4O30

Crystal structure of ATXR5 in complex with histone H3.1 and AdoHcy

PDB DOI: https://doi.org/10.2210/pdb4O30/pdb

Classification: TRANSFERASE
Organism(s): Ricinus communis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-17 Released: 2014-03-26
Deposition Author(s): Bergamin, E., Mongeon, V., Couture, J.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.247
R-Value Work: 0.202
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication.

Jacob, Y., Bergamin, E., Donoghue, M.T., Mongeon, V., LeBlanc, C., Voigt, P., Underwood, C.J., Brunzelle, J.S., Michaels, S.D., Reinberg, D., Couture, J.F., Martienssen, R.A.

(2014) Science 343: 1249-1253

PubMed: 24626927 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1248357
Primary Citation of Related Structures:
4O30

PubMed Abstract:
Histone variants have been proposed to act as determinants for posttranslational modifications with widespread regulatory functions. We identify a histone-modifying enzyme that selectively methylates the replication-dependent histone H3 variant H3.1. The crystal structure of the SET domain of the histone H3 lysine-27 (H3K27) methyltransferase ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) in complex with a H3.1 peptide shows that ATXR5 contains a bipartite catalytic domain that specifically "reads" alanine-31 of H3.1. Variation at position 31 between H3.1 and replication-independent H3.3 is conserved in plants and animals, and threonine-31 in H3.3 is responsible for inhibiting the activity of ATXR5 and its paralog, ATXR6. Our results suggest a simple model for the mitotic inheritance of the heterochromatic mark H3K27me1 and the protection of H3.3-enriched genes against heterochromatization during DNA replication.

Organizational Affiliation

Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

Macromolecule Content

Total Structure Weight: 58 kDa
Atom Count: 3,911
Modelled Residue Count: 459
Deposited Residue Count: 506
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase ATXR6, putative	A, B	234	Ricinus communis	Mutation(s): 0 Gene Names: RCOM_1460410 EC: 2.1.1.43
UniProt
Find proteins for B9RU15 (Ricinus communis) Explore B9RU15 Go to UniProtKB: B9RU15
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9RU15
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	C, D	19	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A]	E [auth A], G [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.247
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.17	α = 90
b = 87.31	β = 127.78
c = 74.51	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Bergamin, E.

Mongeon, V.

Couture, J.F.

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2014-09-24
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations