8Z73 | pdb_00008z73

Crystal Structure of AF9 in complex with H3K9la peptide

• PDB DOI: https://doi.org/10.2210/pdb8Z73/pdb

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


• Deposited: 2024-04-19 Released: 2025-04-23 
• Deposition Author(s): Li, H.T., Ma, H.D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of AF9 in complex with H3K9la peptide

Ma, H.D., Li, H.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 79.13 kDa 
• Atom Count: 5,003 
• Modeled Residue Count: 583 
• Deposited Residue Count: 672 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein AF-9	A, C [auth B], E [auth D], G [auth F]	158	Homo sapiens	Mutation(s): 0  Gene Names: MLLT3, AF9, YEATS3
UniProt & NIH Common Fund Data Resources
Find proteins for P42568 (Homo sapiens) Explore P42568  Go to UniProtKB:  P42568
PHAROS:  P42568 GTEx:  ENSG00000171843

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3C	B [auth P], D [auth C], F [auth E], H [auth G]	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NXT2 (Homo sapiens) Explore Q6NXT2  Go to UniProtKB:  Q6NXT2
PHAROS:  Q6NXT2 GTEx:  ENSG00000188375

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth B], J [auth D], K [auth F], L [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
XRW	B [auth P], D [auth C], F [auth E], H [auth G]	L-PEPTIDE LINKING	C9 H18 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.587	α = 90
b = 116.587	β = 90
c = 168.824	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
MOLREP	phasing
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Li, H.T., Ma, H.D.

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

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release