6JJZ | pdb_00006jjz

Crystal Structure of MAGI2 and Dendrin complex

• PDB DOI: https://doi.org/10.2210/pdb6JJZ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-27 Released: 2019-09-25 
• Deposition Author(s): Lin, Z., Zhang, H., Yang, Z., Ji, Z., Zhang, M., Zhu, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.

Lin, Z., Yang, Z., Xie, R., Ji, Z., Guan, K., Zhang, M.

(2019) Elife 8

• PubMed: 31486770 
• DOI: https://doi.org/10.7554/eLife.49439
• Primary Citation Related Structures: 
  6J68, 6JJW, 6JJX, 6JJY, 6JJZ, 6JK0, 6JK1


• PubMed Abstract: 
  

  WW domain tandem-containing proteins such as KIBRA, YAP, and MAGI play critical roles in cell growth and polarity via binding to and positioning target proteins in specific subcellular regions. An immense disparity exists between promiscuity of WW domain-mediated target bindings and specific roles of WW domain proteins in cell growth regulation. Here, we discovered that WW domain tandems of KIBRA and MAGI, but not YAP, bind to specific target proteins with extremely high affinity and exquisite sequence specificity. Via systematic structural biology and biochemistry approaches, we decoded the target binding rules of WW domain tandems from cell growth regulatory proteins and uncovered a list of previously unknown WW tandem binding proteins including β-Dystroglycan, JCAD, and PTPN21. The WW tandem-mediated target recognition mechanisms elucidated here can guide functional studies of WW domain proteins in cell growth and polarity as well as in other cellular processes including neuronal synaptic signaling.

---

Organizational Affiliation: 
• Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.
Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, United States.
Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China.
Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Kowloon, China.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.08 kDa 
• Atom Count: 1,850 
• Modeled Residue Count: 210 
• Deposited Residue Count: 240 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2	A, B	102	Mus musculus	Mutation(s): 0  Gene Names: Magi2, Acvrinp1, Aip1, Arip1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9WVQ1 (Mus musculus) Explore Q9WVQ1  Go to UniProtKB:  Q9WVQ1
IMPC:  MGI:1354953

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Dendrin	C, D	18	Mus musculus	Mutation(s): 0  Gene Names: Ddn, Gm748, Kiaa0749
UniProt
Find proteins for Q80TS7 (Mus musculus) Explore Q80TS7  Go to UniProtKB:  Q80TS7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	E [auth A], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.899	α = 90
b = 58.582	β = 90
c = 86.298	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Lin, Z., Zhang, H., Yang, Z., Ji, Z., Zhang, M., Zhu, J.

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description