8HR1: SSX1

Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom. Determined by electron microscopy at 3.02 Å resolution. Released 13 Sept 2023.

Method: Electron microscopy
Resolution: 3.02 Å
Organism: Homo sapiens
Chains: 11
Atoms: 12,110
Mol. weight: 178.04 kDa
Released: 13 Sept 2023

Explore 8HR1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HR1 contains 37 α-helices and 18 β-strands across 8 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-112	27
α-helix	121-129	9

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	2

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	3
α-helix	46-72	27
β-strand	77-78	2	4
α-helix	80-88	9
α-helix	92-96	5
β-strand	100-101	2	5
α-helix	102	1

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	4
α-helix	56-83	28
β-strand	88-89	2	3
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	6
α-helix	86-113	28
β-strand	118-119	2	7
α-helix	121-131	11

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	7
α-helix	48-50	3
α-helix	55-75	21
β-strand	80-81	2	6
α-helix	83-92	10
β-strand	96-97	2	5

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	8
α-helix	46-72	27
β-strand	77-78	2	9
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	97	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	B, F	protein	83	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	107	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	D, H	protein	91	Homo sapiens	O60814 (AlphaFold model)
SSX1	S	protein	14	Homo sapiens	Q16384
DNA (147-mer)	I	DNA	147	Homo sapiens
DNA (147-mer)	J	DNA	147	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>8HR1_1 Histone H3 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVGLFEDTNLSAIHAKRVTIMPKDIQLARRIRGER

Sequence of entity 2 (B, F), FASTA

>8HR1_2 Histone H4 (chains B, F)
RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKR
KTVTAMDVVYALKRQGRTLYGFG

Sequence of entity 3 (C, G), FASTA

>8HR1_3 Histone H2A type 1-B/E (chains C, G)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKC

Sequence of entity 4 (D, H), FASTA

>8HR1_4 Histone H2B type 1-K (chains D, H)
KESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSRE
IQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Sequence of entity 5 (S), FASTA

>8HR1_5 SSX1 (chains S)
HAWTHRLRERKQLV

Sequence of entity 6 (I), FASTA

>8HR1_6 DNA (147-MER) (chains I)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 7 (J), FASTA

>8HR1_7 DNA (147-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT

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

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