5C4J	Transferase Dna Rna	date	Jun 18, 2015
title	Crystal Structure Of A Transcribing Rna Polymerase II Comple A Complete Transcription Bubble
authors	C.O.Barnes, M.Calero, I.Malik, H.Spahr, Q.Zhang, F.Pullara, C.D.Ka G.Calero
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 Atcc: 204508
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 Atcc: 204508
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 Atcc: 204508
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 Atcc: 204508
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 Atcc: 204508
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 Atcc: 204508
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 Atcc: 204508
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 Atcc: 204508
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 Atcc: 204508
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 Atcc: 204508
Molecule: Rna (5'-R(Pupcpgpapgpapgpgpa)-3') Chain: R Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Non-Template Strand Dna (38-Mer) Chain: S Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Template Strand Dna (38-Mer) Chain: U Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: C 1 2 1	R_factor 0.212 R_Free 0.271
crystal cell	length a length b length c angle alpha angle beta angle gamma 280.711 223.384 156.422 90.00 98.14 90.00
method	X-Ray Diffraction	resolution	4.00 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... E RNA-directed 5'-3' RNA polym... F 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	Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble., Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA, Kaplan CD, Calero G, Mol Cell. 2015 Jul 16;59(2):258-69. doi: 10.1016/j.molcel.2015.06.034. PMID:26186291

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1312 Kb) [Save to disk] Biological Unit Coordinates (5c4j.pdb1.gz) 1302 Kb LPC: Ligand-Protein Contacts for 5C4J CSU: Contacts of Structural Units for 5C4J Structure Factors (1533 Kb) Retrieve 5C4J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5C4J from S2C, [Save to disk] Re-refined 5c4j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

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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: [5c4j_A] [5c4j_L] [5c4j_B] [5c4j_I] [5c4j_J] [5c4j_R] [5c4j] [5c4j_U] [5c4j_C] [5c4j_S] [5c4j_K] [5c4j_F] [5c4j_H] [5c4j_E] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5C4J: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART

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