8OL1: CGAS-Nucleosome
cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure). Determined by electron microscopy at 3.5 Å resolution. Released 14 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Homo sapiens
- Chains
- 14
- Atoms
- 18,376
- Mol. weight
- 270.83 kDa
- Ligands
- ZN
- Released
- 14 Feb 2024
Explore 8OL1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OL1 contains 73 α-helices and 65 β-strands across 12 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 | 40-42 | 3 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-130 | 10 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 51-75 | 25 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-53 | 8 | |
| α-helix | 55-64 | 10 | |
| α-helix | 65-68 | 4 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-88 | 9 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 6 |
Chain D: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-45 | 8 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-58 | 3 | |
| α-helix | 60-83 | 24 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 96-101 | 6 | |
| α-helix | 106-115 | 10 | |
| α-helix | 120-123 | 4 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 46-56 | 11 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83 | 1 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 51-76 | 26 | |
| β-strand | 80 | 1 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-87 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 3 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-45 | 8 | |
| β-strand | 53-54 | 2 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 9 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
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 | protein | 98 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F | protein | 81 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-H | C | protein | 108 | Homo sapiens | Q96KK5 (AlphaFold model) |
| Histone H2B type 1-H | D | protein | 95 | Homo sapiens | Q93079 (AlphaFold model) |
| Histone H2A type 1-J | G | protein | 107 | Homo sapiens | Q99878 |
| Histone H2B type 1-N | H | protein | 94 | Homo sapiens | Q99877 |
| DNA (145-mer) | I | DNA | 145 | Homo sapiens | |
| DNA (145-mer) | J | DNA | 145 | Homo sapiens | |
| Cyclic GMP-AMP synthase | K | protein | 362 | Homo sapiens | Q8N884 |
| SPRY domain-containing SOCS box protein 3 | L | protein | 244 | Homo sapiens | Q6PJ21 |
| Elongin-C | M | protein | 112 | Homo sapiens | Q15369 |
| Elongin-B | N | protein | 118 | Homo sapiens | Q15370 |
Sequence of entity 1 (A, E), FASTA
>8OL1_1 Histone H3.2 (chains A, E)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS
EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 2 (B, F), FASTA
>8OL1_2 Histone H4 (chains B, F)
LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTV
TAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C), FASTA
>8OL1_3 Histone H2A type 1-H (chains C)
ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLP
Sequence of entity 4 (D), FASTA
>8OL1_4 Histone H2B type 1-H (chains D)
KRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTI
TSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS
Sequence of entity 5 (G), FASTA
>8OL1_5 Histone H2A type 1-J (chains G)
ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLL
Sequence of entity 6 (H), FASTA
>8OL1_6 Histone H2B type 1-N (chains H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS
Sequence of entity 7 (I), FASTA
>8OL1_7 DNA (145-MER) (chains I)
TGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCTG
Sequence of entity 8 (J), FASTA
>8OL1_8 DNA (145-MER) (chains J)
CAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTCCA
Sequence of entity 9 (K), FASTA
>8OL1_9 Cyclic GMP-AMP synthase (chains K)
GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKI
SAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKF
RKIIAEEINDIKDTDVIMKAKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRI
QNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENK
EEKCCRKDCLKLMKYLLEQLKERFKDKAHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDL
GLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFD
EF
Sequence of entity 10 (L), FASTA
>8OL1_10 SPRY domain-containing SOCS box protein 3 (chains L)
SSLHSAHRGRDCRCGEEDEYFDWVWDDLNKSSATLLSCDNRKVSFHMEYSCGTAAIRGTK
ELGEGQHFWEIKMTSPVYGTDMMVGIGTSDVDLDKYRHTFCSLLGRDEDSWGLSYTGLLH
HKGDKTSFSSRFGQGSIIGVHLDTWHGTLTFFKNRKCIGVAATKLQNKRFYPMVCSTAAR
SSMKVTRSCASATSLQYLCCHRLRQLRPDSGDTLEGLPLPPGLKQVLHNKLGWVLSMSCS
RRKA
Sequence of entity 11 (M), FASTA
>8OL1_11 Elongin-C (chains M)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 12 (N), FASTA
>8OL1_12 Elongin-B (chains N)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Xu, P., Liu, Y., Liu, C. et al. Nature (2024) 627:873-879. DOI 10.1038/s41586-024-07112-w · 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 8OL1 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.