9IM4 | pdb_00009im4

Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la

PDB DOI: https://doi.org/10.2210/pdb9IM4/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-07-02 Released: 2025-07-09
Deposition Author(s): Li, H.T., Ma, H.D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.315 (Depositor), 0.323 (DCC)
R-Value Work:
0.266 (Depositor), 0.275 (DCC)
R-Value Observed:
0.271 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la

Ma, H.D., Li, H.T.

To be published.

Macromolecule Content

Total Structure Weight: 39.46 kDa
Atom Count: 2,474
Modeled Residue Count: 296
Deposited Residue Count: 336
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein AF-9	A, C [auth B]	158	Homo sapiens	Mutation(s): 1 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42568
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3C	B [auth P], D [auth C]	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NXT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.315 (Depositor), 0.323 (DCC)
R-Value Work: 0.266 (Depositor), 0.275 (DCC)
R-Value Observed: 0.271 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.081	α = 90
b = 83.081	β = 90
c = 116.259	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.