4A93 Transcription date Nov 23, 2011
title Rna Polymerase II Elongation Complex Containing A Cpd Lesion
authors C.Walmacq, A.C.M.Cheung, M.L.Kireeva, L.Lubkowska, C.Ye, D.Gotte, J.N.Strathern, T.Carell, P.Cramer, M.Kashlev
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 B1, Dna-Directed Rna Polymerase III Largest Subunit, Rna Po 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 B3, B44.5, Dna-Directed Rna Polymerase II 45 Kda Polypeptid

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 Polypept

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 Polypept

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, Abc14.5, Dna-Directed Rna Polymerases I\,II\,And III 14.5 K 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 Polymerase II 14.2 Kda Polypeptide, Dna-Directed Rna Polyme 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 Beta, Abc8, Dna-Directed Rna Polymerases I\,II\,And III 8.3 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 Alpha;

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

Molecule: 5'-D(Tpapapgptpapcptptpgpapgpcptp)-
Chain: N
Synonym: Non Template Dna
Engineered: Yes

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

Molecule: 5'-R(Upupcpgpapcpcpapgpgpapap)-3'
Chain: P
Synonym: Transcript Rna
Engineered: Yes

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

Molecule: 5'-D(Apgpcptpcpapapgptpapcptttptpt Brupgpgptpcpaptpt)-3';
Chain: T
Synonym: Template Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
symmetry Space Group: C 2 2 21
R_factor 0.165 R_Free 0.199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
221.637 391.519 281.774 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 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 referenceMechanism of Translesion Transcription by RNA Polymerase II and Its Role in Cellular Resistance to DNA Damage., Walmacq C, Cheung AC, Kireeva ML, Lubkowska L, Ye C, Gotte D, Strathern JN, Carell T, Cramer P, Kashlev M, Mol Cell. 2012 Apr 13;46(1):18-29. Epub 2012 Mar 8. PMID:22405652
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1398 Kb) [Save to disk]
  • Biological Unit Coordinates (4a93.pdb1.gz) 1382 Kb
  • LPC: Ligand-Protein Contacts for 4A93
  • CSU: Contacts of Structural Units for 4A93
  • Structure Factors (2322 Kb)
  • Retrieve 4A93 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4A93 from S2C, [Save to disk]
  • Re-refined 4a93 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4A93 in 3D
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4A93
  • 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 4A93, from MSDmotif at EBI
  • Fold representative 4a93 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4a93_P] [4a93_C] [4a93_E] [4a93_G] [4a93_K] [4a93_A] [4a93_N] [4a93_J] [4a93_H] [4a93_T] [4a93_D] [4a93_F] [4a93_L] [4a93] [4a93_B] [4a93_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4A93: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
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