2WB1 Transcription date Feb 19, 2009
title The Complete Structure Of The Archaeal 13-Subunit Dna-Direct Polymerase
authors Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P. S.D.Bell, N.G.A.Abrescia
compound source
Molecule: Dna-Directed Rna Polymerase Rpo1n Subunit
Chain: A, W
 Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo2 Subunit
Chain: B, R
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo1c Subunit
Chain: C, Y
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymeraserpo3 Subunit
Chain: D, S
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo7 Subunit
Chain: E, T
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo4 Subunit
Chain: F, U
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo8 Subunit
Chain: G, V
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo5 Subunit
Chain: H, Z
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo6 Subunit
Chain: I, K
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo13 Subunit
Chain: J, Q
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo11 Subunit
Chain: L, M
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo10 Subunit
Chain: N, O
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Rpo12 Subunit
Chain: P, X
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286
symmetry Space Group: P 21 21 21
R_factor 0.333 R_Free 0.384
crystal
cell
length a length b length c angle alpha angle beta angle gamma
196.095 211.871 238.905 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.52 Å
ligand F3S, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, W


B, R


F, U


K, I


M, L


N, O


S, D


T, E


X, P


Y, C


Z, H


Primary referenceEvolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure., Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB, Bell SD, Abrescia NG, PLoS Biol. 2009 May 5;7(5):e102. PMID:19419240
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2208 Kb) [Save to disk]
  • Biological Unit Coordinates (2wb1.pdb1.gz) 1105 Kb
  • Biological Unit Coordinates (2wb1.pdb2.gz) 1105 Kb
  • LPC: Ligand-Protein Contacts for 2WB1
  • CSU: Contacts of Structural Units for 2WB1
  • Likely Quarternary Molecular Structure file(s) for 2WB1
  • Structure Factors (1052 Kb)
  • Retrieve 2WB1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2WB1 from S2C, [Save to disk]
  • Re-refined 2wb1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2WB1 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 2WB1
  • 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 2WB1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1e2wb1, region B:1-168,B:233-251 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2wb1_X] [2wb1_Q] [2wb1_V] [2wb1_S] [2wb1_H] [2wb1_Z] [2wb1_L] [2wb1_R] [2wb1_D] [2wb1_U] [2wb1_C] [2wb1_G] [2wb1_T] [2wb1_J] [2wb1_K] [2wb1_F] [2wb1_I] [2wb1] [2wb1_B] [2wb1_E] [2wb1_M] [2wb1_Y] [2wb1_O] [2wb1_N] [2wb1_P] [2wb1_W] [2wb1_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2WB1: [RNA_pol_Rpb6] [RPOLA_N] [RPOLCX] [RPOLD] [S1 ] by SMART
    • Other resources with information on 2WB1
  • Community annotation for 2WB1 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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