Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.98 kDa 
• Atom Count: 1269 
• Residue Count: 154 
• Unique protein chains: 2

2NDF

Solution NMR structures of AF9 yeats domain in complex with histon H3 acetylation at K18

• DOI: 10.2210/pdb2NDF/pdb
• BMRB: 26059

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


• Deposited: 2016-05-19 Released: 2016-09-07 
• Deposition Author(s): Zeng, L., Zhou, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural Insights into Histone Crotonyl-Lysine Recognition by the AF9 YEATS Domain.

Zhang, Q., Zeng, L., Zhao, C., Ju, Y., Konuma, T., Zhou, M.M.

(2016) Structure 24: 1606-1612

• PubMed: 27545619 
• DOI: 10.1016/j.str.2016.05.023
• Primary Citation of Related Structures:  
  2NDG, 2NDF


• PubMed Abstract: 
  

Histone lysine acylations play an important role in the regulation of gene transcription in chromatin. Unlike histone acetyl-lysine, molecular recognition of a recently identified crotonyl-lysine mark is much less understood. Here, we report that the YEATS domain of AF9 preferentially binds crotonyl-lysine over acetyl-lysine in histone H3. Nuclear magnetic resonance structural analysis reveals that crotonyl-lysine of histone H3 lysine 18 is engulfed deep in an aromatic cage of the YEATS domain where the carbonyl oxygen of crotonyl-lysine forms a hydrogen bond with the backbone amide of protein residue Tyr78. The crotonyl-lysine, through its unique electron-rich double-bond side chain, engages π-π aromatic stacking and extended hydrophobic/aromatic interactions with the YEATS domain compared with acetyl-lysine. Our mutational analysis confirmed key protein residues Phe59 and Tyr78 for crotonyl-lysine recognition. Importantly, our findings present a new structural mechanism of protein-protein interactions mediated by histone lysine crotonylation, and show how the cells interpret acyl-lysine marks in different biological contexts.

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Organizational Affiliation: 

Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein AF-9	A	141	Homo sapiens	Mutation(s): 0  Gene Names: MLLT3, AF9, YEATS3
Find proteins for P42568 (Homo sapiens) Explore P42568  Go to UniProtKB:  P42568
NIH Common Fund Data Resources
PHAROS  P42568 GTEx  ENSG00000171843

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3 peptide	B	13	N/A	Mutation(s): 0
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431 GTEx  ENSG00000197409GTEx  ENSG00000197153GTEx  ENSG00000278828GTEx  ENSG00000275714GTEx  ENSG00000273983GTEx  ENSG00000274750GTEx  ENSG00000275379GTEx  ENSG00000277775

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2NDF Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-19 
• Released Date: 2016-09-07 
Deposition Author(s): Zeng, L., Zhou, M.

Revision History 

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references