8JGM | pdb_00008jgm

Cryo-EM sturcutre of DANGEROUS MIX 3 (DM3) from Hohenlieth (Hh-0)

PDB DOI: https://doi.org/10.2210/pdb8JGM/pdb
EM Map EMD-36239: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
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: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 302.49 kDa
Atom Count: 21,120
Modeled Residue Count: 2,652
Deposited Residue Count: 2,688
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DM3Hh0	A, B, C, D, E A, B, C, D, E, F	448	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9M314 (Arabidopsis thaliana) Explore Q9M314 Go to UniProtKB: Q9M314
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9M314
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

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: 2025-06-25
Changes: Data collection
Version 1.2: 2025-07-23
Changes: Data collection, Database references

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.