3I4W

Crystal Structure of the third PDZ domain of PSD-95

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Novel conformational aspects of the third PDZ domain of the neuronal post-synaptic density-95 protein revealed from two 1.4A X-ray structures

Camara-Artigas, A., Murciano-Calles, J., Gavira, J.A., Cobos, E.S., Martinez, J.C.

(2010) J Struct Biol 170: 565-569

  • DOI: 10.1016/j.jsb.2010.03.005
  • Primary Citation of Related Structures:  
    3K82, 3I4W

  • PubMed Abstract: 

    • The crystal structure of the third PDZ domain of the neuronal post-synaptic density-95 protein (PSD95-PDZ3, residues 302-402) has been solved at 1.4 and 1.35A from two different crystal forms. These structures lack the cloning artefact present in the ...

    The crystal structure of the third PDZ domain of the neuronal post-synaptic density-95 protein (PSD95-PDZ3, residues 302-402) has been solved at 1.4 and 1.35A from two different crystal forms. These structures lack the cloning artefact present in the carboxyl terminal sequence of the former crystallographic structures and they belong to the space groups P4(3) and P1. The new PDZ structures are identical between the two crystal forms and among the four chains of the P1 crystal form. When we compare the new structures with the previous ones, some important conformational differences in the C-terminal alpha-helix and in the loop connecting beta2 and beta3 strands have been found. Additionally, the high resolution of the new structures has allowed us to indentify a succinimide residue at the position corresponding to Asp332 in the beta2-beta3 loop, which may contribute to the alternate conformation of this loop, and at the same time, to the interaction between residues from this loop and the C-terminal alpha-helix. Thus, these features would have implications in the recently proposed allosteric role of this third alpha-helix in the binding of the carboxyl terminal fragments to the PSD95-PDZ3.

    Organizational Affiliation: 

    Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería, 04120 Almería, Spain. acamara@ual.es



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Disks large homolog 4A, B, C, D104Homo sapiensMutation(s): 1 
Gene Names: DLG4, PSD95
Find proteins for P78352 (Homo sapiens)
Explore P78352 
Go to UniProtKB:  P78352
NIH Common Fund Data Resources
PHAROS  P78352
GTEx  ENSG00000132535
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SNN
Query on SNN		A,B,C,DL-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.322α = 90
b = 42.152β = 90
c = 47.602γ = 92.08
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description