5VVR	Transcription Rna Dna	date	May 19, 2017
title	Ternary Complex Of Rna Pol II, Transcription Scaffold And Ra
authors	I.Lahiri, A.E.Leschziner
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 (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 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 (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 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 (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 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 (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: E Synonym: Rna Polymerases I,II,And III Subunit Abc1,Abc27,Dn Rna Polymerases I,And III 27 Kda Polypeptide;		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: F Synonym: Rna Polymerases I,II,And III Subunit Abc2,Abc23,Dn Rna Polymerases I,And III 23 Kda Polypeptide;		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 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 (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: 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 (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
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 (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
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 (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: L Synonym: Rna Polymerases I,II,And III Subunit Abc4,Abc10-Al		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna Repair And Recombination Protein Rad26 Chain: M Synonym: Atp-Dependent Helicase Rad26 Ec: 3.6.4.12		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna (Nts) Chain: N Engineered: Yes		Synthetic: Yes Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Rna Chain: R Engineered: Yes		Synthetic: Yes Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna (Ts) Chain: T Engineered: Yes		Synthetic: Yes Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
symmetry	Space Group: P 1	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 1.000 1.000 1.000 90.00 90.00 90.00
method	Electron Microscopy	resolution	5.80 Å
ligand	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... M DNA helicase activity
Primary reference	Structural basis for the initiation of eukaryotic transcription-coupled DNA repair., Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang D, Nature. 2017 Nov 30;551(7682):653-657. doi: 10.1038/nature24658. Epub 2017 Nov, 22. PMID:29168508

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (766 Kb) [Save to disk] Biological Unit Coordinates (5vvr.pdb1.gz) 756 Kb LPC: Ligand-Protein Contacts for 5VVR CSU: Contacts of Structural Units for 5VVR Retrieve 5VVR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5VVR from S2C, [Save to disk]

View 5VVR in 3D

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Visual 3D analysis of 5VVR

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Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5vvr_E] [5vvr_L] [5vvr_J] [5vvr_A] [5vvr_H] [5vvr_C] [5vvr_T] [5vvr_M] [5vvr_F] [5vvr_K] [5vvr_B] [5vvr_R] [5vvr_G] [5vvr_I] [5vvr_N] [5vvr_D] SWISS-PROT database: Domain organization of by SWISSPFAM

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