9W5C | pdb_00009w5c

Complex structure of MAGI3 WW1 and IQSEC3 PPxY motif

PDB DOI: https://doi.org/10.2210/pdb9W5C/pdb

Classification: PROTEIN BINDING
Organism(s): Rattus norvegicus, Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-01 Released: 2026-02-25
Deposition Author(s): Wang, J., Lin, L., Zhu, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.218 (Depositor), 0.218 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural and Biochemical Dissection of MAGI WW1-IQSEC3 Interactions

Wang, J., Lin, L., Zhu, J.

To be published.

Macromolecule Content

Total Structure Weight: 43.39 kDa
Atom Count: 2,656
Modeled Residue Count: 303
Deposited Residue Count: 372
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3	A, C, E, G, I A, C, E, G, I, K	44	Rattus norvegicus	Mutation(s): 0 Gene Names: Magi3, Slipr
UniProt
Find proteins for Q9JK71 (Rattus norvegicus) Explore Q9JK71 Go to UniProtKB: Q9JK71
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JK71
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IQ motif and SEC7 domain-containing protein 3	B, D, F, H, J B, D, F, H, J, L	18	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q3TES0 (Mus musculus) Explore Q3TES0 Go to UniProtKB: Q3TES0
IMPC: MGI:2677208
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3TES0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.218 (Depositor), 0.218 (DCC)
R-Value Work: 0.180 (Depositor), 0.182 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.472	α = 90
b = 78.971	β = 93.52
c = 48.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-02-25
Type: Initial release

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.