6EZI

PDZK1 domain 4 in complex with C-terminal peptide of human PepT2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Probing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution.

Hajizadeh, N.R.Pieprzyk, J.Skopintsev, P.Flayhan, A.Svergun, D.I.Low, C.

(2018) Structure 26: 1522-1533.e5

  • DOI: 10.1016/j.str.2018.07.016
  • Primary Citation of Related Structures:  
    6EZI

  • PubMed Abstract: 
  • The scaffolding protein PDZK1 has been associated with the regulation of membrane transporters. It contains four conserved PDZ domains, which typically recognize a 3-5-residue long motif at the C terminus of the binding partner. The atomic structures of the individual domains are available but their spatial arrangement in the full-length context influencing the binding properties remained elusive ...

    The scaffolding protein PDZK1 has been associated with the regulation of membrane transporters. It contains four conserved PDZ domains, which typically recognize a 3-5-residue long motif at the C terminus of the binding partner. The atomic structures of the individual domains are available but their spatial arrangement in the full-length context influencing the binding properties remained elusive. Here we report a systematic study of full-length PDZK1 and deletion constructs using small-angle X-ray scattering, complemented with biochemical and functional studies on PDZK1 binding to known membrane protein partners. A hybrid modeling approach utilizing multiple scattering datasets yielded a well-defined, extended, asymmetric L-shaped domain organization of PDZK1 in contrast to a flexible "beads-on-string" model predicted by bioinformatics analysis. The linker regions of PDZK1 appear to play a central role in the arrangement of the four domains underlying the importance of studying scaffolding proteins in their full-length context.


    Organizational Affiliation

    Centre for Systems Structural Biology (CSSB), DESY and European Molecular Biology Laboratory, Notkestrasse 85, Hamburg D-22607, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Insititutet, Scheels väg 2, Stockholm SE-17177, Sweden. Electronic address: christian.loew@embl-hamburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)/H(+) exchange regulatory cofactor NHE-RF3A89Homo sapiensMutation(s): 0 
Gene Names: PDZK1CAP70NHERF3PDZD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T2W1 (Homo sapiens)
Explore Q5T2W1 
Go to UniProtKB:  Q5T2W1
PHAROS:  Q5T2W1
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Solute carrier family 15 member 2B10Homo sapiensMutation(s): 0 
Gene Names: SLC15A2PEPT2
UniProt & NIH Common Fund Data Resources
Find proteins for Q16348 (Homo sapiens)
Explore Q16348 
Go to UniProtKB:  Q16348
PHAROS:  Q16348
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.4α = 90
b = 54.4β = 90
c = 150.76γ = 120
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references