9F2M | pdb_00009f2m

Cross species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants

• PDB DOI: https://doi.org/10.2210/pdb9F2M/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Marchantia polymorpha, Phytophthora infestans
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2024-04-23 Released: 2025-05-21 
• Deposition Author(s): Sanchez de Medina, V., Dagdas, Y.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants

Sanchez de Medina Hernandez, V., Nava-Garcia, M.M., Bianchi, A., Clavel, M., Papareddy, R.K., Benchalel, L., Andreev, V.I., Mathur, V., Mohseni, A., Garcia-Leon, M., Gao, P., de la Concepcion, J.C., Picchianti, L., Grujic, N., Kobylinska, R., Abdrakhmanov, A., Duverge, H., Anand, G., Leibrock, N., Ma, J., Raffeiner, M., Crawford, T.S., Argiro, L., Matuszkiewicz, M., Wun, C.L., Kanne, J.V., Meinhart, A., Roitinger, E., Baurle, I., Kang, B.H., Petersen, M., Ustun, S., Kulathu, Y., Clausen, T., Ramundo, S., Dagdas, Y.

(2026) Dev Cell 61: 655

• DOI: https://doi.org/10.1016/j.devcel.2025.11.001

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.31 kDa 
• Atom Count: 1,056 
• Modeled Residue Count: 114 
• Deposited Residue Count: 114 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein	A	109	Marchantia polymorpha	Mutation(s): 0  Gene Names: MARPO_0001s0494
UniProt
Find proteins for A0A176W124 (Marchantia polymorpha subsp. ruderalis) Explore A0A176W124  Go to UniProtKB:  A0A176W124

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RxLR effector protein 54	B [auth D]	5	Phytophthora infestans	Mutation(s): 0
UniProt
Find proteins for D0NBE6 (Phytophthora infestans (strain T30-4)) Explore D0NBE6  Go to UniProtKB:  D0NBE6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.23	α = 90
b = 36.23	β = 90
c = 69.59	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Sanchez de Medina, V., Dagdas, Y.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101000981

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 1.1: 2026-06-10
  Changes: Database references, Structure summary