2PPB Transferase Dna Rna date Apr 28, 2007
title Crystal Structure Of The T. Thermophilus Rnap Polymerase Elo Complex With The Ntp Substrate Analog And Antibiotic Strept
authors D.G.Vassylyev, M.N.Vassylyeva, I.Artsimovitch, R.Landick
compound source
Molecule: Dna (5'- D(Pcpcpcptpgptpcptpgpgpcpgptptpcpgpcpgpc G)-3');
Chain: G, X
Engineered: Yes
Other_details: Dna Template Strand
Synthetic: Yes

Molecule: Rna (5'- R(Pgpapgpupcpupgpcpgpgpcpgpcpgpcpg)-3');
Chain: H, Y
Engineered: Yes
Other_details: Rna Transcript

Synthetic: Yes

Molecule: Dna (5'-D(Apapcpgpcpcpapgpapcpapgpgp
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 0.234 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
155.379 155.379 496.992 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand APC, MG, STD, 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] (1062 Kb) [Save to disk]
  • Biological Unit Coordinates (2ppb.pdb1.gz) 532 Kb
  • Biological Unit Coordinates (2ppb.pdb2.gz) 531 Kb
  • LPC: Ligand-Protein Contacts for 2PPB
  • CSU: Contacts of Structural Units for 2PPB
  • Likely Quarternary Molecular Structure file(s) for 2PPB
  • Structure Factors (2111 Kb)
  • Retrieve 2PPB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PPB from S2C, [Save to disk]
  • Re-refined 2ppb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PPB 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 2PPB
  • 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 2PPB, from MSDmotif at EBI
  • Fold representative 2ppb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ppb_L] [2ppb_Y] [2ppb_N] [2ppb_Z] [2ppb_O] [2ppb_I] [2ppb_K] [2ppb_D] [2ppb_A] [2ppb_E] [2ppb_X] [2ppb_H] [2ppb_B] [2ppb_M] [2ppb_G] [2ppb_C] [2ppb]
  • SWISS-PROT database: [Q9Z9H6] [Q8RQE9] [Q8RQE8] [Q8RQE7]
  • Domain organization of [RPOA_THETH] [RPOB_THET8] [RPOC_THET8] [RPOZ_THET8] by SWISSPFAM
  • Domains found in 2PPB: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 2PPB
  • Community annotation for 2PPB 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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