1JXM

CRYSTAL STRUCTURE OF THE GMP BOUND SH3-HOOK-GK FRAGMENT OF PSD-95


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1016/s1097-2765(01)00416-6
  • Primary Citation of 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 ...

    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.


    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POSTSYNAPTIC DENSITY PROTEINA301Rattus norvegicusMutation(s): 0 
Gene Names: PSD-95Dlg4Dlgh4Psd95
UniProt
Find proteins for P31016 (Rattus norvegicus)
Explore P31016 
Go to UniProtKB:  P31016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31016
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5GP
Query on 5GP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
GAI
Query on GAI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.724α = 90
b = 59.724β = 90
c = 209.956γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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