2JA5 Transferase date Nov 23, 2006
title Cpd Lesion Containing Rna Polymerase II Elongation Complex A
authors F.Brueckner, U.Hennecke, T.Carell, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit B1,Dna-Directed Rna Poly Largest Subunit,Rna Polymerase II Subunit B220;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Atcc 204508 S288c

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Atcc 204508 S288c

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Atcc 204508 S288c

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Atcc 204508 S288c

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: E
Synonym: Rna Polymerases I,II,And III Subunit Abc1,Abc27,Dn Rna Polymerases I,And III 27 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Atcc 204508 S288c

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F
Synonym: Rna Polymerases I,II,And III Subunit Abc2,Abc23,Dn Rna Polymerases I,And III 23 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Atcc 204508 S288c

Molecule: 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
Strain: Atcc 204508 S288c

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Rna Polymerases I,II,And III Subunit Abc3,Abc14.4, Dna-Directed Rna Polymerases I,And III 14.5 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: Rna Polymerase II Subunit B9,B12.6,Dna-Directed Rn Polymerase II 14.2 Kda Polypeptide,Dna-Directed Rna Polymer Subunit 9;

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: J
Synonym: Rna Polymerases I,II,And III Subunit Abc5,Abc10-Be Dna-Directed Rna Polymerases I,And III 8.3 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: Rna Polymerase II Subunit B11,B13.6,Dna-Directed R 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
Chain: L
Synonym: Rna Polymerases I,II,And III Subunit Abc4,Abc10-Al

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

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

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

Molecule: 5'-D(Apgpcptpcpapapgptpap Cptpttptptpcpcpbrupgpgptpcpaptpt)-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 0.270 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
222.209 392.206 284.032 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand BRU, 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 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] (657 Kb) [Save to disk]
  • Biological Unit Coordinates (2ja5.pdb1.gz) 645 Kb
  • LPC: Ligand-Protein Contacts for 2JA5
  • CSU: Contacts of Structural Units for 2JA5
  • Likely Quarternary Molecular Structure file(s) for 2JA5
  • Structure Factors (2264 Kb)
  • Retrieve 2JA5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JA5 from S2C, [Save to disk]
  • Re-refined 2ja5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2JA5 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 2JA5
  • 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 2JA5, from MSDmotif at EBI
  • Fold representative 2ja5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ja5_H] [2ja5_G] [2ja5_A] [2ja5_I] [2ja5_J] [2ja5] [2ja5_K] [2ja5_N] [2ja5_B] [2ja5_F] [2ja5_C] [2ja5_L] [2ja5_D] [2ja5_E] [2ja5_T] [2ja5_P]
  • 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 2JA5: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 2JA5
  • Community annotation for 2JA5 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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