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Human holo-PIC in the open state

Electron Microscopy
8.6Å resolution
PDB entry 5iy7 coloured by chain, front view.
PDB entry 5iy7 coloured by chain, side view.
PDB entry 5iy7 coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero 29-mer (preferred)
Entry contents: 27 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: General transcription factor TFIIB-TBP complex and DNA
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Multimeric state: hetero 29-mer
Accessible surface area: 357141.0 Å2
Buried surface area: 132715.91 Å2
Dissociation area: 1,587.4 Å2
Dissociation energy (ΔGdiss): -3.77 kcal/mol
Dissociation entropy (TΔSdiss): 27.19 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118816

Macromolecules

DNA-directed RNA polymerase II subunit RPB1
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P24928 (Residues: 1-1970; Coverage: 100%)
Gene names: POLR2, POLR2A
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 5iy7, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB2
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P30876 (Residues: 1-1174; Coverage: 100%)
Gene name: POLR2B
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB2 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB2 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB2 in PDB entry 5iy7, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB3
Chain: C
Length: 275 amino acids
Theoretical weight: 31.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P19387 (Residues: 1-275; Coverage: 100%)
Gene names: A-152E5.7, POLR2C
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB3 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB3 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB3 in PDB entry 5iy7, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB4
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15514 (Residues: 1-142; Coverage: 100%)
Gene name: POLR2D
Pfam: RNA polymerase Rpb4
InterPro:
DNA-directed RNA polymerase II subunit RPB4 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB4 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB4 in PDB entry 5iy7, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC1
Chain: E
Length: 210 amino acids
Theoretical weight: 24.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P19388 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Pfam:
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 5iy7, 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: 14.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61218 (Residues: 1-127; Coverage: 100%)
Gene names: POLR2F, POLRF
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 5iy7, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB7
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62487 (Residues: 1-172; Coverage: 100%)
Gene names: POLR2G, RPB7
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 5iy7, 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: Homo sapiens
UniProt:
  • Canonical: P52434 (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 5iy7, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 5iy7, 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: Homo sapiens
UniProt:
  • Canonical: P36954 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 5iy7, 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: Homo sapiens
UniProt:
  • Canonical: P62875 (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 5iy7, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 5iy7, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB11-a
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P52435 (Residues: 1-117; Coverage: 100%)
Gene names: POLR2J, POLR2J1
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB11-a in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB11-a in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB11-a in PDB entry 5iy7, 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: Homo sapiens
UniProt:
  • Canonical: P53803 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 5iy7, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 5iy7, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 5iy7, 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:
InterPro:
Transcription initiation factor IIB in PDB entry 5iy7, assembly 1, front view.
Transcription initiation factor IIB in PDB entry 5iy7, assembly 1, side view.
Transcription initiation factor IIB in PDB entry 5iy7, assembly 1, top view.
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Transcription initiation factor IIA subunit 1
Chain: N
Length: 376 amino acids
Theoretical weight: 41.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P52655 (Residues: 1-376; Coverage: 100%)
Gene names: GTF2A1, TF2A1
Pfam: Transcription factor IIA, alpha/beta subunit
InterPro:
Transcription initiation factor IIA subunit 1 in PDB entry 5iy7, assembly 1, front view.
Transcription initiation factor IIA subunit 1 in PDB entry 5iy7, assembly 1, side view.
Transcription initiation factor IIA subunit 1 in PDB entry 5iy7, assembly 1, top view.
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Transcription initiation factor IIA subunit 2
Chain: O
Length: 109 amino acids
Theoretical weight: 12.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P52657 (Residues: 1-109; Coverage: 100%)
Gene names: GTF2A2, TF2A2
Pfam:
InterPro:
Transcription initiation factor IIA subunit 2 in PDB entry 5iy7, assembly 1, front view.
Transcription initiation factor IIA subunit 2 in PDB entry 5iy7, assembly 1, side view.
Transcription initiation factor IIA subunit 2 in PDB entry 5iy7, assembly 1, top view.
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TATA-box-binding protein
Chain: P
Length: 339 amino acids
Theoretical weight: 37.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P20226 (Residues: 1-339; Coverage: 100%)
Gene names: GTF2D1, TBP, TF2D, TFIID
Pfam: Transcription factor TFIID (or TATA-binding protein, TBP)
InterPro:
TATA-box-binding protein in PDB entry 5iy7, assembly 1, front view.
TATA-box-binding protein in PDB entry 5iy7, assembly 1, side view.
TATA-box-binding protein in PDB entry 5iy7, assembly 1, top view.
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General transcription factor IIE subunit 1
Chain: Q
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:
