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Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1

Electron Microscopy
3.1Å resolution
PDB entry 6ted coloured by chain, front view.
PDB entry 6ted coloured by chain, side view.
PDB entry 6ted coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 24-mer (preferred)
Entry contents: 21 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DSIF transcription elongation factor complex and RNA and DNA
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Multimeric state: hetero 24-mer
Accessible surface area: 283754.6 Å2
Buried surface area: 115262.59 Å2
Dissociation area: 1,475.49 Å2
Dissociation energy (ΔGdiss): 8.78 kcal/mol
Dissociation entropy (TΔSdiss): 14.59 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-236757

Macromolecules

DNA-directed RNA polymerase subunit
Chain: A
Length: 1984 amino acids
Theoretical weight: 219.05 KDa
Source organism: Sus scrofa
InterPro:
DNA-directed RNA polymerase subunit in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerase subunit in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerase subunit in PDB entry 6ted, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta
Chain: B
Length: 1251 amino acids
Theoretical weight: 142.43 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 50-1300; Coverage: 96%)
Gene name: POLR2B
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 6ted, assembly 1, top view.
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DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
Chain: C
Length: 275 amino acids
Theoretical weight: 31.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCH3 (Residues: 1-275; Coverage: 100%)
Gene name: POLR2C
Pfam:
InterPro:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 6ted, assembly 1, top view.
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RNA polymerase Rpb4/RPC9 core domain-containing protein
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 43-184; Coverage: 77%)
Gene name: POLR2D
Pfam: RNA polymerase Rpb4
InterPro:
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 6ted, assembly 1, front view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 6ted, assembly 1, side view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 6ted, assembly 1, top view.
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DNA-directed RNA polymerase II subunit E
Chain: E
Length: 210 amino acids
Theoretical weight: 24.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LSI7 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit E in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerase II subunit E in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerase II subunit E in PDB entry 6ted, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC2
Chain: F
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 6ted, assembly 1, top view.
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RNA polymerase II subunit G
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
InterPro:
RNA polymerase II subunit G in PDB entry 6ted, assembly 1, front view.
RNA polymerase II subunit G in PDB entry 6ted, assembly 1, side view.
RNA polymerase II subunit G in PDB entry 6ted, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain: H
Length: 150 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCB2 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Pfam: RNA polymerase Rpb8
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6ted, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB9
Chain: I
Length: 125 amino acids
Theoretical weight: 14.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P60899 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 6ted, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC5
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VYD0 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Pfam: RNA polymerases N / 8 kDa subunit
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 6ted, assembly 1, top view.
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DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RKE4 (Residues: 1-117; Coverage: 100%)
Gene name: POLR2J
Pfam: RNA polymerase Rpb3/Rpb11 dimerisation domain
InterPro:
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 6ted, assembly 1, front view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 6ted, assembly 1, side view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 6ted, assembly 1, top view.
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RNA polymerase II, I and III subunit K
Chain: L
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TRS6 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
RNA polymerase II, I and III subunit K in PDB entry 6ted, assembly 1, front view.
RNA polymerase II, I and III subunit K in PDB entry 6ted, assembly 1, side view.
RNA polymerase II, I and III subunit K in PDB entry 6ted, assembly 1, top view.
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Transcription elongation factor SPT6
Chain: M
Length: 1729 amino acids
Theoretical weight: 199.6 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7KZ85 (Residues: 1-1726; Coverage: 100%)
Gene names: KIAA0162, SPT6H, SUPT6H
Pfam:
InterPro:
Transcription elongation factor SPT6 in PDB entry 6ted, assembly 1, front view.
Transcription elongation factor SPT6 in PDB entry 6ted, assembly 1, side view.
Transcription elongation factor SPT6 in PDB entry 6ted, assembly 1, top view.
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RNA polymerase-associated protein CTR9 homolog
