5L83 | pdb_00005l83

Complex of potato ATG8 protein with a peptide from Irish potato famine pathogen effector protein PexRD54

PDB DOI: https://doi.org/10.2210/pdb5L83/pdb

Classification: IMMUNE SYSTEM
Organism(s): Phytophthora infestans, Solanum tuberosum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-06-06 Released: 2016-08-03
Deposition Author(s): Maqbool, A., Hughes, R.K., Banfield, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.200 (Depositor), 0.202 (DCC)
R-Value Work:
0.175 (Depositor), 0.185 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural Basis of Host Autophagy-related Protein 8 (ATG8) Binding by the Irish Potato Famine Pathogen Effector Protein PexRD54.

Maqbool, A., Hughes, R.K., Dagdas, Y.F., Tregidgo, N., Zess, E., Belhaj, K., Round, A., Bozkurt, T.O., Kamoun, S., Banfield, M.J.

(2016) J Biol Chem 291: 20270-20282

PubMed: 27458016 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M116.744995
Primary Citation Related Structures:
5L7S, 5L83

PubMed Abstract:
Filamentous plant pathogens deliver effector proteins to host cells to promote infection. The Phytophthora infestans RXLR-type effector PexRD54 binds potato ATG8 via its ATG8 family-interacting motif (AIM) and perturbs host-selective autophagy. However, the structural basis of this interaction remains unknown. Here, we define the crystal structure of PexRD54, which includes a modular architecture, including five tandem repeat domains, with the AIM sequence presented at the disordered C terminus. To determine the interface between PexRD54 and ATG8, we solved the crystal structure of potato ATG8CL in complex with a peptide comprising the effector's AIM sequence, and we established a model of the full-length PexRD54-ATG8CL complex using small angle x-ray scattering. Structure-informed deletion of the PexRD54 tandem domains reveals retention of ATG8CL binding in vitro and in planta This study offers new insights into structure/function relationships of oomycete RXLR effectors and how these proteins engage with host cell targets to promote disease.

Organizational Affiliation

From the Department of Biological Chemistry, John Innes Centre, and.

Macromolecule Content

Total Structure Weight: 28.11 kDa
Atom Count: 2,239
Modeled Residue Count: 234
Deposited Residue Count: 234
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASP-TRP-GLU-ILE-VAL	A [auth C], B [auth D]	5	Phytophthora infestans	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein	C [auth A], D [auth B]	112	Solanum tuberosum	Mutation(s): 0 Gene Names: PGSC0003DMG402022314, PGSC0003DMG400014422
UniProt
Find proteins for M1C146 (Solanum tuberosum) Explore M1C146 Go to UniProtKB: M1C146
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1C146
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 L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] J [auth B] E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B]