9UBD: Histone H2A.Z

The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP Catalytic Subunit. Determined by X-ray diffraction at 2.53 Å resolution. Released 8 Apr 2026.

Method: X-ray diffraction
Resolution: 2.53 Å
Organism: Homo sapiens
Chains: 5
Atoms: 2,685
Mol. weight: 45.34 kDa
Released: 8 Apr 2026

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

Secondary structure: helices and β-sheets

9UBD contains 19 α-helices and 8 β-strands across 5 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	20-24	5
α-helix	30-39	10
β-strand	46-47	2	1
α-helix	49-76	28
β-strand	81-82	2	2
α-helix	84-92	9
α-helix	95-100	6

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	2
α-helix	57-83	27
β-strand	89-90	2	1
α-helix	92-102	11
α-helix	105-123	19

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	551-554	4

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	20-24	5
α-helix	30-40	11
β-strand	46-47	2	4
α-helix	49-75	27
β-strand	81-82	2	3
α-helix	84-92	9
α-helix	95-105	11

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	3
α-helix	57-82	26
β-strand	89-90	2	4
α-helix	92-102	11
α-helix	105-123	19

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)
Helicase SRCAP	C	protein	30	Homo sapiens	Q6ZRS2

Sequence of entity 1 (A, D), FASTA

>9UBD_1 Histone H2A.Z (chains A, D)
AVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD
LKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHI

Sequence of entity 2 (B, E), FASTA

>9UBD_2 Histone H2B type 1-J (chains B, E)
RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSR
EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSASS

Sequence of entity 3 (C), FASTA

>9UBD_3 Helicase SRCAP (chains C)
SEDAQSQSQADEEEEDDDFGVEYLLARDEE

Primary citation

The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP Catalytic Subunit. Tan, W.S., Yuan, B.Y., Jiang, J.S. et al. To be published.

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…
9INC 2.01 Å, High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z…
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…
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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