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RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)

Electron Microscopy
4Å resolution
PDB entry 8bvw coloured by chain, front view.
PDB entry 8bvw coloured by chain, side view.
PDB entry 8bvw coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 42-mer (preferred)
Entry contents: 36 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: General transcription factor TFIIH complex and DNA
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Multimeric state: hetero 42-mer
Accessible surface area: 445524.59 Å2
Buried surface area: 211169.67 Å2
Dissociation area: 597.48 Å2
Dissociation energy (ΔGdiss): -6.31 kcal/mol
Dissociation entropy (TΔSdiss): 14.18 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-236732

Macromolecules

General transcription and DNA repair factor IIH helicase/translocase subunit XPB
Chain: 0
Length: 772 amino acids
Theoretical weight: 88.09 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P19447 (Residues: 1-772; Coverage: 99%)
Gene names: ERCC3, XPB, XPBC
Pfam:
General transcription and DNA repair factor IIH helicase/translocase subunit XPB in PDB entry 8bvw, assembly 1, front view.
General transcription and DNA repair factor IIH helicase/translocase subunit XPB in PDB entry 8bvw, assembly 1, side view.
General transcription and DNA repair factor IIH helicase/translocase subunit XPB in PDB entry 8bvw, assembly 1, top view.
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General transcription and DNA repair factor IIH helicase subunit XPD
Chain: 1
Length: 760 amino acids
Theoretical weight: 87.02 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P18074 (Residues: 1-760; Coverage: 100%)
Gene names: ERCC2, XPD, XPDC
Pfam:
General transcription and DNA repair factor IIH helicase subunit XPD in PDB entry 8bvw, assembly 1, front view.
General transcription and DNA repair factor IIH helicase subunit XPD in PDB entry 8bvw, assembly 1, side view.
General transcription and DNA repair factor IIH helicase subunit XPD in PDB entry 8bvw, assembly 1, top view.
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General transcription factor IIH subunit 1
Chain: 2
Length: 548 amino acids
Theoretical weight: 62.12 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32780 (Residues: 1-548; Coverage: 100%)
Gene names: BTF2, GTF2H1
Pfam:
General transcription factor IIH subunit 1 in PDB entry 8bvw, assembly 1, front view.
General transcription factor IIH subunit 1 in PDB entry 8bvw, assembly 1, side view.
General transcription factor IIH subunit 1 in PDB entry 8bvw, assembly 1, top view.
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General transcription factor IIH subunit 4
Chain: 3
Length: 462 amino acids
Theoretical weight: 52.25 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92759 (Residues: 1-462; Coverage: 100%)
Gene name: GTF2H4
Pfam:
General transcription factor IIH subunit 4 in PDB entry 8bvw, assembly 1, front view.
General transcription factor IIH subunit 4 in PDB entry 8bvw, assembly 1, side view.
General transcription factor IIH subunit 4 in PDB entry 8bvw, assembly 1, top view.
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General transcription factor IIH subunit 2
Chain: 4
Length: 395 amino acids
Theoretical weight: 44.48 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13888 (Residues: 1-395; Coverage: 100%)
Gene names: BTF2P44, GTF2H2
Pfam:
General transcription factor IIH subunit 2 in PDB entry 8bvw, assembly 1, front view.
General transcription factor IIH subunit 2 in PDB entry 8bvw, assembly 1, side view.
General transcription factor IIH subunit 2 in PDB entry 8bvw, assembly 1, top view.
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General transcription factor IIH subunit 3
Chain: 5
Length: 308 amino acids
Theoretical weight: 34.42 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13889 (Residues: 1-308; Coverage: 100%)
Gene name: GTF2H3
Pfam: Transcription factor Tfb4
General transcription factor IIH subunit 3 in PDB entry 8bvw, assembly 1, front view.
General transcription factor IIH subunit 3 in PDB entry 8bvw, assembly 1, side view.
General transcription factor IIH subunit 3 in PDB entry 8bvw, assembly 1, top view.
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General transcription factor IIH subunit 5
Chain: 6
Length: 71 amino acids
Theoretical weight: 8.06 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6ZYL4 (Residues: 1-71; Coverage: 100%)
Gene names: C6orf175, GTF2H5, TTDA
Pfam: Transcription factor TFIIH complex subunit Tfb5
General transcription factor IIH subunit 5 in PDB entry 8bvw, assembly 1, front view.
General transcription factor IIH subunit 5 in PDB entry 8bvw, assembly 1, side view.
General transcription factor IIH subunit 5 in PDB entry 8bvw, assembly 1, top view.
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CDK-activating kinase assembly factor MAT1
Chain: 7
Length: 309 amino acids
Theoretical weight: 35.87 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P51948 (Residues: 1-309; Coverage: 100%)
Gene names: CAP35, MAT1, MNAT1, RNF66
Pfam:
CDK-activating kinase assembly factor MAT1 in PDB entry 8bvw, assembly 1, front view.
