8HQY: SSX1
Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom. Determined by electron microscopy at 3.05 Å resolution. Released 27 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 3.05 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 12,302
- Mol. weight
- 180.39 kDa
- Released
- 27 Sept 2023
Explore 8HQY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8HQY contains 39 α-helices and 27 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-112 | 27 | |
| 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 | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-87 | 8 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 113-115 | 3 | |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-76 | 27 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
Chain U: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 11 |
| β-strand | 12-16 | 5 | 11 |
| β-strand | 22 | 1 | 12 |
| α-helix | 24-33 | 10 | |
| β-strand | 43-44 | 2 | 11 |
| β-strand | 49 | 1 | 11 |
| β-strand | 55 | 1 | 12 |
| α-helix | 56-58 | 3 | |
| β-strand | 66-69 | 4 | 11 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3 | A, E | protein | 97 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 (Fragment) | B | protein | 83 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C | protein | 107 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-K | D, H | protein | 91 | Homo sapiens | O60814 (AlphaFold model) |
| Histone H4 | F | protein | 81 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | G | protein | 106 | Homo sapiens | P04908 (AlphaFold model) |
| Protein SSX2 | S | protein | 23 | Homo sapiens | Q16385 |
| Polyubiquitin-B (Fragment) | U | protein | 74 | Homo sapiens | P0CG47 |
| DNA (137-mer) | I | DNA | 136 | Homo sapiens | |
| DNA (136-mer) | J | DNA | 136 | Homo sapiens | |
Sequence of entity 1 (A, E), FASTA
>8HQY_1 Histone H3 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVGLFEDTNLSAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 2 (B), FASTA
>8HQY_2 Histone H4 (Fragment) (chains B)
RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKR
KTVTAMDVVYALKRQGRTLYGFG
Sequence of entity 3 (C), FASTA
>8HQY_3 Histone H2A type 1-B/E (chains C)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKC
Sequence of entity 4 (D, H), FASTA
>8HQY_4 Histone H2B type 1-K (chains D, H)
KESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSRE
IQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Sequence of entity 5 (F), FASTA
>8HQY_5 Histone H4 (chains F)
VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGFG
Sequence of entity 6 (G), FASTA
>8HQY_6 Histone H2A type 1-B/E (chains G)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK
Sequence of entity 7 (S), FASTA
>8HQY_7 Protein SSX2 (chains S)
HAWTHRLRERKQLVIYEEISDPE
Sequence of entity 8 (U), FASTA
>8HQY_8 Polyubiquitin-B (Fragment) (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLR
Sequence of entity 9 (I), FASTA
>8HQY_9 DNA (137-MER) (chains I)
ATGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATA
Sequence of entity 10 (J), FASTA
>8HQY_10 DNA (136-MER) (chains J)
TATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGG
ACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCG
GCACCGGGATTCTCAT
Primary citation
Synovial sarcoma X breakpoint 1 protein uses a cryptic groove to selectively recognize H2AK119Ub nucleosomes. Tong, Z., Ai, H., Xu, Z. et al. Nat Struct Mol Biol (2024) 31:300-310. DOI 10.1038/s41594-023-01141-1 · 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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