5IQL

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.253
R-Value Work: 0.204
R-Value Observed: 0.209

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/cr.2016.49
Primary Citation of Related Structures:
5IQL

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ULM3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCR Query on 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
R-Value Work: 0.204
R-Value Observed: 0.209
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Li, H.

Zhao, D.

Guan, H.

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

Revision History (Full details and data files)

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