1JXO | pdb_00001jxo

Crystal Structure of the SH3-HOOK-GK Fragment of PSD-95

• PDB DOI: https://doi.org/10.2210/pdb1JXO/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-07 Released: 2002-01-16 
• Deposition Author(s): Tavares, G.A., Panepucci, E.H., Brunger, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.264 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of the intramolecular interaction between the SH3 and guanylate kinase domains of PSD-95.

Tavares, G.A., Panepucci, E.H., Brunger, A.T.

(2001) Mol Cell 8: 1313-1325

• PubMed: 11779506 
• DOI: https://doi.org/10.1016/s1097-2765(01)00416-6
• Primary Citation Related Structures: 
  1JXM, 1JXO


• PubMed Abstract: 
  

  PSD-95/SAP90 is a member of the MAGUK superfamily. In excitatory synapses, PSD-95 clusters receptors and ion channels at specific sites in the postsynaptic membrane and organizes downstream signaling and cytoskeletal molecules. We have determined the crystal structures of the apo and GMP-bound forms to 2.3 and 2.0 A resolutions, respectively, of a fragment containing the SH3, HOOK, and guanylate kinase (GK) domains of PSD-95. We observe an intramolecular interaction between the SH3 and GK domains involving the formation of a beta sheet including residues N- and C-terminal to the GK domain. Based on amino acid conservation and mutational data available in the literature, we propose that this intramolecular interaction is a common feature among MAGUK proteins.

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Organizational Affiliation: 
• The Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, 1201 Welch Road P210 MSLS, Stanford, CA 94305, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.63 kDa 
• Atom Count: 4,203 
• Modeled Residue Count: 525 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
postsynaptic density protein	A, B	301	Rattus norvegicus	Mutation(s): 0  Gene Names: PSD-95
UniProt
Find proteins for P31016 (Rattus norvegicus) Explore P31016  Go to UniProtKB:  P31016

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.264 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.009	α = 89.96
b = 53.41	β = 90
c = 63.262	γ = 91.78

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-16 
Deposition Author(s): Tavares, G.A., Panepucci, E.H., Brunger, A.T.

Revision History  

• Version 1.0: 2002-01-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description