5SVA Transcription, Transferase Dna date Aug 05, 2016
title Mediator-Rna Polymerase II Pre-Initiation Complex
authors P.J.Robinson, D.A.Bushnell, R.D.Kornberg
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit B1, Dna-Directed Rna Pol III Largest Subunit, Rna Polymerase 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: Rna Polymerase II Subunit 2, B150, Dna-Directed Rn 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 B3, B44.5, Dna-Directed 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, Dna-Directed Rn 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
Chain: E
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Abc27 Directed Rna Polymerases I, And III 27 Kda Polypeptide;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F
Synonym: Rna Polymerases I, II, And III Subunit Abc2, Abc23 Directed Rna Polymerases I, And III 23 Kda Polypeptide;
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
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Rna Polymerases I, II, And III Subunit Abc3, Abc14 Abc14.5, Dna-Directed Rna Polymerases I, And III 14.5 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, Dna-Directed 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
Chain: J
Synonym: Rna Polymerases I, II, And III Subunit Abc5, Abc10 Abc8, Dna-Directed Rna Polymerases I, And III 8.3 Kda Polyp
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, Dna-Directed 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
Chain: L
Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: M
Synonym: Mediator Complex Subunit 6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: N
Synonym: Mediator Complex Subunit 8
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: O
Synonym: Mediator Complex Subunit 11
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: P
Synonym: Mediator Complex Subunit 17, Suppressor Of Rna Pol 4;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: Q
Synonym: Mediator Complex Subunit 18, Suppressor Of Rna Pol 5;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: R
Synonym: Hyper-Recombination Suppressor Protein 2, Mediator Subunit 20, Suppressor Of Rna Polymerase B 2;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: S
Synonym: Mediator Complex Subunit 22, Suppressor Of Rna Pol 6;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: T
Synonym: Mediator Complex Subunit 4
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: U
Synonym: Mediator Complex Subunit 7
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: V
Synonym: Chromosome Segregation Protein 2, Mediator Complex 9;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: W
Synonym: Mediator Complex Subunit 21, Rnapii Complex Compon Suppressor Of Rna Polymerase B 7;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Mediator Of Rna Polymerase II Transcription Subun
Chain: X
Synonym: Hpr1 Suppressor Protein 1, Mediator Complex Subuni
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna Repair Helicase Rad3
Chain: Y
Synonym: General Transcription And Dna Repair Factor Iih Su Rad3, Tfiih Subunit Rad3;
Ec: 3.6.4.12
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna Repair Helicase Rad25
Chain: Z
Synonym: General Transcription And Dna Repair Factor Iih Su Rad25, Tfiih Subunit Rad25, Suppressor Of Stem-Loop Mutatio
Ec: 3.6.4.12
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Rna Polymerase II Transcription Factor B Subunit
Chain: a
Synonym: General Transcription And Dna Repair Factor Iih Su Tfb2, Tfiih Subunit Tfb2, Rna Polymerase II Transcription F Kda Subunit, Rna Polymerase II Transcription Factor B P52 S
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Rna Polymerase II Transcription Factor B Subunit
Chain: b
Synonym: General Transcription And Dna Repair Factor Iih Su Tfb5, Tfiih Subunit Tfb5;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iib
Chain: c
Synonym: General Transcription Factor Tfiib, Transcription
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Sua7, Ypr086w, P9513.4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Initiation Factor Iia Large Subunit
Chain: d
Synonym: Tfiia Large Subunit, Tfiia 32 Kda Subunit
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Toa1, Yor194c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Initiation Factor Iia Subunit 2
Chain: e
Synonym: General Transcription Factor Iia Subunit 2, Tfiia Subunit, Transcription Initiation Factor Iia Small Chain, Transcription Initiation Factor Iia Small Subunit;
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Toa2, Ykl058w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Initiation Factor Iif Subunit Alpha
Chain: f
Synonym: Tfiif-Alpha, Tfiif Large Subunit, Transcription Fa Kda Subunit, P105;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iif Subunit Beta
Chain: g
Synonym: Atp-Dependent Helicase Tfg2, Tfiif Medium Subunit, Beta, Transcription Factor G 54 Kda Subunit;
Ec: 3.6.4.12
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iie Subunit Alpha
Chain: h
Synonym: Tfiie-Alpha, Factor A 66 Kda Subunit, Transcriptio Large Subunit;
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Tfa1, Ykl028w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Initiation Factor Iie Subunit Beta
Chain: I
Synonym: Tfiie-Beta, Factor A 43 Kda Subunit, Transcription Small Subunit;
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Tfa2, Ykr062w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tata-Box-Binding Protein
Chain: j
Synonym: Tata Sequence-Binding Protein, Tbp, Tata-Binding F Tata-Box Factor, Transcription Factor D, Transcription Init Factor Tfiid Tbp Subunit;
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Spt15, Btf1, Tbp1, Yer148w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: k
Synonym: Rna Polymerase II Subunit B1, Dna-Directed Rna Pol III Largest Subunit, Rna Polymerase II Subunit B220;
Ec: 2.7.7.6
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 108bp His4 Promoter Non-Template Strand (-92+16)
Chain: l
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 108bp His4 Promoter Template Strand (+16-92)
Chain: m
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Tfiid Subunit 14
Chain: n
Synonym: Actin Non-Complementing Mutant 1, Chromosome Stabi Protein 10, Swisnf Chromatin-Remodeling Complex Subunit Ta Swisnf Complex 29 Kda Subunit, Swisnf Complex Subunit Taf Associated Factor 14, Tbp-Associated Factor 30 Kda, Transcr Factor G 30 Kda Subunit, Transcription Initiation Factor Tf Subunit
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
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 15.30 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


