2Y0S Transferase date Dec 07, 2010
title Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In P Group
authors M.Wojtas, B.Peralta, M.Ondiviela, M.Mogni, S.D.Bell, N.G.A.Abresc
compound source
Molecule: Dna-Directed Rna Polymerase
Chain: A, W
Ec: 2.7.7.6
 Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase
Chain: B, R
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Subunit A''
Chain: C, Y
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Subunit D
Chain: D, S
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Rna Polymerase Subunit 4
Chain: E, T
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Rna Polymerase Subunit 7
Chain: F, U
Other_details: Rpo4
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Rna Polymerase Subunit 8
Chain: G, V
Fragment: Rpo8
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Subunit H
Chain: H, Z
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Subunit K
Chain: I, K
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Rna Polymerase Subunit 13
Chain: J, Q
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Subunit L
Chain: L, M
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Dna-Directed Rna Polymerase Subunit N
Chain: N, O
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286

Molecule: Rna Polymerase Subunit 12
Chain: P, X
Organism_scientific: Sulfolobus Shibatae
Organism_taxid: 2286
symmetry Space Group: P 1 21 1
R_factor 0.300 R_Free 0.354
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.330 195.909 212.451 90.00 105.73 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand F3S, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
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 referenceArchaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit., Wojtas M, Peralta B, Ondiviela M, Mogni M, Bell SD, Abrescia NG, Biochem Soc Trans. 2011 Jan 19;39(1):25-30. PMID:21265742
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2224 Kb) [Save to disk]
  • Biological Unit Coordinates (2y0s.pdb1.gz) 1112 Kb
  • Biological Unit Coordinates (2y0s.pdb2.gz) 1111 Kb
  • LPC: Ligand-Protein Contacts for 2Y0S
  • CSU: Contacts of Structural Units for 2Y0S
  • Structure Factors (874 Kb)
  • Retrieve 2Y0S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Y0S from S2C, [Save to disk]
  • Re-refined 2y0s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2Y0S 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 2Y0S
  • 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 2Y0S, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2y0s_O] [2y0s_E] [2y0s_W] [2y0s_G] [2y0s_I] [2y0s_A] [2y0s_D] [2y0s_P] [2y0s_J] [2y0s_Z] [2y0s_H] [2y0s_C] [2y0s_T] [2y0s_B] [2y0s_Y] [2y0s_X] [2y0s_L] [2y0s_K] [2y0s_N] [2y0s_U] [2y0s_Q] [2y0s_M] [2y0s] [2y0s_S] [2y0s_R] [2y0s_V] [2y0s_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2Y0S: [RNA_pol_Rpb6] [RPOLA_N] [RPOLCX] [RPOLD] [S1 ] by SMART
    • Other resources with information on 2Y0S
  • Community annotation for 2Y0S 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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