1ZYR Transcription,Transferase date Jun 10, 2005
title Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Streptolydigin
authors S.Tuske, S.G.Sarafianos, X.Wang, B.Hudson, E.Sineva, J.Mukhopadhyay, J.J.Birktoft, O.Leroy, S.Ismail, A.D.Clark, C.Dharia, A.Napoli, O.Laptenko, J.Lee, S.Borukhov, R.H.Ebright, E.Arnold
compound source
Molecule: Dna-Directed Rna Polymerase Alpha Chain
Chain: A, B, K, L
Fragment: Subumit Alpha
Synonym: Rnap Alpha Subunit; Transcriptase Alpha Chain Rna Polymerase Alpha Subunit;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna-Directed Rna Polymerase Sigma Chain
Chain: F, P
Fragment: Subunit Sigma
Synonym: Rna Polymerase Sigma Factor Rpod

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 32
R_factor 0.261 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
237.000 237.000 250.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand MG, STD, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


F, P
  • bacterial sigma factor activ...


  • M, C


    N, D


    O, E


    Primary referenceInhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation., Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark AD Jr, Dharia C, Napoli A, Laptenko O, Lee J, Borukhov S, Ebright RH, Arnold E, Cell 2005 Aug 26;122(4):541-52. PMID:16122422
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1111 Kb) [Save to disk]
  • Biological Unit Coordinates (1zyr.pdb1.gz) 550 Kb
  • Biological Unit Coordinates (1zyr.pdb2.gz) 552 Kb
  • LPC: Ligand-Protein Contacts for 1ZYR
  • CSU: Contacts of Structural Units for 1ZYR
  • Likely Quarternary Molecular Structure file(s) for 1ZYR
  • Structure Factors (1248 Kb)
  • Retrieve 1ZYR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ZYR from S2C, [Save to disk]
  • View 1ZYR 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 1ZYR
  • 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 1ZYR, from MSDmotif at EBI
  • Fold representative 1zyr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1zyr_D] [1zyr_P] [1zyr_K] [1zyr_E] [1zyr_C] [1zyr_A] [1zyr_O] [1zyr_N] [1zyr_F] [1zyr_B] [1zyr_M] [1zyr_L] [1zyr]
  • SWISS-PROT database: [Q5SKW1] [Q5SHR6] [Q8RQE9] [Q8RQE8] [Q8RQE7]
  • Domain organization of [Q5SKW1_THET8] [RPOA_THET8] [RPOB_THET8] [RPOC_THET8] [RPOZ_THET8] by SWISSPFAM
  • Domains found in 1ZYR: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 1ZYR
  • Community annotation for 1ZYR 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