4A3J	Transcription	date	Sep 30, 2011
title	Rna Polymerase II Initial Transcribing Complex With A 2nt Dna-Rna Hybrid And Soaked With Gmpcpp
authors	A.C.M.Cheung, S.Sainsbury, P.Cramer
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 Subunit B1, Dna-Directed Rna Polymerase III Largest Subuni Polymerase 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 Subunit B3, B44.5, Dna-Directed Rna Polymerase II 45 Kda Polypeptide;		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 Polypep		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 Polypep		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, Abc14.4, Abc14.5, Dna-Directed Rna Polymerases I\,II\,And Kda 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 Rna Polymerase II 14.2 Kda Polypeptide, Dna-Directed Rna Polymerase II 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 Abc10-Beta, Abc8, Dna-Directed Rna Polymerases I\,II\,And Kda 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 Abc10-Alpha;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: 5'-D(Gptpapgpapapapgpcptpapgpcptp)- Chain: N Synonym: Non Template Dna		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: 5'-R(Cpap)-3' Chain: P Synonym: Transcript Rna		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: 5'-D(Apgpcptpapgpcptptptpcpbrupapcp Tpgpapapcpapapcptpapapcp)-3'; Chain: T Synonym: Template Dna		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: C 2 2 21	R_factor 0.1567 R_Free 0.1939
crystal cell	length a length b length c angle alpha angle beta angle gamma 223.290 392.790 282.660 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.70 Å
ligand	BRU, G2P, 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	Structural basis of initial RNA polymerase II transcription., Cheung AC, Sainsbury S, Cramer P, EMBO J. 2011 Nov 4. doi: 10.1038/emboj.2011.396. PMID:22056778

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1377 Kb) [Save to disk] Biological Unit Coordinates (4a3j.pdb1.gz) 1361 Kb LPC: Ligand-Protein Contacts for 4A3J CSU: Contacts of Structural Units for 4A3J Structure Factors (1053 Kb) Retrieve 4A3J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 4A3J from S2C, [Save to disk] Re-refined 4a3j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4A3J in 3D

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Visual 3D analysis of 4A3J

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Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 4A3J, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4a3j_I] [4a3j_H] [4a3j_C] [4a3j] [4a3j_J] [4a3j_F] [4a3j_T] [4a3j_L] [4a3j_A] [4a3j_P] [4a3j_G] [4a3j_D] [4a3j_K] [4a3j_N] [4a3j_B] [4a3j_E] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 4A3J: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART

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