4A3I Transcription date Sep 30, 2011
title Rna Polymerase II Binary Complex With Dna
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 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(Gpgpcpapcpapapcptpgpcpgpgpcpt
Chain: N
Synonym: Non Template Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Template Dna 27-Mer
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 2 2 21
R_factor 0.159 R_Free 0.191
crystal
cell
length a length b length c angle alpha angle beta angle gamma
221.140 393.180 282.480 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand BRU, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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 referenceStructural 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] (1379 Kb) [Save to disk]
  • Biological Unit Coordinates (4a3i.pdb1.gz) 1364 Kb
  • LPC: Ligand-Protein Contacts for 4A3I
  • CSU: Contacts of Structural Units for 4A3I
  • Structure Factors (1695 Kb)
  • Retrieve 4A3I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4A3I from S2C, [Save to disk]
  • Re-refined 4a3i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4A3I in 3D
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  • Visual 3D analysis of 4A3I
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  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4A3I, from MSDmotif at EBI
  • Fold representative 4a3i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4a3i_C] [4a3i_F] [4a3i_H] [4a3i_B] [4a3i_T] [4a3i] [4a3i_G] [4a3i_J] [4a3i_E] [4a3i_L] [4a3i_K] [4a3i_N] [4a3i_D] [4a3i_I] [4a3i_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4A3I: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
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