4BBS Transcription date Sep 27, 2012
title Structure Of An Initially Transcribing Rna Polymerase II- Tfiib Complex
authors S.Sainsbury, J.Niesser, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit 1, Rna Polymerase II Sub Dna-Directed Rna Polymerase III Largest Subunit, Rna Polym Subunit B220, Rpb1;
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, B150, Rpb2, 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: Rna Polymerase II Subunit 3, Rna Polymerase II Sub 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: Rna Polymerase II Subunit B4, B32, Rpb4, 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: Rna Polymerases I, II, And III Subunit Abc1, Abc27 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: Rna Polymerases I, II, And III Subunit Abc2, Abc23 Dna-Directed Rna Polymerases I, II, And III 23 Kda Polypep

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, Rpb7

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: Rna Polymerases I, II, And III Subunit Abc3, Abc14 Abc14.5, Rpb8, Dna-Directed Rna Polymerases I, II, And III 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: Rna Polymerase II Subunit B9, B12.6, Rpb9, 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: Rna Polymerases I, II, And III Subunit Abc5, Abc10 Abc8, Rpb10, Dna-Directed Rna Polymerases I, II, And III 8 Polypeptide;

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, B13.6, Rpb11, 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: Rna Polymerases I, II, And III Subunit Abc4, Abc10 Rpb12;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iib
Chain: M
Synonym: General Transcription Factor Tfiib, Transcription E, Tfiib;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Gpgpcpapcpapapcptpgpcpgpcptp)-
Chain: N
Synonym: Non-Template Dna

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5'-D(Apgpcpgpcpapgptptpgptpgpcptp Aptpgpaptpaptptptptptpaptp)-3';
Chain: T
Synonym: Template Dna

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5'-R(Apupapupcpap)-3'
Chain: P
Synonym: Rna Product

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
symmetry Space Group: C 2 2 21
R_factor 0.1847 R_Free 0.2250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
222.170 386.010 254.470 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand 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...


  • M


    Primary referenceStructure and function of the initially transcribing RNA polymerase II-TFIIB complex., Sainsbury S, Niesser J, Cramer P, Nature. 2012 Nov 14. doi: 10.1038/nature11715. PMID:23151482
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1447 Kb) [Save to disk]
  • Biological Unit Coordinates (4bbs.pdb1.gz) 1430 Kb
  • LPC: Ligand-Protein Contacts for 4BBS
  • CSU: Contacts of Structural Units for 4BBS
  • Structure Factors (2157 Kb)
  • Retrieve 4BBS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BBS from S2C, [Save to disk]
  • Re-refined 4bbs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BBS in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4BBS
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  • 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 4BBS, from MSDmotif at EBI
  • Fold representative 4bbs from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bbs_I] [4bbs_H] [4bbs_E] [4bbs_F] [4bbs_C] [4bbs_L] [4bbs_A] [4bbs_B] [4bbs_J] [4bbs_G] [4bbs_D] [4bbs] [4bbs_P] [4bbs_M] [4bbs_K] [4bbs_N] [4bbs_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4BBS: [CYCLIN] [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
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