3AOI Transcription, Transferase Dna Rna date Sep 30, 2010
title Rna Polymerase-Gfh1 Complex (Crystal Type 2)
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(Gpgptpcptpgptpaptpcpapcpgpapgpcpcpacp Pgpcpapt)-3');
Chain: P, R, T
Engineered: Yes
Other_details: Template Dna

Synthetic: Yes
Other_details: Dna Oligomer

Molecule: Rna (5'- R(Cpcpcpgpgpapapgpapupcpapupcpupupcpcpgp Gpapugpcpgpgpcpgpg)-3');
Chain: Q, S, U
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 0.317 R_Free 0.338
crystal
cell
length a length b length c angle alpha angle beta angle gamma
189.230 264.510 193.930 90.00 116.68 90.00
method X-Ray Diffractionresolution 4.30 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] (1478 Kb) [Save to disk]
  • Biological Unit Coordinates (3aoi.pdb1.gz) 505 Kb
  • Biological Unit Coordinates (3aoi.pdb2.gz) 495 Kb
  • Biological Unit Coordinates (3aoi.pdb3.gz) 507 Kb
  • LPC: Ligand-Protein Contacts for 3AOI
  • CSU: Contacts of Structural Units for 3AOI
  • Structure Factors (989 Kb)
  • Retrieve 3AOI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AOI from S2C, [Save to disk]
  • Re-refined 3aoi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AOI 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 3AOI
  • 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 3AOI, from MSDmotif at EBI
  • Fold representative 3aoi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3aoi_X] [3aoi_F] [3aoi_Q] [3aoi_I] [3aoi_R] [3aoi_C] [3aoi_T] [3aoi_O] [3aoi_E] [3aoi_J] [3aoi_G] [3aoi_K] [3aoi_M] [3aoi_A] [3aoi_H] [3aoi_P] [3aoi_Y] [3aoi_L] [3aoi_N] [3aoi_D] [3aoi_U] [3aoi] [3aoi_Z] [3aoi_S] [3aoi_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AOI: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 3AOI
  • Community annotation for 3AOI 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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