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 Diffraction	resolution	3.40 Å
ligand	BRU, MG, TT, ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
Gene Ontology	Chain Function Process Component 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 reference	Mechanism 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] (1365 Kb) [Save to disk] Biological Unit Coordinates (4a93.pdb1.gz) 1351 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

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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 4A93, from MSDmotif at EBI

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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