6Y5D: Human cGAS
Structure of human cGAS (K394E) bound to the nucleosome. Determined by electron microscopy at 4.1 Å resolution. Released 23 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organism
- Homo sapiens
- Chains
- 22
- Atoms
- 30,372
- Mol. weight
- 478.34 kDa
- Ligands
- ZN, PTD
- Released
- 23 Sept 2020
Explore 6Y5D in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6Y5D contains 119 α-helices and 74 β-strands across 18 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.
Chains A, M and Q: 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 | |
Chains B, N and R: 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 | 29-35 | 7 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 47-73 | 27 | |
| 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 | |
Chains D, P and T: 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 | 106-124 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-43 | 2 | |
| α-helix | 46-57 | 12 | |
| α-helix | 65-79 | 15 | |
| 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 | 84-93 | 10 | |
| β-strand | 97-99 | 3 | 6 |
Chain G: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-15 | 3 | |
| α-helix | 18-22 | 5 | |
| α-helix | 29-34 | 6 | |
| 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 | |
4 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, M, Q | protein | 98 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F, N, R | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 2-A | C, G, O, S | protein | 130 | Homo sapiens | Q6FI13 (AlphaFold model) |
| Histone H2B type 1-K | D, H, P, T | protein | 126 | Homo sapiens | O60814 (AlphaFold model) |
| DNA (153-mer) | I, U | DNA | 153 | Homo sapiens | |
| DNA (153-mer) | J, V | DNA | 153 | Homo sapiens | |
| Cyclic GMP-AMP synthase | K, L | protein | 362 | Homo sapiens | Q8N884 |
Sequence of entity 1 (A, E, M, Q), FASTA
>6Y5D_1 Histone H3.2 (chains A, E, M, Q)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVGLFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F, N, R), FASTA
>6Y5D_2 Histone H4 (chains B, F, N, R)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G, O, S), FASTA
>6Y5D_3 Histone H2A type 2-A (chains C, G, O, S)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D, H, P, T), FASTA
>6Y5D_4 Histone H2B type 1-K (chains D, H, P, T)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I, U), FASTA
>6Y5D_5 DNA (153-MER) (chains I, U)
ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCACGTGTCAGATATATACATCCTGTGAT
Sequence of entity 6 (J, V), FASTA
>6Y5D_6 DNA (153-MER) (chains J, V)
ATCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT
Sequence of entity 7 (K, L), FASTA
>6Y5D_7 Cyclic GMP-AMP synthase (chains K, L)
GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKI
SAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKF
RKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRI
QNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSETCCENK
EEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDL
GLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFD
EF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| PTD | Pentanedial | C5 H8 O2 | 9 |
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
About this viewer
MolViewer shows 6Y5D directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.