5HJB | pdb_00005hjb

AF9 YEATS in complex with histone H3 Crotonylation at K9

• PDB DOI: https://doi.org/10.2210/pdb5HJB/pdb

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


• Deposited: 2016-01-12 Released: 2016-04-20 
• Deposition Author(s): Li, Y.Y., Zhao, D., Guan, H.P., Li, H.T.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain

Li, Y.Y., Sabari, B.R., Panchenko, T., Wen, H., Zhao, D., Guan, H.P., Wan, L., Huang, H., Tang, Z., Zhao, Y., Roeder, R.G., Shi, X., Allis, C.D., Li, H.T.

(2016) Mol Cell 62: 181-193

• PubMed: 27105114 
• DOI: https://doi.org/10.1016/j.molcel.2016.03.028
• Primary Citation Related Structures: 
  5HJB, 5HJC, 5HJD


• PubMed Abstract: 
  

  Recognition of histone covalent modifications by chromatin-binding protein modules ("readers") constitutes a major mechanism for epigenetic regulation, typified by bromodomains that bind acetyllysine. Non-acetyl histone lysine acylations (e.g., crotonylation, butyrylation, propionylation) have been recently identified, but readers that prefer these acylations have not been characterized. Here we report that the AF9 YEATS domain displays selectively higher binding affinity for crotonyllysine over acetyllysine. Structural studies revealed an extended aromatic sandwiching cage with crotonyl specificity arising from π-aromatic and hydrophobic interactions between crotonyl and aromatic rings. These features are conserved among the YEATS, but not the bromodomains. Using a cell-based model, we showed that AF9 co-localizes with crotonylated histone H3 and positively regulates gene expression in a YEATS domain-dependent manner. Our studies define the evolutionarily conserved YEATS domain as a family of crotonyllysine readers and specifically demonstrate that the YEATS domain of AF9 directly links histone crotonylation to active transcription.

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Organizational Affiliation: 
• MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Beijing 100084, PRC; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, PRC.
Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA. Electronic address: [e-mail].
MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Beijing 100084, PRC; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, PRC; Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PRC. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 17.54 kDa 
• Atom Count: 1,252 
• Modeled Residue Count: 148 
• Deposited Residue Count: 148 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein AF-9	A	140	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
peptide of Histone H3.1	B	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCR	B	L-PEPTIDE LINKING	C10 H18 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.595	α = 90
b = 97.595	β = 90
c = 39.685	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Li, Y.Y., Zhao, D., Guan, H.P., Li, H.T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91519304

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection