6Y5E: Human cGAS
Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex). Determined by electron microscopy at 3.15 Å resolution. Released 23 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.15 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 15,292
- Mol. weight
- 223.09 kDa
- Ligands
- PTD, ZN
- Released
- 23 Sept 2020
Explore 6Y5E in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6Y5E contains 61 α-helices and 37 β-strands across 9 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-43 | 2 | |
| α-helix | 46-57 | 12 | |
| α-helix | 65-76 | 12 | |
| β-strand | 84-85 | 2 | 1 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 2 |
| α-helix | 122-131 | 10 | |
Chain B: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 2 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 83 | 1 | |
| α-helix | 84-92 | 9 | |
| β-strand | 98-99 | 2 | 3 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-15 | 3 | |
| α-helix | 18-22 | 5 | |
| α-helix | 29-36 | 8 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-89 | 9 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 6 |
| α-helix | 114-116 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| β-strand | 54-55 | 2 | 5 |
| α-helix | 57-84 | 28 | |
| β-strand | 89-90 | 2 | 4 |
| α-helix | 92-102 | 11 | |
| α-helix | 107-124 | 18 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-43 | 2 | |
| α-helix | 46-57 | 12 | |
| α-helix | 65-76 | 12 | |
| β-strand | 84-85 | 2 | 7 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 8 |
| α-helix | 122-132 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 8 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 7 |
| α-helix | 84-92 | 9 | |
| β-strand | 97-99 | 3 | 6 |
Chain G: 9 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-15 | 3 | |
| α-helix | 18-21 | 4 | |
| α-helix | 29-34 | 6 | |
| α-helix | 37-39 | 3 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| α-helix | 101 | 1 | |
| β-strand | 102-103 | 2 | 3 |
| α-helix | 114-116 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| β-strand | 54-55 | 2 | 10 |
| α-helix | 57-84 | 28 | |
| β-strand | 89-90 | 2 | 9 |
| α-helix | 92-102 | 11 | |
| α-helix | 107-122 | 16 | |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.2 | A, E | protein | 96 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B | protein | 81 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 2-C | C | protein | 107 | Homo sapiens | Q16777 (AlphaFold model) |
| Histone H2B type 1-K | D | protein | 93 | Homo sapiens | O60814 (AlphaFold model) |
| Histone H4 | F | protein | 83 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 2-C | G | protein | 108 | Homo sapiens | Q16777 (AlphaFold model) |
| Histone H2B type 1-K | H | protein | 94 | Homo sapiens | O60814 (AlphaFold model) |
| DNA (153-mer) | I | DNA | 153 | Homo sapiens | |
| DNA (153-mer) | J | DNA | 153 | Homo sapiens | |
| Cyclic GMP-AMP synthase | K | protein | 362 | Homo sapiens | Q8N884 |
Sequence of entity 1 (A, E), FASTA
>6Y5E_1 Histone H3.2 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVGLFEDTNLAAIHAKRVTIMPKDIQLARRIRGE
Sequence of entity 2 (B), FASTA
>6Y5E_2 Histone H4 (chains B)
LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTV
TAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C), FASTA
>6Y5E_3 Histone H2A type 2-C (chains C)
RAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLP
Sequence of entity 4 (D), FASTA
>6Y5E_4 Histone H2B type 1-K (chains D)
SRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Sequence of entity 5 (F), FASTA
>6Y5E_5 Histone H4 (chains F)
KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK
TVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 6 (G), FASTA
>6Y5E_6 Histone H2A type 2-C (chains G)
RAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPK
Sequence of entity 7 (H), FASTA
>6Y5E_7 Histone H2B type 1-K (chains H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Sequence of entity 8 (I), FASTA
>6Y5E_8 DNA (153-MER) (chains I)
ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCACGTGTCAGATATATACATCCTGTGAT
Sequence of entity 9 (J), FASTA
>6Y5E_9 DNA (153-MER) (chains J)
ATCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT
Sequence of entity 10 (K), FASTA
>6Y5E_10 Cyclic GMP-AMP synthase (chains K)
GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKI
SAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKF
RKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRI
QNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSETCCENK
EEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDL
GLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFD
EF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PTD | Pentanedial | C5 H8 O2 | 8 |
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structural mechanism of cGAS inhibition by the nucleosome. Pathare, G.R., Decout, A., Gluck, S. et al. Nature (2020) 587:668-672. DOI 10.1038/s41586-020-2750-6 · PubMed
Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
- 2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
- 5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
- 6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
- 7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
- 5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
- 3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
- 4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
- 4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide
Browse structure collections
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