6JJX | pdb_00006jjx

Crystal Structure of KIBRA and Angiomotin complex

• PDB DOI: https://doi.org/10.2210/pdb6JJX/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli str. 'clone D i2, Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.210 (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.

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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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.65 kDa 
• Atom Count: 2,517 
• Modeled Residue Count: 276 
• Deposited Residue Count: 320 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein KIBRA	A, B	134	Mus musculus	Mutation(s): 0  Gene Names: Wwc1, Kiaa0869
UniProt
Find proteins for Q5SXA9 (Mus musculus) Explore Q5SXA9  Go to UniProtKB:  Q5SXA9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Angiomotin	C [auth D], D [auth C]	26	Homo sapiens	Mutation(s): 0  Gene Names: AMOT, KIAA1071
UniProt & NIH Common Fund Data Resources
Find proteins for Q4VCS5 (Homo sapiens) Explore Q4VCS5  Go to UniProtKB:  Q4VCS5
PHAROS:  Q4VCS5 GTEx:  ENSG00000126016

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.627	α = 90
b = 72.283	β = 90
c = 79.374	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary