 274
Strain: Hb8

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

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
Organism_taxid: 300852
Strain: Hb8

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
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: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet
Expression_system_plasmid: Pet21a-Siga

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

Synthetic: Yes

Molecule: Dna (25-Mer)
Chain: H
Engineered: Yes
Other_details: Non-Template Dna

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.256 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
184.487 102.159 294.719 90.00 98.96 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 2TM, 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] (1230 Kb) [Save to disk]
  • Biological Unit Coordinates (4q4z.pdb1.gz) 1215 Kb
  • LPC: Ligand-Protein Contacts for 4Q4Z
  • CSU: Contacts of Structural Units for 4Q4Z
  • Structure Factors (1651 Kb)
  • Retrieve 4Q4Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Q4Z from S2C, [Save to disk]
  • Re-refined 4q4z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q4Z 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 4Q4Z
  • 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 4Q4Z, from MSDmotif at EBI
  • Fold representative 4q4z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q4z_G] [4q4z_E] [4q4z_A] [4q4z_H] [4q4z_C] [4q4z_F] [4q4z_B] [4q4z] [4q4z_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4Q4Z: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4Q4Z
  • Community annotation for 4Q4Z at PDBWiki (http://pdbwiki.org)

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