5WYI | pdb_00005wyi

The Yaf9 YEATS domain Recognizing H3K122suc Peptide

• PDB DOI: https://doi.org/10.2210/pdb5WYI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae RM11-1a, Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): Yes 


• Deposited: 2017-01-13 Released: 2018-01-17 
• Deposition Author(s): Wang, Y., Hao, Q.
• Funding Organization(s): HK-RGC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

The Yaf9 YEATS domain Recognizing H3K122suc Peptide

Wang, Y., Hao, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.15 kDa 
• Atom Count: 3,978 
• Modeled Residue Count: 420 
• Deposited Residue Count: 501 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Yaf9	A	165	Saccharomyces cerevisiae RM11-1a	Mutation(s): 3  Gene Names: SCRG_03242
UniProt
Find proteins for B3LNW5 (Saccharomyces cerevisiae (strain RM11-1a)) Explore B3LNW5  Go to UniProtKB:  B3LNW5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Yaf9	B, C	164	Saccharomyces cerevisiae RM11-1a	Mutation(s): 3  Gene Names: SCRG_03242
UniProt
Find proteins for B3LNW5 (Saccharomyces cerevisiae (strain RM11-1a)) Explore B3LNW5  Go to UniProtKB:  B3LNW5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ILE-MET-PRO-LYS-ASP-ILE-GLN-LEU	D [auth E]	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

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLL	E [auth C]	(2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid C10 H18 N2 O5 ZAFOVBXOMIXMTH-ZETCQYMHSA-N
SIN	F [auth E]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.932	α = 90
b = 136.932	β = 90
c = 26.168	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Wang, Y., Hao, Q.

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Funding Organization	Location	Grant Number
HK-RGC	Hong Kong	C7037-14G

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Structure summary