5IY9 Transcription, Transferase Dna Rna date Mar 24, 2016
title Human Holo-Pic In The Initial Transcribing State (No Iis)
authors Y.He, C.Yan, J.Fang, C.Inouye, R.Tjian, I.Ivanov, E.Nogales
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit B1, Dna-Directed Rna Pol Subunit A, Dna-Directed Rna Polymerase III Largest Subunit, Directed Rna Polymerase II Subunit Rpb1;
Ec: 2.7.7.6,2.7.7.48
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Synonym: Dna-Directed Rna Polymerase II 140 Kda Polypeptide Directed Rna Polymerase II Subunit B, Rna Polymerase II Sub Rna Polymerase II Subunit B2;
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit B3, Dna-Directed Rna Pol 33 Kda Polypeptide, Rpb33, Dna-Directed Rna Polymerase II S Rpb31;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4
Chain: D
Synonym: Rna Polymerase II Subunit B4, Dna-Directed Rna Pol Subunit D, Rna Polymerase II 16 Kda Subunit, Rpb16;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb5
Chain: E
Synonym: Rna Polymerases I,II,And III Subunit Abc1, Dna-Dir Dna-Directed Rna Polymerases I, II, And III Subunit Rpabc1, Polymerase II 23 Kda Polypeptide, Dna-Directed Rna Polymera Subunit E, Xap4;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb6
Chain: F
Synonym: Dna-Directed Rna Polymerases I, II, And III Subuni Rna Polymerases I,II,And III Subunit Abc2, Dna-Directed Rna Polymerase II Subunit F, Dna-Directed Rna Polymerases I,And Kda Polypeptide, Rpabc14.4, Rpb14.4, Rpc15;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Rna Polymerase II Subunit B7, Dna-Directed Rna Pol Subunit G, Rna Polymerase II 19 Kda Subunit, Rpb19;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb8
Chain: H
Synonym: Dna-Directed Rna Polymerases I, II, And III Subuni Rna Polymerases I,II,And III Subunit Abc3, Dna-Directed Rna Polymerase II Subunit H, Dna-Directed Rna Polymerases I, II 17.1 Kda Polypeptide, Rpb17, Hrpb8;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9, Dna-Directed Rna Pol Subunit I, Rna Polymerase II 14.5 Kda Subunit, Rpb14.5;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb10
Chain: J
Synonym: Dna-Directed Rna Polymerases I, II, And III Subuni Rna Polymerases I,II,And III Subunit Abc5, Dna-Directed Rna Polymerase III Subunit L, Rna Polymerase II 7.6 Kda Subunit
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11-A
Chain: K
Synonym: Rpb11a, Dna-Directed Rna Polymerase II Subunit J-1 Polymerase II 13.3 Kda Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb12
Chain: L
Synonym: Dna-Directed Rna Polymerases I, II, And III Subuni Rna Polymerases I,II,And III Subunit Abc4, Abc10-Alpha, Dna Rna Polymerase II Subunit K, Rna Polymerase II 7.0 Kda Subu Rpb7.0, Rpb10alpha;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Transcription Initiation Factor Iib
Chain: M
Synonym: General Transcription Factor Tfiib, S300-II
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gtf2b, Tf2b, Tfiib
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Initiation Factor Iia Subunit 1
Chain: N
Synonym: General Transcription Factor Iia Subunit 1, Tfiial Transcription Initiation Factor Tfiia 42 Kda Subunit, Tfiia
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gtf2a1, Tf2a1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Initiation Factor Iia Subunit 2
Chain: O
Synonym: General Transcription Factor Iia Subunit 2, Tfiia Subunit, Tfiias, Transcription Initiation Factor Iia Gamma Tfiia-Gamma;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gtf2a2, Tf2a2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tata-Box-Binding Protein
Chain: P
Synonym: Tata Sequence-Binding Protein, Tata-Binding Factor Factor, Transcription Initiation Factor Tfiid Tbp Subunit;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tbp, Gtf2d1, Tf2d, Tfiid
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: General Transcription Factor Iie Subunit 1
Chain: Q
Synonym: General Transcription Factor Iie 56 Kda Subunit, Transcription Initiation Factor Iie Subunit Alpha, Tfiie-Al
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gtf2e1, Tf2e1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Initiation Factor Iie Subunit Beta
Chain: R
Synonym: Tfiie-Beta, General Transcription Factor Iie Subun
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gtf2e2, Tf2e2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: General Transcription Factor Iif Subunit 1
Chain: S
Synonym: General Transcription Factor Iif 74 Kda Subunit, Transcription Initiation Factor Iif Subunit Alpha, Tfiif-Al Transcription Initiation Factor Rap74;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gtf2f1, Rap74
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: General Transcription Factor Iif Subunit 2
Chain: T
Synonym: Atp-Dependent Helicase Gtf2f2, General Transcripti Iif 30 Kda Subunit, Transcription Initiation Factor Iif Sub Tfiif-Beta, Transcription Initiation Factor Rap30;
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gtf2f2, Rap30
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tfiih Basal Transcription Factor Complex Helicase Subunit;
Chain: V
Synonym: Basic Transcription Factor 2 89 Kda Subunit, Btf2 Excision Repair Protein Ercc-3, Dna Repair Protein Compleme Cells, Tfiih Basal Transcription Factor Complex 89 Kda Subu P89, Xeroderma Pigmentosum Group B-Complementing Protein;
Ec: 3.6.4.12
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Tfiih Basal Transcription Factor Complex Helicase Subunit;
Chain: W
Synonym: Basic Transcription Factor 2 80 Kda Subunit,Btf2 P Dna Excision Repair Protein Ercc-2, Dna Repair Protein Comp Xp-D Cells, Tfiih Basal Transcription Factor Complex 80 Kda Tfiih P80, Xeroderma Pigmentosum Group D-Complementing Prot
Ec: 3.6.4.12
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: General Transcription Factor Iih Subunit 2
Chain
Synonym: Basic Transcription Factor 2 44 Kda Subunit,Btf2 P General Transcription Factor Iih Polypeptide 2, Tfiih Basal Transcription Factor Complex P44 Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: General Transcription Factor Iih Subunit 5
Chain: 1
Synonym: General Transcription Factor Iih Polypeptide 5, Tf Ortholog,Tfiih Basal Transcription Factor Complex Ttd-A Sub
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: General Transcription Factor Iih Subunit 4
Chain: 2
Synonym: Basic Transcription Factor 2 52 Kda Subunit, Btf2 General Transcription Factor Iih Polypeptide 4, Tfiih Basal Transcription Factor Complex P52 Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: General Transcription Factor Iih Subunit 3
Chain: 3
Synonym: Basic Transcription Factor 2 34 Kda Subunit, Btf2 General Transcription Factor Iih Polypeptide 3, Tfiih Basal Transcription Factor Complex P34 Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Scp-X
Chain: X
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Scp-Y
Chain: Y
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Rna
Chain: Z
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
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 6.30 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
0
  • RNA polymerase II carboxy-te...


