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Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex)

Electron Microscopy
3.15Å resolution
PDB entry 6y5e coloured by chain, front view.
PDB entry 6y5e coloured by chain, side view.
PDB entry 6y5e coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero undecamer (preferred)
Entry contents: 8 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero undecamer
Accessible surface area: 92988.22 Å2
Buried surface area: 60338.43 Å2
Dissociation area: 4,725.65 Å2
Dissociation energy (ΔGdiss): 68.46 kcal/mol
Dissociation entropy (TΔSdiss): 13.61 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120988

Macromolecules

Histone H3.2
Chains: A, E
Length: 96 amino acids
Theoretical weight: 11.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q71DI3 (Residues: 39-134; Coverage: 71%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H3.2 in PDB entry 6y5e, assembly 1, front view.
Histone H3.2 in PDB entry 6y5e, assembly 1, side view.
Histone H3.2 in PDB entry 6y5e, assembly 1, top view.
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Histone H4
Chain: B
Length: 81 amino acids
Theoretical weight: 9.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P62805 (Residues: 23-103; Coverage: 79%)
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 6y5e, assembly 1, front view.
Histone H4 in PDB entry 6y5e, assembly 1, side view.
Histone H4 in PDB entry 6y5e, assembly 1, top view.
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Histone H2A type 2-C
Chain: C
Length: 107 amino acids
Theoretical weight: 11.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q16777 (Residues: 12-118; Coverage: 83%)
Gene names: H2AC20, H2AFQ, HIST2H2AC
Pfam:
InterPro:
Histone H2A type 2-C in PDB entry 6y5e, assembly 1, front view.
Histone H2A type 2-C in PDB entry 6y5e, assembly 1, side view.
Histone H2A type 2-C in PDB entry 6y5e, assembly 1, top view.
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Histone H2B type 1-K
Chain: D
Length: 93 amino acids
Theoretical weight: 10.32 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: O60814 (Residues: 33-125; Coverage: 74%)
Gene names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B type 1-K in PDB entry 6y5e, assembly 1, front view.
Histone H2B type 1-K in PDB entry 6y5e, assembly 1, side view.
Histone H2B type 1-K in PDB entry 6y5e, assembly 1, top view.
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Histone H4
Chain: F
Length: 83 amino acids
Theoretical weight: 9.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P62805 (Residues: 21-103; Coverage: 81%)
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 6y5e, assembly 1, front view.
Histone H4 in PDB entry 6y5e, assembly 1, side view.
Histone H4 in PDB entry 6y5e, assembly 1, top view.
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Histone H2A type 2-C
Chain: G
Length: 108 amino acids
Theoretical weight: 11.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q16777 (Residues: 12-119; Coverage: 84%)
Gene names: H2AC20, H2AFQ, HIST2H2AC
Pfam:
InterPro:
Histone H2A type 2-C in PDB entry 6y5e, assembly 1, front view.
Histone H2A type 2-C in PDB entry 6y5e, assembly 1, side view.
Histone H2A type 2-C in PDB entry 6y5e, assembly 1, top view.
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Histone H2B type 1-K
Chain: H
Length: 94 amino acids
Theoretical weight: 10.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: O60814 (Residues: 32-125; Coverage: 75%)
Gene names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B type 1-K in PDB entry 6y5e, assembly 1, front view.
Histone H2B type 1-K in PDB entry 6y5e, assembly 1, side view.
Histone H2B type 1-K in PDB entry 6y5e, assembly 1, top view.
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Cyclic GMP-AMP synthase
Chain: K
Length: 362 amino acids
Theoretical weight: 42.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q8N884 (Residues: 161-522; Coverage: 69%)
Gene names: C6orf150, CGAS, MB21D1
Pfam:
InterPro:
Cyclic GMP-AMP synthase in PDB entry 6y5e, assembly 1, front view.
Cyclic GMP-AMP synthase in PDB entry 6y5e, assembly 1, side view.
Cyclic GMP-AMP synthase in PDB entry 6y5e, assembly 1, top view.
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DNA chain I
Name: DNA (153-MER)
Representative chains: I
Length: 153 nucleotides
Theoretical weight: 47 KDa
DNA (153-MER) in PDB entry 6y5e, assembly 1, front view.
DNA (153-MER) in PDB entry 6y5e, assembly 1, side view.
DNA (153-MER) in PDB entry 6y5e, assembly 1, top view.
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DNA chain J
Name: DNA (153-MER)
Representative chains: J
Length: 153 nucleotides
Theoretical weight: 47.46 KDa
DNA (153-MER) in PDB entry 6y5e, assembly 1, front view.
DNA (153-MER) in PDB entry 6y5e, assembly 1, side view.
DNA (153-MER) in PDB entry 6y5e, assembly 1, top view.
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