Chain: Q
Length: 1179 amino acids
Theoretical weight: 134.51 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6PD62 (Residues: 1-1173; Coverage: 100%)
Gene names: CTR9, KIAA0155, SH2BP1
Pfam:
InterPro:
RNA polymerase-associated protein CTR9 homolog in PDB entry 6ted, assembly 1, front view.
RNA polymerase-associated protein CTR9 homolog in PDB entry 6ted, assembly 1, side view.
RNA polymerase-associated protein CTR9 homolog in PDB entry 6ted, assembly 1, top view.
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RNA polymerase-associated protein RTF1 homolog
Chain: R
Length: 713 amino acids
Theoretical weight: 80.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92541 (Residues: 1-710; Coverage: 100%)
Gene names: KIAA0252, RTF1
Pfam: Plus-3 domain
InterPro:
RNA polymerase-associated protein RTF1 homolog in PDB entry 6ted, assembly 1, front view.
RNA polymerase-associated protein RTF1 homolog in PDB entry 6ted, assembly 1, side view.
RNA polymerase-associated protein RTF1 homolog in PDB entry 6ted, assembly 1, top view.
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RNA polymerase-associated protein LEO1
Chain: U
Length: 666 amino acids
Theoretical weight: 75.51 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8WVC0 (Residues: 1-666; Coverage: 100%)
Gene names: LEO1, RDL
Pfam: Leo1-like protein
InterPro: Leo1-like protein
RNA polymerase-associated protein LEO1 in PDB entry 6ted, assembly 1, front view.
RNA polymerase-associated protein LEO1 in PDB entry 6ted, assembly 1, side view.
RNA polymerase-associated protein LEO1 in PDB entry 6ted, assembly 1, top view.
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RNA polymerase II-associated factor 1 homolog
Chain: V
Length: 531 amino acids
Theoretical weight: 60.05 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8N7H5 (Residues: 1-531; Coverage: 100%)
Gene names: PAF1, PD2
Pfam: Paf1
InterPro: RNA polymerase II associated factor Paf1
RNA polymerase II-associated factor 1 homolog in PDB entry 6ted, assembly 1, front view.
RNA polymerase II-associated factor 1 homolog in PDB entry 6ted, assembly 1, side view.
RNA polymerase II-associated factor 1 homolog in PDB entry 6ted, assembly 1, top view.
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Superkiller complex protein 8
Chain: W
Length: 305 amino acids
Theoretical weight: 33.62 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9GZS3 (Residues: 1-305; Coverage: 100%)
Gene names: SKIC8, WDR61
Pfam: WD domain, G-beta repeat
InterPro:
Superkiller complex protein 8 in PDB entry 6ted, assembly 1, front view.
Superkiller complex protein 8 in PDB entry 6ted, assembly 1, side view.
Superkiller complex protein 8 in PDB entry 6ted, assembly 1, top view.
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Parafibromin
Chain: X
Length: 531 amino acids
Theoretical weight: 60.67 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6P1J9 (Residues: 1-531; Coverage: 100%)
Gene names: C1orf28, CDC73, HRPT2
Pfam:
InterPro:
Parafibromin in PDB entry 6ted, assembly 1, front view.
Parafibromin in PDB entry 6ted, assembly 1, side view.
Parafibromin in PDB entry 6ted, assembly 1, top view.
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Transcription elongation factor SPT4
Chain: Y
Length: 121 amino acids
Theoretical weight: 13.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P63272 (Residues: 1-117; Coverage: 100%)
Gene names: SPT4H, SUPT4H, SUPT4H1
Pfam: Spt4/RpoE2 zinc finger
InterPro:
Transcription elongation factor SPT4 in PDB entry 6ted, assembly 1, front view.
Transcription elongation factor SPT4 in PDB entry 6ted, assembly 1, side view.
Transcription elongation factor SPT4 in PDB entry 6ted, assembly 1, top view.
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Transcription elongation factor SPT5
Chain: Z
Length: 1087 amino acids
Theoretical weight: 121.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O00267 (Residues: 1-1087; Coverage: 100%)
Gene names: SPT5, SPT5H, SUPT5H
Pfam:
InterPro:
Transcription elongation factor SPT5 in PDB entry 6ted, assembly 1, front view.
Transcription elongation factor SPT5 in PDB entry 6ted, assembly 1, side view.
Transcription elongation factor SPT5 in PDB entry 6ted, assembly 1, top view.
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DNA chain N
Name: DNA (37-MER)
Representative chains: N
Length: 48 nucleotides
Theoretical weight: 14.93 KDa
DNA (37-MER) in PDB entry 6ted, assembly 1, front view.
DNA (37-MER) in PDB entry 6ted, assembly 1, side view.
DNA (37-MER) in PDB entry 6ted, assembly 1, top view.
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DNA chain T
Name: Template DNA
Representative chains: T
Length: 48 nucleotides
Theoretical weight: 14.67 KDa
Template DNA in PDB entry 6ted, assembly 1, front view.
Template DNA in PDB entry 6ted, assembly 1, side view.
Template DNA in PDB entry 6ted, assembly 1, top view.
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RNA chain P
Name: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')
Representative chains: P
Length: 46 nucleotides
Theoretical weight: 14.84 KDa
RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3') in PDB entry 6ted, assembly 1, front view.
RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3') in PDB entry 6ted, assembly 1, side view.
RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3') in PDB entry 6ted, assembly 1, top view.
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