5OQJ Transcription date Aug 11, 2017
title Structure Of Yeast Transcription Pre-Initiation Complex With
authors S.Schilbach, M.Hantsche, D.Tegunov, C.Dienemann, C.Wigge, U.Henni 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 Bl21(De3)
Expression_system_taxid: 469008

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 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 Bl21(De3)
Expression_system_taxid: 469008

Molecule: Transcription Initiation Factor Iif Subunit Alpha
Chain: Q
Synonym: Tfiif-Alpha,Tfiif Large Subunit,Transcription Fact Kda Subunit,P105;
Engineered: Yes
Mutation: 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 Bl21(De3)
Expression_system_taxid: 469008

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 Bl21(De3)
Expression_system_taxid: 469008

Molecule: Template 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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Toa1, Yor194c
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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 Bl21(De3)
Expression_system_taxid: 469008

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfa1, Ykl028w
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfa2, Ykr062w
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna Repair Helicase Rad3
Chain
Synonym: General Transcription And Dna Repair Factor Iih Su Rad3,Tfiih Subunit Rad3,General Transcription And Dna Repai Iih Subunit Rad3,Tfiih Subunit Rad3,General Transcription A Repair Factor Iih Subunit Rad3,Tfiih Subunit Rad3;
Ec: 3.6.4.12,3.6.4.12,3.6.4.12
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Rad3, Rem1, Yer171w
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Rna Polymerase II Transcription Factor B Subunit
Chain: 1
Synonym: General Transcription And Dna Repair Factor Iih Su Tfb1,Tfiih Subunit Tfb1,Rna Polymerase II Transcription Fac Kda Subunit,Rna Polymerase II Transcription Factor B P73 Su General Transcription And Dna Repair Factor Iih Subunit Tfb Subunit Tfb1,Rna Polymerase II Transcription Factor B 73 Kd Rna Polymerase II Transcription Factor B P73 Subunit,Genera Transcription And Dna Repair Factor Iih Subunit Tfb1,Tfiih Tfb1,Rna Polymerase II Transcription Factor B 73 Kda Subuni Polymerase II Transcription Factor B P73 Subunit,General Transcription And Dna Repair Factor Iih Subunit Tfb1,Tfiih Tfb1,Rna Polymerase II Transcription Factor B 73 Kda Subuni Polymerase II Transcription Factor B P73 Subunit,General Transcription And Dna Repair Factor Iih Subunit Tfb1,Tfiih Tfb1,Rna Polymerase II Transcription Factor B 73 Kda Subuni Polymerase II Transcription Factor B P73 Subunit;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfb1, Ydr311w, D9740.3
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Rna Polymerase II Transcription Factor B Subunit
Chain: 2
Synonym: General Transcription And Dna Repair Factor Iih Su Tfb2,Tfiih Subunit Tfb2,Rna Polymerase II Transcription Fac Kda Subunit,Rna Polymerase II Transcription Factor B P52 Su General Transcription And Dna Repair Factor Iih Subunit Tfb Subunit Tfb2,Rna Polymerase II Transcription Factor B 52 Kd Rna Polymerase II Transcription Factor B P52 Subunit,Genera Transcription And Dna Repair Factor Iih Subunit Tfb2,Tfiih Tfb2,Rna Polymerase II Transcription Factor B 52 Kda Subuni Polymerase II Transcription Factor B P52 Subunit,General Transcription And Dna Repair Factor Iih Subunit Tfb2,Tfiih Tfb2,Rna Polymerase II Transcription Factor B 52 Kda Subuni Polymerase II Transcription Factor B P52 Subunit,General Transcription And Dna Repair Factor Iih Subunit Tfb2,Tfiih Tfb2,Rna Polymerase II Transcription Factor B 52 Kda Subuni Polymerase II Transcription Factor B P52 Subunit,General Transcription And Dna Repair Factor Iih Subunit Tfb2,Tfiih Tfb2,Rna Polymerase II Transcription Factor B 52 Kda Subuni Polymerase II Transcription Factor B P52 Subunit,General Transcription And Dna Repair Factor Iih Subunit Tfb2,Tfiih Tfb2,Rna Polymerase II Transcription Factor B 52 Kda Subuni Polymerase II Transcription Factor B P52 Subunit;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfb2, Ypl122c
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Rna Polymerase II Transcription Factor B Subunit
Chain: 3
Synonym: Rna Polymerase II Transcription Factor B 38 Kda Su Polymerase II Transcription Factor B P38 Subunit;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfb3, Rig2, Ydr460w
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Rna Polymerase II Transcription Factor B Subunit
Chain: 4
Synonym: General Transcription And Dna Repair Factor Iih Su Tfb4,Tfiih Subunit Tfb4,Rna Polymerase II Transcription Fac Kda Subunit,Rna Polymerase II Transcription Factor B P34 Su General Transcription And Dna Repair Factor Iih Subunit Tfb Subunit Tfb4,Rna Polymerase II Transcription Factor B 34 Kd Rna Polymerase II Transcription Factor B P34 Subunit,Genera Transcription And Dna Repair Factor Iih Subunit Tfb4,Tfiih Tfb4,Rna Polymerase II Transcription Factor B 34 Kda Subuni Polymerase II Transcription Factor B P34 Subunit,General Transcription And Dna Repair Factor Iih Subunit Tfb4,Tfiih Tfb4,Rna Polymerase II Transcription Factor B 34 Kda Subuni Polymerase II Transcription Factor B P34 Subunit,General Transcription And Dna Repair Factor Iih Subunit Tfb4,Tfiih Tfb4,Rna Polymerase II Transcription Factor B 34 Kda Subuni Polymerase II Transcription Factor B P34 Subunit;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfb4, Ypr056w
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Rna Polymerase II Transcription Factor B Subunit
Chain: 5
Synonym: General Transcription And Dna Repair Factor Iih Su Tfb5,Tfiih Subunit Tfb5;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Tfb5, Ydr079c-A
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Suppressor Of Stem-Loop Protein 1
Chain: 6
Synonym: General Transcription And Dna Repair Factor Iih Su Ssl1,Tfiih Subunit Ssl1,General Transcription And Dna Repai Iih Subunit Ssl1,Tfiih Subunit Ssl1,General Transcription A Repair Factor Iih Subunit Ssl1,Tfiih Subunit Ssl1,General Transcription And Dna Repair Factor Iih Subunit Ssl1,Tfiih Ssl1,General Transcription And Dna Repair Factor Iih Subuni Tfiih Subunit Ssl1,General Transcription And Dna Repair Fac Subunit Ssl1,Tfiih Subunit Ssl1,General Transcription And D Factor Iih Subunit Ssl1,Tfiih Subunit Ssl1;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Ssl1, Ylr005w
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Dna Repair Helicase Rad25
Chain: 7
Synonym: General Transcription And Dna Repair Factor Iih Su Rad25,Tfiih Subunit Rad25,Suppressor Of Stem-Loop Mutation Transcription And Dna Repair Factor Iih Subunit Rad25,Tfiih Rad25,Suppressor Of Stem-Loop Mutation 2,General Transcript Dna Repair Factor Iih Subunit Rad25,Tfiih Subunit Rad25,Sup Stem-Loop Mutation 2,General Transcription And Dna Repair F Subunit Rad25,Tfiih Subunit Rad25,Suppressor Of Stem-Loop M General Transcription And Dna Repair Factor Iih Subunit Rad Subunit Rad25,Suppressor Of Stem-Loop Mutation 2;
Ec: 3.6.4.12,3.6.4.12,3.6.4.12,3.6.4.12,3.6.4.12
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Ssl2, Lom3, Rad25, Uvs112, Yil143c
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Unknown Protein
Chain: Z
Engineered: Yes
Other_details: Residues Indicated As Unk With The Chain Ide Are Part Of An Assembly Between The Clutch Domains Of Tfb2 But Could Not Be Assigned To Any Of The Two Proteins With C Since Domain Swappingbeta-Strand Exchange May Occur. To Ac This Uncertainty, A Theoretical Chain Z Was Introduced For Residue Range But Not Assigned To Any Of The Pic Components

