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Cryo-EM structure of human RNA Polymerase I Open Complex

Electron Microscopy
3.3Å resolution
PDB entry 7obb coloured by chain, front view.
PDB entry 7obb coloured by chain, side view.
PDB entry 7obb coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero pentadecamer (preferred)
Entry contents: 13 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA-directed RNA polymerase I complex and DNA
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Multimeric state: hetero pentadecamer
Accessible surface area: 162344.31 Å2
Buried surface area: 77410.37 Å2
Dissociation area: 720.49 Å2
Dissociation energy (ΔGdiss): 1.87 kcal/mol
Dissociation entropy (TΔSdiss): 10.77 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-121722

Macromolecules

DNA-directed RNA polymerase I subunit RPA1
Chain: A
Length: 1720 amino acids
Theoretical weight: 195.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95602 (Residues: 1-1720; Coverage: 100%)
Gene name: POLR1A
Pfam:
InterPro:
DNA-directed RNA polymerase I subunit RPA1 in PDB entry 7obb, assembly 1, front view.
DNA-directed RNA polymerase I subunit RPA1 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerase I subunit RPA1 in PDB entry 7obb, assembly 1, top view.
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DNA-directed RNA polymerase I subunit RPA2
Chain: B
Length: 1135 amino acids
Theoretical weight: 128.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H9Y6 (Residues: 1-1135; Coverage: 100%)
Gene name: POLR1B
Pfam:
InterPro:
DNA-directed RNA polymerase I subunit RPA2 in PDB entry 7obb, assembly 1, front view.
DNA-directed RNA polymerase I subunit RPA2 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerase I subunit RPA2 in PDB entry 7obb, assembly 1, top view.
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DNA-directed RNA polymerases I and III subunit RPAC1
Chain: C
Length: 346 amino acids
Theoretical weight: 39.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15160 (Residues: 1-346; Coverage: 100%)
Gene names: POLR1C, POLR1E
Pfam:
InterPro:
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 7obb, assembly 1, front view.
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 7obb, 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: 24.64 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 7obb, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 7obb, 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 7obb, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 7obb, assembly 1, top view.
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DNA-directed RNA polymerase I subunit RPA43
Chain: G
Length: 338 amino acids
Theoretical weight: 37.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q3B726 (Residues: 1-338; Coverage: 100%)
Gene names: POLR1F, TWISTNB
Pfam:
InterPro:
DNA-directed RNA polymerase I subunit RPA43 in PDB entry 7obb, assembly 1, front view.
DNA-directed RNA polymerase I subunit RPA43 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerase I subunit RPA43 in PDB entry 7obb, 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 7obb, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 7obb, assembly 1, top view.
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DNA-directed RNA polymerase I subunit RPA12
Chain: I
Length: 126 amino acids
Theoretical weight: 13.92 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P1U0 (Residues: 1-126; Coverage: 100%)
Gene names: POLR1H, RPA12, ZNRD1
Pfam: Transcription factor S-II (TFIIS)
InterPro:
DNA-directed RNA polymerase I subunit RPA12 in PDB entry 7obb, assembly 1, front view.
DNA-directed RNA polymerase I subunit RPA12 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerase I subunit RPA12 in PDB entry 7obb, 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 7obb, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 7obb, assembly 1, top view.
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DNA-directed RNA polymerases I and III subunit RPAC2
Chain: K
Length: 133 amino acids
Theoretical weight: 15.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0DPB6 (Residues: 1-133; Coverage: 100%)
Gene name: POLR1D
Pfam: RNA polymerase Rpb3/Rpb11 dimerisation domain
InterPro:
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 7obb, assembly 1, front view.
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 7obb, 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 7obb, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 7obb, assembly 1, top view.
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DNA-directed RNA polymerase I subunit RPA49
Chain: M
Length: 419 amino acids
Theoretical weight: 47.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9GZS1 (Residues: 1-419; Coverage: 100%)
Gene names: PAF53, POLR1E, PRAF1
Pfam: A49-like RNA polymerase I associated factor
InterPro: RNA polymerase I associated factor, A49-like
DNA-directed RNA polymerase I subunit RPA49 in PDB entry 7obb, assembly 1, front view.
DNA-directed RNA polymerase I subunit RPA49 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerase I subunit RPA49 in PDB entry 7obb, assembly 1, top view.
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DNA-directed RNA polymerase I subunit RPA34
Chain: N
Length: 510 amino acids
Theoretical weight: 55.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15446 (Residues: 1-510; Coverage: 100%)
  • Best match: O15446-2 (Residues: 1-512)
Gene names: ASE1, CAST, CD3EAP, PAF49, POLR1G
Pfam: DNA-directed RNA polymerase I subunit RPA34.5
InterPro: DNA-directed RNA polymerase I, subunit RPA34
DNA-directed RNA polymerase I subunit RPA34 in PDB entry 7obb, assembly 1, front view.
DNA-directed RNA polymerase I subunit RPA34 in PDB entry 7obb, assembly 1, side view.
DNA-directed RNA polymerase I subunit RPA34 in PDB entry 7obb, assembly 1, top view.
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DNA chain T
Name: DNA template strand
Representative chains: T
Length: 43 nucleotides
Theoretical weight: 13.27 KDa
DNA template strand in PDB entry 7obb, assembly 1, front view.
DNA template strand in PDB entry 7obb, assembly 1, side view.
DNA template strand in PDB entry 7obb, assembly 1, top view.
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DNA chain S
Name: DNA non-template strand
Representative chains: S
Length: 43 nucleotides
Theoretical weight: 13.27 KDa
DNA non-template strand in PDB entry 7obb, assembly 1, front view.
DNA non-template strand in PDB entry 7obb, assembly 1, side view.
DNA non-template strand in PDB entry 7obb, assembly 1, top view.
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