CDK-activating kinase assembly factor MAT1 in PDB entry 8bvw, assembly 1, side view.
CDK-activating kinase assembly factor MAT1 in PDB entry 8bvw, assembly 1, top view.
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Cyclin-dependent kinase 7
Chain: 8
Length: 346 amino acids
Theoretical weight: 39.09 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P50613 (Residues: 1-346; Coverage: 100%)
Gene names: CAK, CAK1, CDK7, CDKN7, MO15, STK1
Pfam: Protein kinase domain
Cyclin-dependent kinase 7 in PDB entry 8bvw, assembly 1, front view.
Cyclin-dependent kinase 7 in PDB entry 8bvw, assembly 1, side view.
Cyclin-dependent kinase 7 in PDB entry 8bvw, assembly 1, top view.
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Cyclin-H
Chain: 9
Length: 323 amino acids
Theoretical weight: 37.7 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P51946 (Residues: 1-323; Coverage: 100%)
Gene name: CCNH
Pfam:
Cyclin-H in PDB entry 8bvw, assembly 1, front view.
Cyclin-H in PDB entry 8bvw, assembly 1, side view.
Cyclin-H in PDB entry 8bvw, assembly 1, top view.
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DNA-directed RNA polymerase subunit
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A7M4DUC2 (Residues: 1-1984; Coverage: 99%)
Pfam:
DNA-directed RNA polymerase subunit in PDB entry 8bvw, assembly 1, front view.
DNA-directed RNA polymerase subunit in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerase subunit in PDB entry 8bvw, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 127-1300; Coverage: 90%)
Gene name: POLR2B
Pfam:
DNA-directed RNA polymerase subunit beta in PDB entry 8bvw, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 8bvw, 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 8bvw, assembly 1, front view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 8bvw, 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
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 8bvw, assembly 1, front view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 8bvw, assembly 1, side view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 8bvw, 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 8bvw, assembly 1, front view.
DNA-directed RNA polymerase II subunit E in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerase II subunit E in PDB entry 8bvw, 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 8bvw, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 8bvw, 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 8bvw, assembly 1, front view.
DNA-directed RNA polymerase subunit in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerase subunit in PDB entry 8bvw, 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 8bvw, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 8bvw, 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 8bvw, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 8bvw, 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
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 8bvw, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 8bvw, 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 8bvw, assembly 1, front view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 8bvw, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC4
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 8bvw, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 8bvw, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 8bvw, assembly 1, top view.
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Transcription initiation factor IIB
Chain: M
Length: 316 amino acids
Theoretical weight: 34.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00403 (Residues: 1-316; Coverage: 100%)
Gene names: GTF2B, TF2B, TFIIB
Pfam:
Transcription initiation factor IIB in PDB entry 8bvw, assembly 1, front view.
Transcription initiation factor IIB in PDB entry 8bvw, assembly 1, side view.
Transcription initiation factor IIB in PDB entry 8bvw, assembly 1, top view.
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TATA-box-binding protein
Chain: O
Length: 339 amino acids
Theoretical weight: 37.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P20226 (Residues: 1-339; Coverage: 100%)
Gene names: GTF2D1, TBP, TF2D, TFIID
Pfam: Transcription factor TFIID (or TATA-binding protein, TBP)
TATA-box-binding protein in PDB entry 8bvw, assembly 1, front view.
TATA-box-binding protein in PDB entry 8bvw, assembly 1, side view.
TATA-box-binding protein in PDB entry 8bvw, assembly 1, top view.
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General transcription factor IIF subunit 1
Chain: Q
Length: 517 amino acids
Theoretical weight: 58.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P35269 (Residues: 1-517; Coverage: 100%)
Gene names: GTF2F1, RAP74
Pfam: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
General transcription factor IIF subunit 1 in PDB entry 8bvw, assembly 1, front view.
General transcription factor IIF subunit 1 in PDB entry 8bvw, assembly 1, side view.
General transcription factor IIF subunit 1 in PDB entry 8bvw, assembly 1, top view.
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General transcription factor IIF subunit 2
Chain: R
Length: 249 amino acids
Theoretical weight: 28.43 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P13984 (Residues: 1-249; Coverage: 100%)
Gene names: GTF2F2, RAP30
Pfam:
General transcription factor IIF subunit 2 in PDB entry 8bvw, assembly 1, front view.
General transcription factor IIF subunit 2 in PDB entry 8bvw, assembly 1, side view.
General transcription factor IIF subunit 2 in PDB entry 8bvw, assembly 1, top view.
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Transcription initiation factor IIA subunit 1
Chain: U
Length: 376 amino acids
Theoretical weight: 41.54 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P52655 (Residues: 1-376; Coverage: 100%)
Gene names: GTF2A1, TF2A1
Pfam: Transcription factor IIA, alpha/beta subunit
Transcription initiation factor IIA subunit 1 in PDB entry 8bvw, assembly 1, front view.
