5IQL | pdb_00005iql

Crystal structure of YEATS2 YEATS bound to H3K27cr peptide

• PDB DOI: https://doi.org/10.2210/pdb5IQL/pdb

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


• Deposited: 2016-03-11 Released: 2016-07-20 
• Deposition Author(s): Li, H., Zhao, D., Guan, H.
• Funding Organization(s): National Natural Science Foundation of China, MOST

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

YEATS2 is a selective histone crotonylation reader.

Zhao, D., Guan, H., Zhao, S., Mi, W., Wen, H., Li, Y., Zhao, Y., Allis, C.D., Shi, X., Li, H.

(2016) Cell Res 26: 629-632

• PubMed: 27103431 
• DOI: https://doi.org/10.1038/cr.2016.49
• Primary Citation Related Structures: 
  5IQL

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Organizational Affiliation: 
• MOE Key Laboratory of Protein Sciences, Beijing Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
College of Life Sciences, Peking University, Beijing 100871, China.
Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
Genes and Development and Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.66 kDa 
• Atom Count: 1,210 
• Modeled Residue Count: 138 
• Deposited Residue Count: 141 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YEATS domain-containing protein 2	A	133	Homo sapiens	Mutation(s): 0  Gene Names: YEATS2, KIAA1197
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULM3 (Homo sapiens) Explore Q9ULM3  Go to UniProtKB:  Q9ULM3
PHAROS:  Q9ULM3 GTEx:  ENSG00000163872

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
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: 2.10 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.791	α = 90
b = 75.791	β = 90
c = 119.331	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Li, H., Zhao, D., Guan, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91519304
MOST	China	2015CB910503

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection