2JA6 Transferase date Nov 23, 2006
title Cpd Lesion Containing Rna Polymerase II Elongation Complex B
authors F.Brueckner, U.Hennecke, T.Carell, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Largest Subunit
Chain: A
Synonym: Rna Polymerase II Subunit 1, B220
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 140 Kda Polypeptid
Chain: B
Synonym: B150, Rna Polymerase II Subunit 2
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 45kda Polypeptide
Chain: C
Synonym: B44.5
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 32kda Polypeptide
Chain: D
Synonym: B32
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III 27 Kd Polypeptide;
Chain: E
Synonym: Abc27
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III 23 Kd Polypeptide;
Chain: F
Synonym: Abc23
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 19kda Polypeptide
Chain: G
Synonym: B16
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III 14.5 Polypeptide;
Chain: H
Synonym: Abc14.4
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit 9
Chain: I
Synonym: Dna-Directed Rna Polymerase II 14.2 Kda Polypeptid
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases IIIIII Subunit 10
Chain: J
Synonym: Dna-Directed Rna Polymerases I, II, And III 8.3 Kd Polypeptide, Abc10-Beta, Abc8;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 13.6 Kda Polypepti
Chain: K
Synonym: B13.6
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III 7.7 K Polypeptide;
Chain: L
Synonym: Abc10-Alpha
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: 5'-D(Tpapapgptpapcptptpgp Apgpcpt)-
Chain: N
Synonym: Nontemplate Dna Of Complex B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide

Molecule: 5'-R(Upupcpgpapcpcpapgpgpap)-3'
Chain: P
Synonym: Product Rna Of Complex B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide

Molecule: 5'-D(Apgpcptpcpapapgptpap Cptptpttptpcpcpbrupgpgptpcpaptpt)-3';
Chain: T
Synonym: Thymine-Thymine Cpd Containing Template Dna Of Com
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide
symmetry Space Group: C 2 2 21
R_factor 0.292 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
223.580 393.491 283.505 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.00 Å
ligand BRU, MG, TT, 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 referenceCPD damage recognition by transcribing RNA polymerase II., Brueckner F, Hennecke U, Carell T, Cramer P, Science. 2007 Feb 9;315(5813):859-62. PMID:17290000
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (664 Kb) [Save to disk]
  • Biological Unit Coordinates (2ja6.pdb1.gz) 652 Kb
  • LPC: Ligand-Protein Contacts for 2JA6
  • CSU: Contacts of Structural Units for 2JA6
  • Likely Quarternary Molecular Structure file(s) for 2JA6
  • Retrieve 2JA6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JA6 from S2C, [Save to disk]
  • View 2JA6 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 2JA6
  • 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 2JA6, from MSDmotif at EBI
  • Fold representative 2ja6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ja6_G] [2ja6_L] [2ja6_K] [2ja6_B] [2ja6_E] [2ja6_D] [2ja6_H] [2ja6_I] [2ja6_N] [2ja6_F] [2ja6_C] [2ja6_T] [2ja6_J] [2ja6_P] [2ja6] [2ja6_A]
  • SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P20433] [P34087] [P27999]
  • Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB4_YEAST] [RPB7_YEAST] [RPB9_YEAST] by SWISSPFAM
  • Domains found in 2JA6: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 2JA6
  • Community annotation for 2JA6 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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