6O9L Transcription Dna date Mar 14, 2019
title Human Holo-Pic In The Closed State
authors C.L.Yan, T.Dodd, Y.He, J.A.Tainer, S.E.Tsutakawa, I.Ivanov
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit B1,Dna-Directed Rna Poly Subunit A,Dna-Directed Rna Polymerase III Largest Subunit,R 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 Subu 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 Poly 33 Kda Polypeptide,Rpb33,Dna-Directed Rna Polymerase II Sub 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 Poly 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 Polymerases I, II, And III Subun
Chain: F
Synonym: Rna Polymerases I,II,And III Subunit Abc2,Dna-Dire Polymerase II Subunit F,Dna-Directed Rna Polymerases I,And Kda Polypeptide,Rpabc14.4,Rpb14.4,Rpb6 Homolog,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 Poly Subunit G,Rna Polymerase II 19 Kda Subunit,Rpb19;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Rna Polymerases I,II,And III Subunit Abc3,Dna-Dire Polymerase II Subunit H,Dna-Directed Rna Polymerases I,And Kda Polypeptide,Rpb17,Rpb8 Homolog,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 Poly 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 Polymerases I, II, And III Subun
Chain: J
Synonym: Rna Polymerases I,II,And III Subunit Abc5,Dna-Dire Polymerase III Subunit L,Rna Polymerase II 7.6 Kda Subunit, Rpb10 Homolog;

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 Polymerases I, II, And III Subun
Chain: L
Synonym: Rna Polymerases I,II,And III Subunit Abc4,Abc10-Al Directed Rna Polymerase II Subunit K,Rna Polymerase II 7.0 Subunit,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
Ec: 2.3.1.48
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-

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Transcription Initiation Factor Iia Subunit 2
Chain: O
Synonym: General Transcription Factor Iia Subunit 2,Tfiia P Subunit,Tfiias,Transcription Initiation Factor Iia Gamma Ch 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-Alp
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 Subuni
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-Alp 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 Transcriptio Iif 30 Kda Subunit,Transcription Initiation Factor Iif Subu 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: Transcription Elongation Factor A Protein 1
Chain: U
Synonym: Transcription Elongation Factor S-II Protein 1, Transcription Elongation Factor Tfiis.O;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Tfiih Basal Transcription Factor Complex Helicase Subunit;
Chain
Synonym: Basic Transcription Factor 2 80 Kda Subunit, Btf2 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
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ercc2, Xpd, Xpdc
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: General Transcription Factor Iih Subunit 1
Chain: 1
Synonym: Basic Transcription Factor 2 62 Kda Subunit,Btf2 P Transcription Factor Iih Polypeptide 1,Tfiih Basal Transcri Factor Complex P62 Subunit;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: General Transcription Factor Iih Subunit 4, P52
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: Cdk-Activating Kinase Assembly Factor Mat1
Chain: 3
Synonym: Cdk7cyclin-H Assembly Factor,Cyclin-G1-Interactin Menage A Trois,Ring Finger Protein 66,Ring Finger Protein M P36;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: General Transcription Factor Iih Subunit 3
Chain: 4
Synonym: P34, Basic Transcription Factor 2 44 Kda Subunit, 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: 5
Synonym: General Transcription Factor Iih Polypeptide 5, Tf Ortholog, Tfiih Basal Transcription Factor Complex Ttd-A Su

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: General Transcription Factor Iih Subunit 2
Chain: 6
Synonym: Basic Transcription Factor 2 44 Kda Subunit, Btf2 General Transcription Factor Iih Polypeptide 2, Tfiih Basal Transcription Factor Complex P44 Subunit;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Tfiih Basal Transcription Factor Complex Helicase Subunit;
Chain: 7
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: Cyclin-Dependent Kinase 7
Chain: 8
Synonym: 39 Kda Protein Kinase,P39 Mo15,Cdk-Activating Kina Division Protein Kinase 7,Serinethreonine-Protein Kinase 1 Basal Transcription Factor Complex Kinase Subunit;
Ec: 2.7.11.22,2.7.11.23

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Cyclin-H
Chain: 9
Synonym: Mo15-Associated Protein,P34,P37

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (65-Mer)
Chain: X
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (65-Mer)
Chain: Y
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
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 7.20 Å
ligand MG, SF4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
0


1


2
  • ATPase activator activity


  • 3


    4


    5


    6


    7


    8


    9


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


  • B


    C


    D


    E


    F


    G


    H


    I


    J


    K


    L


    M
  • histone acetyltransferase ac...


  • N


    O


    P

  • transcription factor TFIID c...
  • Q


    R


    S
  • phosphatase activator activi...


  • T
  • DNA helicase activity


  • U


    Primary referenceTranscription preinitiation complex structure and dynamics provide insight into genetic diseases., Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I, Nat Struct Mol Biol. 2019 May 20. pii: 10.1038/s41594-019-0220-3. doi:, 10.1038/s41594-019-0220-3. PMID:31110295
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1425 Kb) [Save to disk]
  • Biological Unit Coordinates (6o9l.pdb1.gz) 1407 Kb
  • LPC: Ligand-Protein Contacts for 6O9L
  • CSU: Contacts of Structural Units for 6O9L
  • Retrieve 6O9L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6O9L from S2C, [Save to disk]
  • View 6O9L 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 6O9L
  • 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 6o9l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6o9l_U] [6o9l_B] [6o9l_E] [6o9l_F] [6o9l_Q] [6o9l_3] [6o9l_C] [6o9l_M] [6o9l_O] [6o9l_5] [6o9l_R] [6o9l_S] [6o9l_4] [6o9l_6] [6o9l_G] [6o9l_D] [6o9l_I] [6o9l_Y] [6o9l_K] [6o9l_1] [6o9l_T] [6o9l_9] [6o9l_0] [6o9l_8] [6o9l_N] [6o9l_2] [6o9l_A] [6o9l_J] [6o9l_L] [6o9l_X] [6o9l_H] [6o9l_7] [6o9l_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6O9L
  • Community annotation for 6O9L at PDBWiki (http://pdbwiki.org)

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