6KIP | pdb_00006kip

Crystal structure of PTPRD phosphatase domain in complex with Liprin-alpha3 tandem SAM domains

• PDB DOI: https://doi.org/10.2210/pdb6KIP/pdb

• Classification: HYDROLASE/PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-07-19 Released: 2020-02-12 
• Deposition Author(s): Wakita, M., Yamagata, A., Fukai, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Models: experimental

Literature

Structural insights into selective interaction between type IIa receptor protein tyrosine phosphatases and Liprin-alpha.

Wakita, M., Yamagata, A., Shiroshima, T., Izumi, H., Maeda, A., Sendo, M., Imai, A., Kubota, K., Goto-Ito, S., Sato, Y., Mori, H., Yoshida, T., Fukai, S.

(2020) Nat Commun 11: 649-649

• PubMed: 32005855 
• DOI: https://doi.org/10.1038/s41467-020-14516-5
• Primary Citation Related Structures: 
  6KIP


• PubMed Abstract: 
  

  Synapse formation is induced by transsynaptic interaction of neuronal cell-adhesion molecules termed synaptic organizers. Type IIa receptor protein tyrosine phosphatases (IIa RPTPs) function as presynaptic organizers. The cytoplasmic domain of IIa RPTPs consists of two phosphatase domains, and the membrane-distal one (D2) is essential for synapse formation. Liprin-α, which is an active zone protein critical for synapse formation, interacts with D2 via its C-terminal domain composed of three tandem sterile alpha motifs (tSAM). Structural mechanisms of this critical interaction for synapse formation remain elusive. Here, we report the crystal structure of the complex between mouse PTPδ D2 and Liprin-α3 tSAM at 1.91 Å resolution. PTPδ D2 interacts with the N-terminal helix and the first and second SAMs (SAM1 and SAM2, respectively) of Liprin-α3. Structure-based mutational analyses in vitro and in cellulo demonstrate that the interactions with Liprin-α SAM1 and SAM2 are essential for the binding and synaptogenic activity.

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Organizational Affiliation: 
• Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
CREST, JST, Saitama, 332-0012, Japan.
RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan.
Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.
Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, 680-8582, Japan.
Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan. [e-mail].
PRESTO, JST, Saitama, 332-0012, Japan. [e-mail].
Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. [e-mail].
Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. [e-mail].
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan. [e-mail].
CREST, JST, Saitama, 332-0012, Japan. [e-mail].

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: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 73.09 kDa 
• Atom Count: 5,016 
• Modeled Residue Count: 565 
• Deposited Residue Count: 636 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase delta	A	305	Mus musculus	Mutation(s): 0  Gene Names: Ptprd EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q64487 (Mus musculus) Explore Q64487  Go to UniProtKB:  Q64487
IMPC:  MGI:97812

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Liprin-alpha-3	B	331	Mus musculus	Mutation(s): 0  Gene Names: Ppfia3
UniProt & NIH Common Fund Data Resources
Find proteins for P60469 (Mus musculus) Explore P60469  Go to UniProtKB:  P60469
IMPC:  MGI:1924037

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.012	α = 90
b = 98.012	β = 90
c = 140	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Wakita, M., Yamagata, A., Fukai, S.

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description