5VNB

YEATS in complex with histone H3

PDB DOI: https://doi.org/10.2210/pdb5VNB/pdb

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

Deposited: 2017-04-29 Released: 2018-09-05
Deposition Author(s): Cho, H.J., Cierpicki, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.248
R-Value Work: 0.186
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

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

Literature

GAS41 Recognizes Diacetylated Histone H3 through a Bivalent Binding Mode.

Cho, H.J., Li, H., Linhares, B.M., Kim, E., Ndoj, J., Miao, H., Grembecka, J., Cierpicki, T.

(2018) ACS Chem Biol 13: 2739-2746

PubMed: 30071723 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acschembio.8b00674
Primary Citation of Related Structures:
5VNA, 5VNB

PubMed Abstract:
GAS41 is a chromatin-associated protein that belongs to the YEATS family and is involved in the recognition of acetyl-lysine in histone proteins. A unique feature of GAS41 is the presence of a C-terminal coiled-coil domain, which is responsible for protein dimerization. Here, we characterized the specificity of the GAS41 YEATS domain and found that it preferentially binds to acetylated H3K18 and H3K27 peptides. Interestingly, we found that full-length, dimeric GAS41 binds to diacetylated H3 peptides with an enhanced affinity when compared to those for monoacetylated peptides, through a bivalent binding mode. We determined the crystal structure of the GAS41 YEATS domain with H3K23acK27ac to visualize the molecular basis of diacetylated histone binding. Our results suggest a unique binding mode in which full-length GAS41 is a reader of diacetylated histones.

Organizational Affiliation

Department of Pathology , University of Michigan , Ann Arbor , Michigan 48109 , United States.

Macromolecule Content

Total Structure Weight: 71.32 kDa
Atom Count: 4,457
Modelled Residue Count: 515
Deposited Residue Count: 602
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 4	A, B, C, D	148	Homo sapiens	Mutation(s): 0 Gene Names: YEATS4, GAS41
UniProt & NIH Common Fund Data Resources
Find proteins for O95619 (Homo sapiens) Explore O95619 Go to UniProtKB: O95619
PHAROS: O95619 GTEx: ENSG00000127337
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95619
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K23acK27ac peptide	E [auth K]	10	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
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C]	G [auth A], N [auth B], O [auth B], P [auth B], Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	F [auth A] H [auth B] I [auth B] J [auth B] K [auth B] F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	E [auth K]	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.248
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.79	α = 90
b = 80.305	β = 90
c = 121.663	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Cho, H.J.

Cierpicki, T.

Revision History (Full details and data files)

Version 1.0: 2018-09-05
Type: Initial release
Version 1.1: 2018-10-03
Changes: Data collection, Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection