2O5J Transferase Dna-Rna Hybrid date Dec 06, 2006
title Crystal Structure Of The T. Thermophilus Rnap Polymerase Elo Complex With The Ntp Substrate Analog
authors D.G.Vassylyev, M.N.Vassylyeva
compound source
Molecule: 5'-D(Pcpcpcptpgptpcptpgpgpcpgptptp Pcpgpcpcpg)-3';
Chain: G, X
Engineered: Yes
Other_details: Dna Template Strand
Synthetic: Yes

Molecule: 5'-R(Pgpapgpupcpupgpcpgpgpcpgpcpgp
Chain: H, Y
Engineered: Yes
Other_details: Rna Transcript

Synthetic: Yes

Molecule: 5'-D(Apapcpgpcpcpapgpapcpapgpgpg)-3
Chain: I, Z
Engineered: Yes
Other_details: Dna Non-Template Strand

Synthetic: Yes

Molecule: Dna-Directed Rna Polymerase Alpha Chain
Chain: A, B, K, L
Synonym: Rnap Alpha Subunit, Transcriptase Alpha Chain, Rna Polymerase Subunit Alpha;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 41
R_factor 0.225 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.340 152.340 524.567 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand APC, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


M, C


N, D


O, E


Primary referenceStructural basis for substrate loading in bacterial RNA polymerase., Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R, Nature. 2007 Jun 20;. PMID:17581591
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1047 Kb) [Save to disk]
  • Biological Unit Coordinates (2o5j.pdb1.gz) 525 Kb
  • Biological Unit Coordinates (2o5j.pdb2.gz) 524 Kb
  • LPC: Ligand-Protein Contacts for 2O5J
  • CSU: Contacts of Structural Units for 2O5J
  • Likely Quarternary Molecular Structure file(s) for 2O5J
  • Structure Factors (2169 Kb)
  • Retrieve 2O5J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2O5J from S2C, [Save to disk]
  • Re-refined 2o5j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2O5J 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 2O5J
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2O5J, from MSDmotif at EBI
  • Fold representative 2o5j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2o5j_Y] [2o5j_O] [2o5j_D] [2o5j_H] [2o5j_E] [2o5j_G] [2o5j_B] [2o5j_C] [2o5j_A] [2o5j_M] [2o5j_N] [2o5j_Z] [2o5j_I] [2o5j] [2o5j_L] [2o5j_X] [2o5j_K]
  • SWISS-PROT database: [Q5SHR6] [Q8RQE9] [Q8RQE8] [Q8RQE7]
  • Domain organization of [RPOA_THET8] [RPOB_THET8] [RPOC_THET8] [RPOZ_THET8] by SWISSPFAM
  • Domains found in 2O5J: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 2O5J
  • Community annotation for 2O5J at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • 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
    Bioinformatics Unit
    Weizmann Institute of Science