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RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome

Electron Microscopy
7Å resolution
PDB entry 6a5p coloured by chain, front view.
PDB entry 6a5p coloured by chain, side view.
PDB entry 6a5p coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 23-mer (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 23-mer
Accessible surface area: 239001.54 Å2
Buried surface area: 125491.23 Å2
Dissociation area: 992.88 Å2
Dissociation energy (ΔGdiss): 1.36 kcal/mol
Dissociation entropy (TΔSdiss): 14.87 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111397

Macromolecules

DNA-directed RNA polymerase subunit
Chain: A
Length: 1743 amino acids
Theoretical weight: 194.11 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R4Y0 (Residues: 1-1743; Coverage: 100%)
Gene name: PAS_chr3_0568
Pfam:
InterPro:
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, front view.
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, side view.
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta
Chain: B
Length: 1227 amino acids
Theoretical weight: 139.75 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QZQ7 (Residues: 1-1227; Coverage: 100%)
Gene name: PAS_chr2-1_0125
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta in PDB entry 6a5p, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 6a5p, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 6a5p, assembly 1, top view.
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DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
Chain: C
Length: 304 amino acids
Theoretical weight: 34.22 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R7L2 (Residues: 1-304; Coverage: 100%)
Gene name: PAS_chr4_0344
Pfam:
InterPro:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 6a5p, assembly 1, front view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 6a5p, assembly 1, side view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 6a5p, assembly 1, top view.
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RNA polymerase Rpb4/RPC9 core domain-containing protein
Chain: D
Length: 186 amino acids
Theoretical weight: 20.62 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R2U9 (Residues: 1-186; Coverage: 100%)
Gene name: PAS_chr2-2_0104
Pfam: RNA polymerase Rpb4
InterPro:
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 6a5p, assembly 1, front view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 6a5p, assembly 1, side view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 6a5p, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC1
Chain: E
Length: 214 amino acids
Theoretical weight: 24.96 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R3P8 (Residues: 1-214; Coverage: 100%)
Gene name: PAS_chr3_0157
Pfam:
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 6a5p, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 6a5p, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 6a5p, assembly 1, top view.
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RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
Chain: F
Length: 155 amino acids
Theoretical weight: 17.8 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R1V1 (Residues: 1-155; Coverage: 100%)
Gene name: PAS_chr2-2_0434
Pfam: RNA polymerase Rpb6
InterPro:
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III in PDB entry 6a5p, assembly 1, front view.
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III in PDB entry 6a5p, assembly 1, side view.
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III in PDB entry 6a5p, assembly 1, top view.
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DNA-directed RNA polymerase subunit
Chain: G
Length: 171 amino acids
Theoretical weight: 18.8 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R9A1 (Residues: 1-171; Coverage: 100%)
Gene name: PAS_chr4_0906
Pfam:
InterPro:
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, front view.
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, side view.
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain: H
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R273 (Residues: 1-145; Coverage: 100%)
Gene name: PAS_chr2-2_0309
Pfam: RNA polymerase Rpb8
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6a5p, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6a5p, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6a5p, assembly 1, top view.
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DNA-directed RNA polymerase subunit
Chain: I
Length: 115 amino acids
Theoretical weight: 13.61 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: F2QPE6 (Residues: 1-115; Coverage: 100%)
Gene names: PP7435_Chr1-1144, RPB9
Pfam:
InterPro:
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, front view.
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, side view.
DNA-directed RNA polymerase subunit in PDB entry 6a5p, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC5
Chain: J
Length: 72 amino acids
Theoretical weight: 8.55 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R009 (Residues: 1-72; Coverage: 100%)
Gene name: PAS_chr2-1_0223
Pfam: RNA polymerases N / 8 kDa subunit
InterPro:
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III in PDB entry 6a5p, assembly 1, front view.
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III in PDB entry 6a5p, assembly 1, side view.
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III in PDB entry 6a5p, assembly 1, top view.
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DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
Chain: K
Length: 118 amino acids
Theoretical weight: 13.83 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R3Z5 (Residues: 1-118; Coverage: 100%)
Gene name: PAS_chr3_0244
Pfam: RNA polymerase Rpb3/Rpb11 dimerisation domain
InterPro:
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 6a5p, assembly 1, front view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 6a5p, assembly 1, side view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 6a5p, assembly 1, top view.
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RNA polymerase subunit ABC10-alpha
Chain: L
Length: 72 amino acids
Theoretical weight: 7.86 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: F2QMI1 (Residues: 1-72; Coverage: 100%)
Gene names: PP7435_Chr1-0476, RPC10
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
RNA polymerase subunit ABC10-alpha in PDB entry 6a5p, assembly 1, front view.
RNA polymerase subunit ABC10-alpha in PDB entry 6a5p, assembly 1, side view.
RNA polymerase subunit ABC10-alpha in PDB entry 6a5p, assembly 1, top view.
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Histone H3.3
Chains: a, e
Length: 139 amino acids
Theoretical weight: 15.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P84243 (Residues: 1-136; Coverage: 100%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H3.3 in PDB entry 6a5p, assembly 1, front view.
Histone H3.3 in PDB entry 6a5p, assembly 1, side view.
Histone H3.3 in PDB entry 6a5p, assembly 1, top view.
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Histone H4
Chains: b, f
Length: 106 amino acids
Theoretical weight: 11.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
Histone H4 in PDB entry 6a5p, assembly 1, front view.
Histone H4 in PDB entry 6a5p, assembly 1, side view.
Histone H4 in PDB entry 6a5p, assembly 1, top view.
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Histone H2A type 1-B/E
Chains: c, g
Length: 133 amino acids
Theoretical weight: 14.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Pfam:
InterPro:
Histone H2A type 1-B/E in PDB entry 6a5p, assembly 1, front view.
Histone H2A type 1-B/E in PDB entry 6a5p, assembly 1, side view.
Histone H2A type 1-B/E in PDB entry 6a5p, assembly 1, top view.
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Histone H2B type 1-J
Chains: d, h
Length: 129 amino acids
Theoretical weight: 14.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B type 1-J in PDB entry 6a5p, assembly 1, front view.
Histone H2B type 1-J in PDB entry 6a5p, assembly 1, side view.
Histone H2B type 1-J in PDB entry 6a5p, assembly 1, top view.
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DNA chain T
Name: DNA (198-MER)
Representative chains: T
Length: 198 nucleotides
Theoretical weight: 60.87 KDa
DNA (198-MER) in PDB entry 6a5p, assembly 1, front view.
DNA (198-MER) in PDB entry 6a5p, assembly 1, side view.
DNA (198-MER) in PDB entry 6a5p, assembly 1, top view.
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DNA chain N
Name: DNA (198-MER)
Representative chains: N
Length: 198 nucleotides
Theoretical weight: 61.38 KDa
DNA (198-MER) in PDB entry 6a5p, assembly 1, front view.
DNA (198-MER) in PDB entry 6a5p, assembly 1, side view.
DNA (198-MER) in PDB entry 6a5p, assembly 1, top view.
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RNA chain P
Name: RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*C)-3')
Representative chains: P
Length: 11 nucleotides
Theoretical weight: 3.6 KDa
RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*C)-3') in PDB entry 6a5p, assembly 1, front view.
RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*C)-3') in PDB entry 6a5p, assembly 1, side view.
RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*C)-3') in PDB entry 6a5p, assembly 1, top view.
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