8JGN | pdb_00008jgn

Cryo-EM structure of alpha/beta hydrolase DANGEROUS MIX 3 (DM3) forms compartmentalized hexamer structure

PDB DOI: https://doi.org/10.2210/pdb8JGN/pdb
EM Map EMD-36240: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-05-21 Released: 2024-12-25
Deposition Author(s): Kim, G., Song, J.J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8JGN

This is version 1.1 of the entry. See complete history.

Literature

Structure determinants of DANGEROUS MIX 3, an alpha/beta hydrolase, for triggering NLR-mediated genetic incompatibility in plants

Kim, G., Song, J.J.

(2025) Mol Cell

Macromolecule Content

Total Structure Weight: 302.6 kDa
Atom Count: 21,360
Modeled Residue Count: 2,688
Deposited Residue Count: 2,688
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT3g61540/F2A19_140	A, B, C, D, E A, B, C, D, E, F	448	Arabidopsis thaliana	Mutation(s): 0 Gene Names: F2A19.140, At3g61540
UniProt
Find proteins for Q9M314 (Arabidopsis thaliana) Explore Q9M314 Go to UniProtKB: Q9M314
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9M314
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020R1A2B5B03001517

Revision History (Full details and data files)

Version 1.0: 2024-12-25
Type: Initial release
Version 1.1: 2025-07-23
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.