1KJW

SH3-Guanylate Kinase Module from PSD-95

• PDB DOI: https://doi.org/10.2210/pdb1KJW/pdb

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


• Deposited: 2001-12-05 Released: 2002-01-09 
• Deposition Author(s): McGee, A.W., Dakoji, S.R., Olsen, O., Bredt, D.S., Lim, W.A., Prehoda, K.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.250 
• R-Value Work: 0.230 

Literature

Structure of the SH3-Guanylate Kinase Module from PSD-95 Suggests a Mechanism for Regulated Assembly of MAGUK Scaffolding Proteins

McGee, A.W., Dakoji, S.R., Olsen, O., Bredt, D.S., Lim, W.A., Prehoda, K.E.

(2001) Mol Cell 8: 1291-1301

• PubMed: 11779504 
• DOI: https://doi.org/10.1016/s1097-2765(01)00411-7
• Primary Citation of Related Structures:  
  1KJW


• PubMed Abstract: 
  

  Membrane-associated guanylate kinases (MAGUKs), such as PSD-95, are modular scaffolds that organize signaling complexes at synapses and other cell junctions. MAGUKs contain PDZ domains, which recruit signaling proteins, as well as a Src homology 3 (SH3) and a guanylate kinase-like (GK) domain, implicated in scaffold oligomerization. The crystal structure of the SH3-GK module from PSD-95 reveals that these domains form an integrated unit: the SH3 fold comprises noncontiguous sequence elements divided by a hinge region and the GK domain. These elements compose two subdomains that can assemble in either an intra- or intermolecular fashion to complete the SH3 fold. We propose a model for MAGUK oligomerization in which complementary SH3 subdomains associate by 3D domain swapping. This model provides a possible mechanism for ligand regulation of oligomerization.

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Organizational Affiliation: 

Department of Physiology, University of California-San Francisco, San Francisco, CA 94143, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.43 kDa 
• Atom Count: 2,529 
• Modelled Residue Count: 292 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POSTSYNAPTIC DENSITY PROTEIN 95	A	295	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P31016 (Rattus norvegicus) Explore P31016  Go to UniProtKB:  P31016

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.250 
• R-Value Work: 0.230 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.509	α = 90
b = 60.509	β = 90
c = 209.956	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-09 
Deposition Author(s): McGee, A.W., Dakoji, S.R., Olsen, O., Bredt, D.S., Lim, W.A., Prehoda, K.E.

Revision History  

• Version 1.0: 2002-01-09
  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: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations