5FMF Transcription date Nov 03, 2015
title The P-Lobe Of Rna Polymerase II Pre-Initiation Complex
authors K.Murakami, K.Tsai, N.Kalisman, D.A.Bushnell, F.J.Asturias, R.D.K
compound source
Molecule: Dna Repair Helicase Rad25, Ssl2
Chain: 1
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: Transcription Elongation Factor S-II, Dst1
Chain: 2
Synonym: Dna Strand Transfer Protein Alpha, Stp-Alpha, Dna Transferase 1, Pyrimidine Pathway Regulatory Protein 2;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

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: Rna Polymerase II Pre-Initiation Complex, Rpb4
Chain: D
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Rpb5;
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 Rpb6;
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 Rpb8;
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 Rpb10;
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 Rpb12;
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: Rna Polymerase II Pre-Initiation Complex, Toa1
Chain: M
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Non-Template Strand Dna
Chain: N
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iia Subunit 2, To
Chain: O
Synonym: General Transcription Factor Iia Subunit 2, Tfiia Subunit, Transcription Initiation Factor Iia Small Chain, Transcription Initiation Factor Iia Small Subunit;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iib, Sua7
Chain: P
Synonym: General Transcription Factor Tfiib, Transcription
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Tata-Box-Binding Protein, Tbp
Chain: Q
Synonym: Tata Sequence-Binding Protein, Tbp, Tata-Binding F Tata- Box Factor, Transcription Factor D, Transcription Ini Factor Tfiid Tbp Subunit;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iie Subunit Alpha
Chain: R
Synonym: Tfiie-Alpha, Factor A 66 Kda Subunit, Transcriptio Large Subunit;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iie Subunit Beta,
Chain: S
Synonym: Tfiie-Beta, Factor A 43 Kda Subunit, Transcription Small Subunit;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Template Strand Dna
Chain: T
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Rna Polymerase II Pre-Initiation Complex, Tfg1
Chain: U
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Transcription Initiation Factor Iif Subunit Beta,
Chain: V
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: Rna Polymerase II Transcription Factor B Subunit
Chain: W
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: X
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: 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
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 6.00 Å
ligand MG, ZN enzyme Hydrolase E.C.3.6.4.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
1


2


A
  • RNA-directed 5'-3' RNA polym...


    • B
  • RNA-directed 5'-3' RNA polym...


    • C


    D


    E
  • RNA-directed 5'-3' RNA polym...


    • F


    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


    M


    O


    P


    Q


    R


    S


    U


    V


    W


    X


    Y


    Primary referenceStructure of an RNA polymerase II preinitiation complex., Murakami K, Tsai KL, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD, Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13543-8. doi:, 10.1073/pnas.1518255112. Epub 2015 Oct 19. PMID:26483468
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (971 Kb) [Save to disk]
  • Biological Unit Coordinates (5fmf.pdb1.gz) 956 Kb
  • LPC: Ligand-Protein Contacts for 5FMF
  • CSU: Contacts of Structural Units for 5FMF
  • Retrieve 5FMF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FMF from S2C, [Save to disk]
    • View 5FMF 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 5FMF
  • 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: [5fmf_D] [5fmf_H] [5fmf_V] [5fmf_X] [5fmf_C] [5fmf_L] [5fmf_T] [5fmf_O] [5fmf_Y] [5fmf_P] [5fmf_F] [5fmf_B] [5fmf_A] [5fmf_2] [5fmf_1] [5fmf_K] [5fmf_J] [5fmf_Q] [5fmf] [5fmf_G] [5fmf_N] [5fmf_U] [5fmf_M] [5fmf_E] [5fmf_R] [5fmf_I] [5fmf_W] [5fmf_S]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5FMF: [CYCLIN] [DEXDc] [DEXDc2] [HELICc] [HELICc2] [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [TFIIA] [TFIIE] [TFS2M] [Tbf5] [ZnF_C2C2 ] by SMART
    • Other resources with information on 5FMF
  • Community annotation for 5FMF at PDBWiki (http://pdbwiki.org)

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