4GZY Transcription Dna Rna date Sep 06, 2012
title Crystal Structures Of Bacterial Rna Polymerase Paused Elonga Complexes
authors A.Weixlbaumer, K.Leon, R.Landick, S.A.Darst
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
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Rpoa, Ttha1664
Expression_system: Thermus Thermophilus
Expression_system_taxid: 274
Expression_system_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
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Rpob, Ttha1813
Expression_system: Thermus Thermophilus
Expression_system_taxid: 274
Expression_system_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
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Rpoc, Ttha1812
Expression_system: Thermus Thermophilus
Expression_system_taxid: 274
Expression_system_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
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Rpoz, Ttha1561
Expression_system: Thermus Thermophilus
Expression_system_taxid: 274
Expression_system_strain: Hb8

Molecule: Non-Template Dna
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic
Organism_taxid: 32630

Molecule: Rna Transcript
Chain: R
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic
Organism_taxid: 32630

Molecule: Template Dna
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic
Organism_taxid: 32630
symmetry Space Group: P 31 2 1
R_factor 0.263 R_Free 0.322
crystal
cell
length a length b length c angle alpha angle beta angle gamma
207.210 207.210 203.223 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.51 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


Primary referenceStructural basis of transcriptional pausing in bacteria., Weixlbaumer A, Leon K, Landick R, Darst SA, Cell. 2013 Jan 31;152(3):431-41. doi: 10.1016/j.cell.2012.12.020. PMID:23374340
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1078 Kb) [Save to disk]
  • Biological Unit Coordinates (4gzy.pdb1.gz) 1066 Kb
  • LPC: Ligand-Protein Contacts for 4GZY
  • CSU: Contacts of Structural Units for 4GZY
  • Structure Factors (445 Kb)
  • Retrieve 4GZY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GZY from S2C, [Save to disk]
  • Re-refined 4gzy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GZY 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 4GZY
  • 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 4GZY, from MSDmotif at EBI
  • Fold representative 4gzy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gzy_B] [4gzy_C] [4gzy_D] [4gzy] [4gzy_E] [4gzy_N] [4gzy_R] [4gzy_A] [4gzy_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4GZY: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4GZY
  • Community annotation for 4GZY at PDBWiki (http://pdbwiki.org)

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