    N


    O


    P
  • transcription factor activit...


    • Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    a
  • ATPase activator activity


    • b

  • holo TFIIH complex
    • c


    d
  • transcription cofactor activ...


    • e


    f

  • transcription factor TFIIF c...
    • g

  • transcription factor TFIIF c...
    • h


    i


    j


    k


    n

  • transcription factor TFIID c...
  • transcription factor TFIIF c...
  • SWI/SNF complex
  • Ino80 complex
    • Primary referenceStructure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex., Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD, Cell. 2016 Sep 8;166(6):1411-1422.e16. doi: 10.1016/j.cell.2016.08.050. PMID:27610567
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1240 Kb) [Save to disk]
  • Biological Unit Coordinates (5sva.pdb1.gz) 1204 Kb
  • LPC: Ligand-Protein Contacts for 5SVA
  • CSU: Contacts of Structural Units for 5SVA
  • Retrieve 5SVA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5SVA from S2C, [Save to disk]
    • View 5SVA 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 5SVA
  • 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: [5sva_l] [5sva_M] [5sva_Y] [5sva_N] [5sva_S] [5sva_T] [5sva_J] [5sva_Q] [5sva_R] [5sva_h] [5sva_n] [5sva_I] [5sva_C] [5sva_P] [5sva_A] [5sva_a] [5sva_D] [5sva_f] [5sva_K] [5sva_i] [5sva] [5sva_B] [5sva_F] [5sva_d] [5sva_g] [5sva_c] [5sva_X] [5sva_j] [5sva_E] [5sva_W] [5sva_k] [5sva_e] [5sva_U] [5sva_H] [5sva_Z] [5sva_V] [5sva_O] [5sva_G] [5sva_L] [5sva_m] [5sva_b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5SVA: [BAG] [CYCLIN] [DEXDc] [DEXDc2] [HELICc] [HELICc2] [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [TFIIA] [TFIIE] [Tbf5] [ZnF_C2C2 ] by SMART
    • Other resources with information on 5SVA
  • Community annotation for 5SVA at PDBWiki (http://pdbwiki.org)

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