4A3J Transcription date Sep 30, 2011
title Rna Polymerase II Initial Transcribing Complex With A 2nt Dna-Rna Hybrid And Soaked With Gmpcpp
authors A.C.M.Cheung, S.Sainsbury, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Fragment: Residues 1-1732
Synonym: Rpb1, Rna Polymerase II Subunit 1, Rna Polymerase Subunit B1, Dna-Directed Rna Polymerase III Largest Subuni Polymerase II Subunit B220;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Synonym: Rpb2, Rna Polymerase II Subunit 2, B150, Dna-Direc Polymerase II 140 Kda Polypeptide;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rpb3, Rna Polymerase II Subunit 3, Rna Polymerase Subunit B3, B44.5, Dna-Directed Rna Polymerase II 45 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4
Chain: D
Synonym: Rpb4, Rna Polymerase II Subunit B4, B32, Dna-Direc Polymerase II 32 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 1;
Chain: E
Synonym: Rpb5, Rna Polymerases I\,II\,And III Subunit Abc1, Dna-Directed Rna Polymerases I\,II\,And III 27 Kda Polypep

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 2;
Chain: F
Synonym: Rpb6, Rna Polymerases I\,II\,And III Subunit Abc2, Dna-Directed Rna Polymerases I\,II\,And III 23 Kda Polypep

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Rpb7, Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Rna Polymerase II Subunit B7, B16

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 3;
Chain: H
Synonym: Rpb8, Rna Polymerases I\,II\,And III Subunit Abc3, Abc14.4, Abc14.5, Dna-Directed Rna Polymerases I\,II\,And Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rbp9, Rna Polymerase II Subunit B9, B12.6, Dna-Dir Rna Polymerase II 14.2 Kda Polypeptide, Dna-Directed Rna Polymerase II Subunit 9;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 5;
Chain: J
Synonym: Rpb10, Rna Polymerases I\,II\,And III Subunit Abc5 Abc10-Beta, Abc8, Dna-Directed Rna Polymerases I\,II\,And Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Rpb11, Rna Polymerase II Subunit B11, B13.6, Dna-D Rna Polymerase II 13.6 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 4;
Chain: L
Synonym: Rpb12, Rna Polymerases I\,II\,And III Subunit Abc4 Abc10-Alpha;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5'-D(Gptpapgpapapapgpcptpapgpcptp)-
Chain: N
Synonym: Non Template Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-R(Cpap)-3'
Chain: P
Synonym: Transcript Rna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Apgpcptpapgpcptptptpcpbrupapcp Tpgpapapcpapapcptpapapcp)-3';
Chain: T
Synonym: Template Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 2 2 21
R_factor 0.1567 R_Free 0.1939
crystal
cell
length a length b length c angle alpha angle beta angle gamma
223.290 392.790 282.660 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.70 Å
ligand BRU, G2P, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA-directed 5'-3' RNA polym...


  • B
  • RNA-directed 5'-3' RNA polym...


  • C
  • RNA-directed 5'-3' RNA polym...


  • D
  • RNA-directed 5'-3' RNA polym...


  • E
  • RNA-directed 5'-3' RNA polym...


  • F
  • RNA-directed 5'-3' RNA polym...


  • G
  • RNA-directed 5'-3' RNA polym...


  • H
  • RNA-directed 5'-3' RNA polym...


  • I
  • RNA-directed 5'-3' RNA polym...


  • J
  • RNA-directed 5'-3' RNA polym...

  • DNA-directed RNA polymerase ...
  • K
  • RNA-directed 5'-3' RNA polym...


  • L
  • RNA-directed 5'-3' RNA polym...


  • Primary referenceStructural basis of initial RNA polymerase II transcription., Cheung AC, Sainsbury S, Cramer P, EMBO J. 2011 Nov 4. doi: 10.1038/emboj.2011.396. PMID:22056778
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1377 Kb) [Save to disk]
  • Biological Unit Coordinates (4a3j.pdb1.gz) 1361 Kb
  • LPC: Ligand-Protein Contacts for 4A3J
  • CSU: Contacts of Structural Units for 4A3J
  • Structure Factors (1053 Kb)
  • Retrieve 4A3J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4A3J from S2C, [Save to disk]
  • Re-refined 4a3j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4A3J 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 4A3J
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4A3J, from MSDmotif at EBI
  • Fold representative 4a3j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4a3j_I] [4a3j_H] [4a3j_C] [4a3j] [4a3j_J] [4a3j_F] [4a3j_T] [4a3j_L] [4a3j_A] [4a3j_P] [4a3j_G] [4a3j_D] [4a3j_K] [4a3j_N] [4a3j_B] [4a3j_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4A3J: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 4A3J
  • Community annotation for 4A3J at PDBWiki (http://pdbwiki.org)
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