9INC | pdb_00009inc

High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain

• PDB DOI: https://doi.org/10.2210/pdb9INC/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-06 Released: 2025-07-09 
• Deposition Author(s): Tan, W.S., Liu, Y., Hong, J.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Models: experimental

Literature

Structural basis of human histone variant H2AZ recognized by human YL1 providing a conserved structural mechanism

Tan, W.S., Liu, Y., Hong, J.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.02 kDa 
• Atom Count: 3,735 
• Modeled Residue Count: 475 
• Deposited Residue Count: 558 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.Z	A, D	98	Homo sapiens	Mutation(s): 0  Gene Names: H2AZ1, H2AFZ, H2AZ
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S5 (Homo sapiens) Explore P0C0S5  Go to UniProtKB:  P0C0S5
PHAROS:  P0C0S5 GTEx:  ENSG00000164032

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	B, E	94	Homo sapiens	Mutation(s): 0  Gene Names: H2BC11, H2BFR, HIST1H2BJ
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
PHAROS:  P06899 GTEx:  ENSG00000124635

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 72 homolog	C, F	87	Homo sapiens	Mutation(s): 0  Gene Names: VPS72, TCFL1, YL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15906 (Homo sapiens) Explore Q15906  Go to UniProtKB:  Q15906
PHAROS:  Q15906 GTEx:  ENSG00000163159

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.093	α = 90
b = 126.99	β = 90
c = 70.757	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Tan, W.S., Liu, Y., Hong, J.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31970669

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release