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
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 4.70 Å
ligand MG, SF4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
0


1


2
  • ATPase activator activity


  • 3

  • holo TFIIH complex
  • 4

  • holo TFIIH complex
  • 5

  • holo TFIIH complex
  • 6
  • ubiquitin protein ligase act...


  • 7


    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 referenceStructures of transcription pre-initiation complex with TFIIH and Mediator., Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P, Nature. 2017 Nov 9;551(7679):204-209. doi: 10.1038/nature24282. Epub 2017 Nov 1. PMID:29088706
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1119 Kb) [Save to disk]
  • Biological Unit Coordinates (5oqj.pdb1.gz) 1086 Kb
  • LPC: Ligand-Protein Contacts for 5OQJ
  • CSU: Contacts of Structural Units for 5OQJ
  • Retrieve 5OQJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OQJ from S2C, [Save to disk]
  • View 5OQJ 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 5OQJ
  • 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 5oqj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5oqj_X] [5oqj_4] [5oqj_0] [5oqj_D] [5oqj_U] [5oqj_1] [5oqj_B] [5oqj_M] [5oqj_7] [5oqj_O] [5oqj_R] [5oqj_V] [5oqj_J] [5oqj_F] [5oqj_I] [5oqj_W] [5oqj_L] [5oqj_E] [5oqj_G] [5oqj_C] [5oqj_K] [5oqj_3] [5oqj_H] [5oqj_2] [5oqj_Z] [5oqj_5] [5oqj_A] [5oqj_T] [5oqj_Q] [5oqj_N] [5oqj_6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5OQJ
  • Community annotation for 5OQJ at PDBWiki (http://pdbwiki.org)

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