6GYK Transcription date Jun 30, 2018
title Structure Of A Yeast Closed Complex (Core Cc1)
authors C.Dienemann, B.Schwalb, S.Schilbach, P.Cramer
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

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

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

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

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

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

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Rna Polymerase II Subunit B7,B16

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

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

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

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

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

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

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Sua7, Ypr086w, P9513.4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Gat1 Promoter
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Spt15, Btf1, Tbp1, Yer148w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfg1, Ssu71, Ygr186w, G7526
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfg2, Ygr005c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Gat1 Promoter Dna
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Toa1, Yor194c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Initiation Factor Iia Subunit 2
Chain: V
Synonym: General Transcription Factor Iia Subunit 2,Tfiia 1 Subunit,Transcription Initiation Factor Iia Small Chain,Tra Initiation Factor Iia Small Subunit;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Toa2, Ykl058w
Expression_system: Escherichia Coli
Expression_system_taxid: 562
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 5.10 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


    V


    Primary referencePromoter Distortion and Opening in the RNA Polymerase II Cleft., Dienemann C, Schwalb B, Schilbach S, Cramer P, Mol Cell. 2018 Nov 16. pii: S1097-2765(18)30846-3. doi:, 10.1016/j.molcel.2018.10.014. PMID:30472190
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (719 Kb) [Save to disk]
  • Biological Unit Coordinates (6gyk.pdb1.gz) 703 Kb
  • LPC: Ligand-Protein Contacts for 6GYK
  • CSU: Contacts of Structural Units for 6GYK
  • Retrieve 6GYK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6GYK from S2C, [Save to disk]
  • View 6GYK 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 6GYK
  • Ramachandran plot from PDBSum
  • 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: [6gyk_H] [6gyk_O] [6gyk_M] [6gyk_N] [6gyk_J] [6gyk_Q] [6gyk_R] [6gyk_L] [6gyk_V] [6gyk_B] [6gyk_T] [6gyk_C] [6gyk_F] [6gyk_I] [6gyk_A] [6gyk_E] [6gyk_G] [6gyk_K] [6gyk_U] [6gyk_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6GYK
  • Community annotation for 6GYK at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science