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Structure of the mammalian Pol II-SPT6-Elongin complex, lacking ELOA latch (composite structure, structure 3)

Electron Microscopy
2.86Å resolution
PDB entry 8oev coloured by chain, front view.
PDB entry 8oev coloured by chain, side view.
PDB entry 8oev coloured by chain, top view.
Source organisms:
Assembly composition:
hetero nonadecamer (preferred)
Entry contents: 16 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero nonadecamer
Accessible surface area: 206327.12 Å2
Buried surface area: 81891.0 Å2
Dissociation area: 1,152.92 Å2
Dissociation energy (ΔGdiss): -11.33 kcal/mol
Dissociation entropy (TΔSdiss): 16.92 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-240658

Macromolecules

DNA-directed RNA polymerase subunit
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1DPV6 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
Pfam:
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 8oev, 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:
DNA-directed RNA polymerase subunit beta in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 8oev, 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:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 8oev, assembly 1, top view.
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RNA polymerase Rpb4/RPC9 core domain-containing protein
Chain: D
Length: 184 amino acids
Theoretical weight: 20.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 1-184; Coverage: 100%)
Gene name: POLR2D
Pfam: RNA polymerase Rpb4
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 8oev, assembly 1, front view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 8oev, assembly 1, side view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 8oev, 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:
DNA-directed RNA polymerase II subunit E in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerase II subunit E in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerase II subunit E in PDB entry 8oev, 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
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 8oev, assembly 1, top view.
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DNA-directed RNA polymerase subunit
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VKG7 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
Pfam:
DNA-directed RNA polymerase subunit in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerase subunit in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerase subunit in PDB entry 8oev, 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
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 8oev, 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:
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 8oev, 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: A0A8W4F9W9 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Pfam: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 8oev, 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
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 8oev, 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
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 8oev, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 8oev, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 8oev, assembly 1, top view.
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Elongin-A
Chain: M
Length: 801 amino acids
Theoretical weight: 90.36 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q14241 (Residues: 1-772; Coverage: 100%)
  • Best match: Q14241-1 (Residues: 1-798)
Gene names: ELOA, MSTP059, TCEB3
Pfam:
Elongin-A in PDB entry 8oev, assembly 1, front view.
Elongin-A in PDB entry 8oev, assembly 1, side view.
Elongin-A in PDB entry 8oev, assembly 1, top view.
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Elongin-C
Chain: O
Length: 112 amino acids
Theoretical weight: 12.49 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15369 (Residues: 1-112; Coverage: 100%)
Gene names: ELOC, TCEB1
Pfam: Skp1 family, tetramerisation domain
Elongin-C in PDB entry 8oev, assembly 1, front view.
Elongin-C in PDB entry 8oev, assembly 1, side view.
Elongin-C in PDB entry 8oev, assembly 1, top view.
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Elongin-B
Chain: Q
Length: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15370 (Residues: 1-118; Coverage: 100%)
Gene names: ELOB, TCEB2
Pfam: Ubiquitin family
Elongin-B in PDB entry 8oev, assembly 1, front view.
Elongin-B in PDB entry 8oev, assembly 1, side view.
Elongin-B in PDB entry 8oev, assembly 1, top view.
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Transcription elongation factor SPT6
Chain: S
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:
Transcription elongation factor SPT6 in PDB entry 8oev, assembly 1, front view.
Transcription elongation factor SPT6 in PDB entry 8oev, assembly 1, side view.
Transcription elongation factor SPT6 in PDB entry 8oev, assembly 1, top view.
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DNA chain N
Name: Non-Template DNA
Representative chains: N
Length: 48 nucleotides
Theoretical weight: 14.93 KDa
Non-Template DNA in PDB entry 8oev, assembly 1, front view.
Non-Template DNA in PDB entry 8oev, assembly 1, side view.
Non-Template DNA in PDB entry 8oev, 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 8oev, assembly 1, front view.
Template DNA in PDB entry 8oev, assembly 1, side view.
Template DNA in PDB entry 8oev, assembly 1, top view.
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RNA chain P
Name: RNA
Representative chains: P
Length: 46 nucleotides
Theoretical weight: 14.84 KDa
RNA in PDB entry 8oev, assembly 1, front view.
RNA in PDB entry 8oev, assembly 1, side view.
RNA in PDB entry 8oev, assembly 1, top view.
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