6TED Transcription date Nov 11, 2019
title Structure Of Complete, Activated Transcription Complex Pol I Paf-Spt6 Uncovers Allosteric Elongation Activation By Rtf1
authors S.M.Vos, L.Farnung, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase Subunit
Chain: A
Ec: 2.7.7.6
 Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: B
Ec: 2.7.7.6
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Rna Polymerase II Subunit C
Chain: C
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Rna Polymerase II Subunit D
Chain: D
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Rna Polymerase II Subunit E
Chain: E
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Rna Polymerase II Subunit F
Chain: F
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Rna Polymerase II Subunit G
Chain: G
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

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

Molecule: Uncharacterized Protein
Chain: J
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Uncharacterized Protein
Chain: K
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Uncharacterized Protein
Chain: L
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Transcription Elongation Factor Spt6
Chain: M
Synonym: Hspt6,Histone Chaperone Suppressor Of Ty6,Tat- Cotransactivator 2 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_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Dna (37-Mer)
Chain: N
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'- R(Pupapapcpcpgpgpapgpapgpgpgpapapcpcpcpa 3');
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna Polymerase-Associated Protein Ctr9 Homolog
Chain: Q
Synonym: Sh2 Domain-Binding Protein 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ctr9, Kiaa0155, Sh2bp1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Rna Polymerase-Associated Protein Rtf1 Homolog
Chain: R
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rtf1, Kiaa0252
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Template Dna
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 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_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Rna Polymerase II-Associated Factor 1 Homolog
Chain: V
Synonym: Hpaf1,Pancreatic Differentiation Protein 2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Paf1, Pd2
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
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_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Parafibromin
Chain: X
Synonym: Cell Division Cycle Protein 73 Homolog,Hyperparath Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc73, C1orf28, Hrpt2
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
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: Escherichia Coli
Expression_system_taxid: 562

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: Escherichia Coli
Expression_system_taxid: 562
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 MG, SEP, TPO, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B


C


E


F


G


H


I


K


L


M


Q


R


U


V


W


X


Y


Z


Primary referenceStructure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation., Vos SM, Farnung L, Linden A, Urlaub H, Cramer P, Nat Struct Mol Biol. 2020 Jul;27(7):668-677. doi: 10.1038/s41594-020-0437-1. Epub, 2020 Jun 15. PMID:32541898
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1075 Kb) [Save to disk]
  • Biological Unit Coordinates (6ted.pdb1.gz) 1039 Kb
  • LPC: Ligand-Protein Contacts for 6TED
  • CSU: Contacts of Structural Units for 6TED
  • Retrieve 6TED in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6TED from S2C, [Save to disk]
    • View 6TED in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6TED
  • 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: [6ted_Y] [6ted_Z] [6ted_T] [6ted_L] [6ted_I] [6ted_G] [6ted_K] [6ted_M] [6ted_R] [6ted_C] [6ted_V] [6ted_Q] [6ted_H] [6ted_P] [6ted_A] [6ted_F] [6ted_J] [6ted_N] [6ted_D] [6ted_W] [6ted_B] [6ted_E] [6ted_U] [6ted_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6TED
  • Community annotation for 6TED at PDBWiki (http://pdbwiki.org)

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