9IM4 | pdb_00009im4

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


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

Validation slider image for 9IM4

This is version 1.1 of the entry. See complete history

Literature

AF9-KLF2 gene regulatory circuit links histone lactylation to metabolic reprogramming and breast cancer progression.

Ma, H.Yuan, M.Yang, C.Yuan, Y.Li, Y.Wang, X.Tang, Z.Li, H.

(2026) Cell Rep 45: 117429-117429

  • DOI: https://doi.org/10.1016/j.celrep.2026.117429
  • Primary Citation Related Structures: 
    9IM4

  • PubMed Abstract: 

    Histone lysine L-lactylation (hereafter referred to as histone Kla) is a chromatin modification induced by glycolytic metabolism, linking metabolic reprogramming and chromatin-mediated regulation. In this study, we uncover a transcriptional regulatory circuit involving AF9 and KLF2 that drives luminal breast cancer progression. AF9, identified as a reader of H3K9la, promotes KLF2 expression, while KLF2, functioning as a transcription factor for AF9, forms a positive feedback loop amplifying lactylation-dependent effects. This circuit activates tumor-associated pathways, including TGF-β1, glucose and lactate transporters, and metabolic enzymes essential for glycolysis and serine biosynthesis, driving tumorigenesis. Spatial and single-cell transcriptomics show AF9-positive tumor cells enriched in regions of active lactylation, correlating with immune evasion via M2 macrophage interactions. Together, AF9, H3K9la, and KLF2 integrate metabolism, chromatin regulation, and signaling to promote tumor progression, highlighting AF9's central role as a histone lactylation reader and potential therapeutic target in breast cancer.


  • Organizational Affiliation
    • State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China.

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

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein AF-9A,
C [auth B]
158Homo sapiensMutation(s): 1 
Gene Names: MLLT3AF9YEATS3
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42568
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3.3CB [auth P],
D [auth C]
10Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NXT2
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
XRW
Query on XRW
B [auth P],
D [auth C]
L-PEPTIDE LINKINGC9 H18 N2 O4LYS

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 = 83.081α = 90
b = 83.081β = 90
c = 116.259γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant 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
  • Version 1.1: 2026-07-22
    Changes: Database references