5FYW Transcription date Mar 10, 2016
title Transcription Initiation Complex Structures Elucidate Dna Op
authors C.Plaschka, M.Hantsche, C.Dienemann, C.Burzinski, J.Plitzko, P.Cr
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 Polyme Subunit B220, Rpb1;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Synonym: Rna Polymerase II Subunit 2, B150, Dna-Directed Rn Polymerase II 140 Kda Polypeptide, Rpb2;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

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, R

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4
Chain: D
Synonym: Rna Polymerase II Subunit B4, B32, Dna-Directed Rn Polymerase II 32 Kda Polypeptide, Rpb4;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 1;
Chain: E
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Abc27 Directed Rna Polymerases I, II, And III 27 Kda Polypeptide,

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 2;
Chain: F
Synonym: Rna Polymerases I, II, And III Subunit Abc2, Abc23 Directed Rna Polymerases I, II, And III 23 Kda Polypeptide,

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

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
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 3;
Chain: H
Synonym: Rna Polymerases I, II, And III Subunit Abc3, Abc14 .5, Dna-Directed Rna Polymerases I, II, And III 14.5 Kda Po Rpb8;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9, B12.6, Dna-Directed Polymerase II 14.2 Kda Polypeptide, Dna-Directed Rna Polyme Subunit 9, Rpb9;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 5;
Chain: J
Synonym: Rna Polymerases I, II, And III Subunit Abc5, Abc10 C8, Dna-Directed Rna Polymerases I, II, And III 8.3 Kda Pol Rpb10;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Rna Polymerase II Subunit B11, B13.6, Dna-Directed Polymerase II 13.6 Kda Polypeptide, Rpb11;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 4;
Chain: L
Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10 Pb12;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet21b

Molecule: Nontemplate Dna
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Tata-Box-Binding Protein
Chain: O
Synonym: Tata Sequence-Binding Protein, Tbp, Tata-Binding F Ta-Box Factor, Transcription Factor D, Transcription Initia Factor Tfiid Tbp Subunit;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Popine

Molecule: Transcription Initiation Factor Iif Subunit Alpha
Chain: Q
Synonym: Tfiif-Alpha, Tfiif Large Subunit, Transcription Fa Kda Subunit, P105, Tfg1;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Petduet-1

Molecule: Transcription Initiation Factor Iif Subunit Beta
Chain: R
Synonym: Atp-Dependent Helicase Tfg2, Tfiif Medium Subunit, Beta, Transcription Factor G 54 Kda Subunit, Tfg2;
Ec: 3.6.4.12
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Petduet-1

Molecule: Nontemplate Dna
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Transcription Initiation Factor Iia Large Subunit
Chain: U
Synonym: Tfiia Large Subunit, Tfiia 32 Kda Subunit, Toa1
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Popine

Molecule: Transcription Initiation Factor Iia Subunit 2
Chain: V
Synonym: General Transcription Factor Iia Subunit 2, Tfiia Subunit, Transcription Initiation Factor Iia Small Chain, Transcription Initiation Factor Iia Small Subunit, Toa2;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Popine

Molecule: Transcription Initiation Factor Iie Subunit Alpha
Chain: W
Synonym: Tfiie-Alpha, Factor A 66 Kda Subunit, Transcriptio Large Subunit, Tfa1;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet21

Molecule: Transcription Initiation Factor Iie Subunit Beta
Chain: X
Synonym: Tfiie-Beta, Factor A 43 Kda Subunit, Transcription Small Subunit, Tfa2;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet21
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 Microscopyresolution 4.35 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


    O


    Q

  • transcription factor TFIIF c...
  • R

  • transcription factor TFIIF c...
  • U
  • transcription cofactor activ...


  • V


    W


    X


    Primary referenceTranscription initiation complex structures elucidate DNA opening., Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P, Nature. 2016 May 11;533(7603):353-8. doi: 10.1038/nature17990. PMID:27193681
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (866 Kb) [Save to disk]
  • Biological Unit Coordinates (5fyw.pdb1.gz) 842 Kb
  • LPC: Ligand-Protein Contacts for 5FYW
  • CSU: Contacts of Structural Units for 5FYW
  • Retrieve 5FYW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FYW from S2C, [Save to disk]
  • View 5FYW in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5FYW
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5fyw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5fyw_D] [5fyw_Q] [5fyw_R] [5fyw_C] [5fyw_E] [5fyw_U] [5fyw_N] [5fyw_B] [5fyw_X] [5fyw_I] [5fyw_M] [5fyw_G] [5fyw_V] [5fyw_W] [5fyw_H] [5fyw_F] [5fyw] [5fyw_A] [5fyw_O] [5fyw_T] [5fyw_K] [5fyw_J] [5fyw_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5FYW: [CYCLIN] [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [TFIIA] [TFIIE] [ZnF_C2C2 ] by SMART
  • Other resources with information on 5FYW
  • Community annotation for 5FYW at PDBWiki (http://pdbwiki.org)

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