7YQK: GammaH2AXK15ub-H4K20me2 nucleosome

cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1. Determined by electron microscopy at 3.38 Å resolution. Released 17 Aug 2022.

Method: Electron microscopy
Resolution: 3.38 Å
Organisms: Homo sapiens, synthetic construct
Chains: 13
Atoms: 13,745
Mol. weight: 201.82 kDa
Released: 17 Aug 2022

Explore 7YQK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YQK contains 42 α-helices and 40 β-strands across 10 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	46-54	9
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	51-75	25
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-71	26
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	93-96	4
β-strand	100-102	3	6

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	30-33	4
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	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	119	1	8
α-helix	121-131	11

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	46	1	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-87	8
α-helix	91-96	6
β-strand	100-102	3	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	10
α-helix	56-83	28
β-strand	88-89	2	9
α-helix	91-101	11
α-helix	105-123	19

2 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 H3.1	A, E	protein	100	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	83	Homo sapiens	P62805 (AlphaFold model)
Histone H2AX	C, G	protein	112	synthetic construct	P16104 (AlphaFold model)
Histone H2B	D, H	protein	96	Homo sapiens	O60814 (AlphaFold model)
DNA (145-mer)	I	DNA	145	synthetic construct
DNA (145-mer)	J	DNA	145	synthetic construct
Polyubiquitin-B	O	protein	75	Homo sapiens	P0CG47
UDR motif of 53BP1	K	protein	18	Homo sapiens	Q12888
TP53-binding protein 1	N	protein	118	Homo sapiens	Q12888

Sequence of entity 1 (A, E), FASTA

>7YQK_1 Histone H3.1 (chains A, E)
KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA
CEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>7YQK_2 Histone H4 (chains B, F)
KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK
TVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>7YQK_3 Histone H2AX (chains C, G)
ARAKACTRSSRAGLQFPVGRVHRLLRKGHYSERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTE

Sequence of entity 4 (D, H), FASTA

>7YQK_4 Histone H2B (chains D, H)
RKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRST
ITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Sequence of entity 5 (I), FASTA

>7YQK_5 DNA (145-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT

Sequence of entity 6 (J), FASTA

>7YQK_6 DNA (145-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT

Sequence of entity 7 (O), FASTA

>7YQK_7 Polyubiquitin-B (chains O)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Sequence of entity 8 (K), FASTA

>7YQK_8 UDR motif of 53BP1 (chains K)
KAADISLDNLVEGKRKRR

Sequence of entity 9 (N), FASTA

>7YQK_9 TP53-binding protein 1 (chains N)
SFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEV
TALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGL

Primary citation

Chemical Synthesis of Post-Translationally Modified H2AX Reveals Redundancy in Interplay between Histone Phosphorylation, Ubiquitination, and Methylation on the Binding of 53BP1 with Nucleosomes. Ai, H., Chu, G.C., Gong, Q. et al. J Am Chem Soc (2022) 144:18329-18337. DOI 10.1021/jacs.2c06156 · PubMed

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

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