9INC: Histone H2A.Z

High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain. Determined by X-ray diffraction at 2.01 Å resolution. Released 9 Jul 2025.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,735
Mol. weight: 61.02 kDa
Released: 9 Jul 2025

Explore 9INC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9INC contains 28 α-helices and 12 β-strands across 6 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	19-22	4
α-helix	29-38	10
β-strand	46	1	1
α-helix	48-72	25
β-strand	80-81	2	2
α-helix	83-91	9
α-helix	94-104	11

Chains B and E: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	2
β-strand	55	1	3
α-helix	56-83	28
β-strand	89	1	1
α-helix	91-101	11
α-helix	104-122	19

Chains C and F: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	17-32	16
α-helix	33-35	3
α-helix	44	1
β-strand	45	1	3
α-helix	46	1
α-helix	56-58	3

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-23	5
α-helix	29-38	10
β-strand	46	1	4
α-helix	48-72	25
β-strand	80-81	2	5
α-helix	83-91	9
α-helix	94-104	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2A.Z	A, D	protein	98	Homo sapiens	P0C0S5 (AlphaFold model)
Histone H2B type 1-J	B, E	protein	94	Homo sapiens	P06899 (AlphaFold model)
Vacuolar protein sorting-associated protein 72 homolog	C, F	protein	87	Homo sapiens	Q15906 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9INC_1 Histone H2A.Z (chains A, D)
AVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD
LKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHI

Sequence of entity 2 (B, E), FASTA

>9INC_2 Histone H2B type 1-J (chains B, E)
RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSR
EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSASS

Sequence of entity 3 (C, F), FASTA

>9INC_3 Vacuolar protein sorting-associated protein 72 homolog (chains C, F)
MGSSHHHHHHSSGLVPRGSHMAPRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEY
QGDQSDTEDEVDSDFDIDEGDEPSSDG

Primary citation

Structural insights into specific recognition of the histone variant H2A.Z by the YL1 subunit of SRCAP chromatin-remodeling complex. Tan, W., Liu, Y., Hong, J. J Biol Chem (2026) 302:111294-111294. DOI 10.1016/j.jbc.2026.111294 · PubMed

Other PDB entries of the same protein (UniProt P0C0S5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4CAY 1.48 Å, Crystal structure of a human Anp32e-H2A.Z-H2B complex
6KO2 1.5 Å, Crystal Structure of BRD4-Brmo2 in complex with H2A.ZK4acK7ac peptide
5CHL 1.89 Å, Structural basis of H2A.Z recognition by YL1 histone chaperone component of SRCAP/SWR1…
6JOU 2.17 Å, Crystal structure of the human nucleosome containing H2A.Z.1 S42R
5B31 2.2 Å, The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1.
5B32 2.35 Å, The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3.
5Z30 2.45 Å, The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z…
9UBD 2.53 Å, The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP…
1F66 2.6 Å, 2.6 a crystal structure of a nucleosome core particle containing the variant histone H2A.Z
8T9F 2.6 Å, Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
4NFT 2.61 Å, Crystal structure of human lnkH2B-h2A.Z-Anp32e
5FUG 2.7 Å, Crystal structure of a human YL1-H2A.Z-H2B complex

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