Transcription initiation factor IIA subunit 1 in PDB entry 8bvw, assembly 1, side view.
Transcription initiation factor IIA subunit 1 in PDB entry 8bvw, assembly 1, top view.
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Transcription initiation factor IIA subunit 2
Chain: V
Length: 109 amino acids
Theoretical weight: 12.47 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P52657 (Residues: 1-109; Coverage: 100%)
Gene names: GTF2A2, TF2A2
Pfam:
Transcription initiation factor IIA subunit 2 in PDB entry 8bvw, assembly 1, front view.
Transcription initiation factor IIA subunit 2 in PDB entry 8bvw, assembly 1, side view.
Transcription initiation factor IIA subunit 2 in PDB entry 8bvw, assembly 1, top view.
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General transcription factor IIE subunit 1
Chain: W
Length: 439 amino acids
Theoretical weight: 49.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P29083 (Residues: 1-439; Coverage: 100%)
Gene names: GTF2E1, TF2E1
Pfam:
General transcription factor IIE subunit 1 in PDB entry 8bvw, assembly 1, front view.
General transcription factor IIE subunit 1 in PDB entry 8bvw, assembly 1, side view.
General transcription factor IIE subunit 1 in PDB entry 8bvw, assembly 1, top view.
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Transcription initiation factor IIE subunit beta
Chain: X
Length: 291 amino acids
Theoretical weight: 33.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P29084 (Residues: 1-291; Coverage: 100%)
Gene names: GTF2E2, TF2E2
Pfam:
Transcription initiation factor IIE subunit beta in PDB entry 8bvw, assembly 1, front view.
Transcription initiation factor IIE subunit beta in PDB entry 8bvw, assembly 1, side view.
Transcription initiation factor IIE subunit beta in PDB entry 8bvw, assembly 1, top view.
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Unassigned peptide, likely XPB
Chain: Y
Length: 8 amino acids
Theoretical weight: 699 Da
Source organism: Homo sapiens
Expression system: Escherichia coli
Unassigned peptide, likely XPB in PDB entry 8bvw, assembly 1, front view.
Unassigned peptide, likely XPB in PDB entry 8bvw, assembly 1, side view.
Unassigned peptide, likely XPB in PDB entry 8bvw, assembly 1, top view.
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Unassigned peptide, likely TFIIE-beta
Chain: Z
Length: 19 amino acids
Theoretical weight: 1.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Unassigned peptide, likely TFIIE-beta in PDB entry 8bvw, assembly 1, front view.
Unassigned peptide, likely TFIIE-beta in PDB entry 8bvw, assembly 1, side view.
Unassigned peptide, likely TFIIE-beta in PDB entry 8bvw, assembly 1, top view.
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Histone H3.2
Chains: a, e
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Pfam: Core histone H2A/H2B/H3/H4
Histone H3.2 in PDB entry 8bvw, assembly 1, front view.
Histone H3.2 in PDB entry 8bvw, assembly 1, side view.
Histone H3.2 in PDB entry 8bvw, assembly 1, top view.
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Histone H4
Chains: b, f
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Pfam: Centromere kinetochore component CENP-T histone fold
Histone H4 in PDB entry 8bvw, assembly 1, front view.
Histone H4 in PDB entry 8bvw, assembly 1, side view.
Histone H4 in PDB entry 8bvw, assembly 1, top view.
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Histone H2A type 1
Chains: c, g
Length: 130 amino acids
Theoretical weight: 14.09 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Pfam:
Histone H2A type 1 in PDB entry 8bvw, assembly 1, front view.
Histone H2A type 1 in PDB entry 8bvw, assembly 1, side view.
Histone H2A type 1 in PDB entry 8bvw, assembly 1, top view.
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Histone H2B 1.1
Chains: d, h
Length: 126 amino acids
Theoretical weight: 13.97 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Pfam: Core histone H2A/H2B/H3/H4
Histone H2B 1.1 in PDB entry 8bvw, assembly 1, front view.
Histone H2B 1.1 in PDB entry 8bvw, assembly 1, side view.
Histone H2B 1.1 in PDB entry 8bvw, assembly 1, top view.
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DNA chain N
Name: Non-template DNA
Representative chains: N
Length: 218 nucleotides
Theoretical weight: 67.22 KDa
Non-template DNA in PDB entry 8bvw, assembly 1, front view.
Non-template DNA in PDB entry 8bvw, assembly 1, side view.
Non-template DNA in PDB entry 8bvw, assembly 1, top view.
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DNA chain T
Name: Template DNA
Representative chains: T
Length: 218 nucleotides
Theoretical weight: 67.41 KDa
Template DNA in PDB entry 8bvw, assembly 1, front view.
Template DNA in PDB entry 8bvw, assembly 1, side view.
Template DNA in PDB entry 8bvw, assembly 1, top view.
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