6GMH Transcription date May 26, 2018
title Structure Of Activated Transcription Complex Pol II-Dsif-Paf
authors S.M.Vos, L.Farnung, M.Boehing, A.Linden, C.Wigge, H.Urlaub, P.Cram
compound source
Molecule: Rpb1
Chain: A
Ec: 2.7.7.6
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: B
Ec: 2.7.7.6

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit C
Chain: C

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit D
Chain: D

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit E
Chain: E

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit F
Chain: F

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit G
Chain: G

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

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: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rpb10
Chain: J

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rpb11
Chain: K

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rpb12
Chain: L

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Transcription Elongation Factor Spt6,Transcriptio Elongation Factor Spt6,Transcription Elongation Factor Spt6
Chain: M
Synonym: Hspt6,Histone Chaperone Suppressor Of Ty6,Tat- Cotransactivator 2 Protein,Tat-Ct2 Protein,Hspt6,Histone Ch Suppressor Of Ty6,Tat-Cotransactivator 2 Protein,Tat-Ct2 Pr Hspt6,Histone Chaperone Suppressor Of Ty6,Tat-Cotransactiva Protein,Tat-Ct2 Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Supt6h, Kiaa0162, Spt6h
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_plasmid: 438c

Molecule: Non-Template Dna
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Ctr9,Rna Polymerase-Associated Protein Ctr9 Homol Polymerase-Associated Protein Ctr9 Homolog;
Chain: Q
Synonym: Sh2 Domain-Binding Protein 1,Sh2 Domain-Binding Pr
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ctr9, Kiaa0155, Sh2bp1
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_vector_type: 438a

Molecule: Template Dna
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Leo1,Leo1,Rna Polymerase-Associated Protein Leo1
Chain: U
Synonym: Replicative Senescence Down-Regulated Leo1-Like Pr
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Leo1, Rdl
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Paf1,Rna Polymerase II-Associated Factor 1 Homolo Polymerase II-Associated Factor 1 Homolog;
Chain: V
Synonym: Hpaf1,Pancreatic Differentiation Protein 2,Hpaf1,P Differentiation Protein 2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Paf1, Pd2
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Wd Repeat-Containing Protein 61
Chain: W
Synonym: Meiotic Recombination Rec14 Protein Homolog,Ski8 H Ski8;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Wdr61
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Cdc73
Chain: X
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Transcription Elongation Factor Spt4
Chain: Y
Synonym: Hspt4,Drb Sensitivity-Inducing Factor 14 Kda Subun P14,Drb Sensitivity-Inducing Factor Small Subunit,Dsif Smal
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Supt4h1, Spt4h, Supt4h
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Transcription Elongation Factor Spt5
Chain: Z
Synonym: Hspt5,Drb Sensitivity-Inducing Factor 160 Kda Subu P160,Drb Sensitivity-Inducing Factor Large Subunit,Dsif Lar Subunit,Tat-Cotransactivator 1 Protein,Tat-Ct1 Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Supt5h, Spt5, Spt5h
Expression_system: Trichoplusia Ni
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 3.10 Å
ligand
enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F
  • RNA polymerase I activity
  • RNA polymerase II activity
  • RNA polymerase III activity


  • G


    H
  • RNA polymerase I activity


  • I


    J


    K


    L
  • RNA polymerase I activity
  • RNA polymerase III activity


  • M


    Q


    U


    V


    W


    Y


    Z


    Primary referenceStructure of activated transcription complex Pol II-DSIF-PAF-SPT6., Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P, Nature. 2018 Aug;560(7720):607-612. doi: 10.1038/s41586-018-0440-4. Epub 2018 Aug, 22. PMID:30135578
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (952 Kb) [Save to disk]
  • Biological Unit Coordinates (6gmh.pdb1.gz) 920 Kb
  • CSU: Contacts of Structural Units for 6GMH
  • Retrieve 6GMH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6GMH from S2C, [Save to disk]
  • View 6GMH 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 6GMH
  • 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 6gmh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6gmh_W] [6gmh_I] [6gmh_G] [6gmh_Y] [6gmh_J] [6gmh_V] [6gmh_A] [6gmh_E] [6gmh_K] [6gmh_Z] [6gmh_L] [6gmh_D] [6gmh_H] [6gmh_M] [6gmh_X] [6gmh_P] [6gmh_Q] [6gmh_N] [6gmh_B] [6gmh_U] [6gmh_F] [6gmh_C] [6gmh_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6GMH
  • Community annotation for 6GMH at PDBWiki (http://pdbwiki.org)

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