InterPro:
General transcription factor IIE subunit 1 in PDB entry 5iy7, assembly 1, front view.
General transcription factor IIE subunit 1 in PDB entry 5iy7, assembly 1, side view.
General transcription factor IIE subunit 1 in PDB entry 5iy7, assembly 1, top view.
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Transcription initiation factor IIE subunit beta
Chain: R
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:
InterPro:
Transcription initiation factor IIE subunit beta in PDB entry 5iy7, assembly 1, front view.
Transcription initiation factor IIE subunit beta in PDB entry 5iy7, assembly 1, side view.
Transcription initiation factor IIE subunit beta in PDB entry 5iy7, assembly 1, top view.
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General transcription factor IIF subunit 1
Chain: S
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)
InterPro:
General transcription factor IIF subunit 1 in PDB entry 5iy7, assembly 1, front view.
General transcription factor IIF subunit 1 in PDB entry 5iy7, assembly 1, side view.
General transcription factor IIF subunit 1 in PDB entry 5iy7, assembly 1, top view.
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General transcription factor IIF subunit 2
Chain: T
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:
InterPro:
General transcription factor IIF subunit 2 in PDB entry 5iy7, assembly 1, front view.
General transcription factor IIF subunit 2 in PDB entry 5iy7, assembly 1, side view.
General transcription factor IIF subunit 2 in PDB entry 5iy7, assembly 1, top view.
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Transcription elongation factor A protein 1
Chain: U
Length: 301 amino acids
Theoretical weight: 34.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23193 (Residues: 1-301; Coverage: 100%)
Gene names: GTF2S, TCEA1, TFIIS
Pfam:
InterPro:
Transcription elongation factor A protein 1 in PDB entry 5iy7, assembly 1, front view.
Transcription elongation factor A protein 1 in PDB entry 5iy7, assembly 1, side view.
Transcription elongation factor A protein 1 in PDB entry 5iy7, assembly 1, top view.
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General transcription and DNA repair factor IIH helicase/translocase subunit XPB
Chain: V
Length: 782 amino acids
Theoretical weight: 89.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P19447 (Residues: 1-782; Coverage: 100%)
Gene names: ERCC3, XPB, XPBC
Pfam:
InterPro:
General transcription and DNA repair factor IIH helicase subunit XPB in PDB entry 5iy7, assembly 1, front view.
General transcription and DNA repair factor IIH helicase subunit XPB in PDB entry 5iy7, assembly 1, side view.
General transcription and DNA repair factor IIH helicase subunit XPB in PDB entry 5iy7, assembly 1, top view.
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General transcription and DNA repair factor IIH helicase subunit XPD
Chain: W
Length: 760 amino acids
Theoretical weight: 87.02 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P18074 (Residues: 1-760; Coverage: 100%)
Gene names: ERCC2, XPD, XPDC
Pfam:
InterPro:
General transcription and DNA repair factor IIH helicase subunit XPD in PDB entry 5iy7, assembly 1, front view.
General transcription and DNA repair factor IIH helicase subunit XPD in PDB entry 5iy7, assembly 1, side view.
General transcription and DNA repair factor IIH helicase subunit XPD in PDB entry 5iy7, assembly 1, top view.
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General transcription factor IIH subunit 2
Chain: 0
Length: 395 amino acids
Theoretical weight: 44.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13888 (Residues: 1-395; Coverage: 100%)
Gene names: BTF2P44, GTF2H2
Pfam:
InterPro:
General transcription factor IIH subunit 2 in PDB entry 5iy7, assembly 1, front view.
General transcription factor IIH subunit 2 in PDB entry 5iy7, assembly 1, side view.
General transcription factor IIH subunit 2 in PDB entry 5iy7, assembly 1, top view.
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General transcription factor IIH subunit 5
Chain: 1
Length: 71 amino acids
Theoretical weight: 8.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6ZYL4 (Residues: 1-71; Coverage: 100%)
Gene names: C6orf175, GTF2H5, TTDA
Pfam: Transcription factor TFIIH complex subunit Tfb5
InterPro:
General transcription factor IIH subunit 5 in PDB entry 5iy7, assembly 1, front view.
General transcription factor IIH subunit 5 in PDB entry 5iy7, assembly 1, side view.
General transcription factor IIH subunit 5 in PDB entry 5iy7, assembly 1, top view.
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General transcription factor IIH subunit 4
Chain: 2
Length: 462 amino acids
Theoretical weight: 52.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92759 (Residues: 1-462; Coverage: 100%)
Gene name: GTF2H4
Pfam:
InterPro:
General transcription factor IIH subunit 4 in PDB entry 5iy7, assembly 1, front view.
General transcription factor IIH subunit 4 in PDB entry 5iy7, assembly 1, side view.
General transcription factor IIH subunit 4 in PDB entry 5iy7, assembly 1, top view.
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General transcription factor IIH subunit 3
Chain: 3
Length: 308 amino acids
Theoretical weight: 34.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13889 (Residues: 1-308; Coverage: 100%)
Gene name: GTF2H3
Pfam: Transcription factor Tfb4
InterPro:
General transcription factor IIH subunit 3 in PDB entry 5iy7, assembly 1, front view.
General transcription factor IIH subunit 3 in PDB entry 5iy7, assembly 1, side view.
General transcription factor IIH subunit 3 in PDB entry 5iy7, assembly 1, top view.
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DNA chain X
Name: SCP-X
Representative chains: X
Length: 77 nucleotides
Theoretical weight: 23.95 KDa
SCP-X in PDB entry 5iy7, assembly 1, front view.
SCP-X in PDB entry 5iy7, assembly 1, side view.
SCP-X in PDB entry 5iy7, assembly 1, top view.
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DNA chain Y
Name: SCP-Y
Representative chains: Y
Length: 77 nucleotides
Theoretical weight: 23.57 KDa
SCP-Y in PDB entry 5iy7, assembly 1, front view.
SCP-Y in PDB entry 5iy7, assembly 1, side view.
SCP-Y in PDB entry 5iy7, assembly 1, top view.
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