3AOH Transcription, Transferase Dna Rna date Sep 28, 2010
title Rna Polymerase-Gfh1 Complex (Crystal Type 1)
authors S.Tagami, S.Sekine, T.Kumarevel, M.Yamamoto, S.Yokoyama, Riken St Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, F, G, K, L
Synonym: Rnap Subunit Alpha, Transcriptase Subunit Alpha, R Polymerase Subunit Alpha;
Ec: 2.7.7.6
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, H, M
Synonym: Rnap Subunit Beta, Transcriptase Subunit Beta, Rna Polymerase 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, I, N
Synonym: Rnap Subunit Beta', Transcriptase Subunit Beta', R Polymerase 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, J, O
Synonym: Rnap Omega Subunit, Transcriptase Subunit Omega, R Polymerase Omega Subunit;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Dna (5'- D(Gpgptpcptpgptpaptpcpapcpgpapgpcpcpapcp Cpgpcpapt)-3');
Chain: P
Engineered: Yes
Other_details: Template Dna
Synthetic: Yes
Other_details: Dna Oligomer

Molecule: Rna (5'- R(Cpcpcpcpgpgpapapgpapupcpapupcpupupcpcp Gpgpapugpcpgpgpcpgpg)-3');
Chain: Q
Engineered: Yes
Synthetic: Yes
Other_details: Rna Oligomer

Molecule: Anti-Cleavage Anti-Grea Transcription Factor Gfh1
Chain: X, Y, Z
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Ttha1042
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.262 R_Free 0.318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
192.760 260.700 198.560 90.00 117.58 90.00
method X-Ray Diffractionresolution 4.10 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
E, J, O


F, K, L, A, B, G


M, C, H


N, D, I


Y, Z, X


Primary referenceCrystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein., Tagami S, Sekine S, Kumarevel T, Hino N, Murayama Y, Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S, Nature. 2010 Dec 16;468(7326):978-82. Epub 2010 Dec 1. PMID:21124318
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1480 Kb) [Save to disk]
  • Biological Unit Coordinates (3aoh.pdb1.gz) 507 Kb
  • Biological Unit Coordinates (3aoh.pdb2.gz) 494 Kb
  • Biological Unit Coordinates (3aoh.pdb3.gz) 503 Kb
  • LPC: Ligand-Protein Contacts for 3AOH
  • CSU: Contacts of Structural Units for 3AOH
  • Structure Factors (1162 Kb)
  • Retrieve 3AOH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AOH from S2C, [Save to disk]
  • Re-refined 3aoh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3AOH 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 3AOH
  • 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
  • 3D motif for 3AOH, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3aoh_D] [3aoh_M] [3aoh_Z] [3aoh_P] [3aoh_N] [3aoh_G] [3aoh_Y] [3aoh] [3aoh_A] [3aoh_F] [3aoh_B] [3aoh_O] [3aoh_E] [3aoh_C] [3aoh_Q] [3aoh_K] [3aoh_H] [3aoh_L] [3aoh_X] [3aoh_I] [3aoh_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AOH: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
    • Other resources with information on 3AOH
  • Community annotation for 3AOH at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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