    • 1


    2
  • ATPase activator activity


    • 3


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


    • B


    C


    D


    E
  • RNA polymerase III activity


    • F
  • RNA polymerase III activity


    • G


    H
  • RNA polymerase III activity


    • I


    J


    K


    L


    M
  • histone acetyltransferase ac...


    • N
  • transcription coactivator ac...


    • O


    P

  • transcription factor TFIID c...
    • Q


    R


    S
  • phosphatase activator activi...


    • T
  • DNA helicase activity


    • V
  • protein kinase activity
  • RNA polymerase II carboxy-te...


    • W
  • protein kinase activity
  • RNA polymerase II carboxy-te...


    • Primary referenceNear-atomic resolution visualization of human transcription promoter opening., He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E, Nature. 2016 May 11;533(7603):359-65. doi: 10.1038/nature17970. PMID:27193682
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1075 Kb) [Save to disk]
  • Biological Unit Coordinates (5iy9.pdb1.gz) 1065 Kb
  • LPC: Ligand-Protein Contacts for 5IY9
  • CSU: Contacts of Structural Units for 5IY9
  • Retrieve 5IY9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IY9 from S2C, [Save to disk]
    • View 5IY9 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 5IY9
  • 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 5iy9 from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5iy9] [5iy9_K] [5iy9_R] [5iy9_L] [5iy9_0] [5iy9_S] [5iy9_A] [5iy9_J] [5iy9_W] [5iy9_Z] [5iy9_O] [5iy9_G] [5iy9_H] [5iy9_2] [5iy9_P] [5iy9_3] [5iy9_1] [5iy9_C] [5iy9_D] [5iy9_X] [5iy9_B] [5iy9_N] [5iy9_Y] [5iy9_F] [5iy9_Q] [5iy9_M] [5iy9_V] [5iy9_E] [5iy9_I] [5iy9_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IY9: [C1_4] [CYCLIN] [DEXDc] [DEXDc2] [HELICc] [HELICc2] [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [TFIIA] [TFIIE] [Tbf5] [VWA] [ZnF_C2C2 ] by SMART
    • Other resources with information on 5IY9
  • Community annotation for 5IY9 at PDBWiki (http://pdbwiki.org)

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