2R7Z	Transcription Dna-Rna Hybrid	date	Sep 10, 2007
title	Cisplatin Lesion Containing Rna Polymerase II Elongation Com
authors	G.E.Damsma, A.Alt, F.Brueckner, T.Carell, P.Cramer
compound		source
Molecule: 5'-D(Tpapcptptpgupcpcpcptpcpcptpcp Chain: T Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Cpapapgptpapg)-3' Chain: N Engineered: Yes		Synthetic: Yes
Molecule: 5'-R(Upupupgpapgpgpapgpg)-3' Chain: P Engineered: Yes		Synthetic: Yes
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1 Chain: A Synonym: Rna Polymerase II Subunit B1; Rna Polymerase II Su Dna-Directed Rna Polymerase III Largest 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: Rna Polymerase II Subunit 2; Dna-Directed Rna Poly 140 Kda Polypeptide; B150; 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: Rna Polymerase II Subunit B3; Rna Polymerase II Su Dna-Directed Rna Polymerase II 45 Kda Polypeptide; B44.5; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4 Chain: D Synonym: Rna Polymerase II Subunit B4; Dna-Directed Rna Pol 32 Kda Polypeptide; B32; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: E Synonym: 'Rna Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: F Synonym: Rna Polymerases I, II, And III Subunit Abc2; Dna-D Rna Polymerases I, II, And III 23 Kda Polypeptide; Abc23; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7 Chain: G Synonym: Rna Polymerase II Subunit B7; B16 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: H Synonym: Rna Polymerases I, II, And III Subunit Abc3; Dna-D Rna Polymerases I, II, And III 14.5 Kda Polypeptide; Abc14. Abc14.5; Ec: 2.7.7.6		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; Dna-Directed Rna Pol Subunit 9; Dna-Directed Rna Polymerase II 14.2 Kda Polypept B12.6; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: J Synonym: Rna Polymerases I, II, And III Subunit Abc5; Dna-D Rna Polymerases I, II, And III 8.3 Kda Polypeptide; Abc10-B Ec: 2.7.7.6		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; Dna-Directed Rna Po II 13.6 Kda Polypeptide; B13.6; Ec: 2.7.7.6		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 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
symmetry	Space Group: C 2 2 21	R_factor 0.215 R_Free 0.240
crystal cell	length a length b length c angle alpha angle beta angle gamma 222.062 393.123 283.733 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.80 Å
ligand	CPT, MG, 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 transcriptional stalling at cisplatin-damaged DNA., Damsma GE, Alt A, Brueckner F, Carell T, Cramer P, Nat Struct Mol Biol. 2007 Nov 11;. PMID:17994106

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (658 Kb) [Save to disk] Biological Unit Coordinates (2r7z.pdb1.gz) 647 Kb LPC: Ligand-Protein Contacts for 2R7Z CSU: Contacts of Structural Units for 2R7Z Likely Quarternary Molecular Structure file(s) for 2R7Z Structure Factors (1053 Kb) Retrieve 2R7Z in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2R7Z from S2C, [Save to disk] Re-refined 2r7z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2R7Z 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 2R7Z

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 2R7Z, from MSDmotif at EBI Fold representative 2r7z from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2r7z_B] [2r7z_E] [2r7z_D] [2r7z] [2r7z_P] [2r7z_H] [2r7z_K] [2r7z_C] [2r7z_J] [2r7z_A] [2r7z_N] [2r7z_L] [2r7z_F] [2r7z_I] [2r7z_G] [2r7z_T] 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 2R7Z: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART

Other resources with information on 2R7Z

Community annotation for 2R7Z at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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