6ECM

Crystal Structure of SNX15 PX domain in domain swapped conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.250 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities.

Chandra, M.Chin, Y.K.Mas, C.Feathers, J.R.Paul, B.Datta, S.Chen, K.E.Jia, X.Yang, Z.Norwood, S.J.Mohanty, B.Bugarcic, A.Teasdale, R.D.Henne, W.M.Mobli, M.Collins, B.M.

(2019) Nat Commun 10: 1528-1528

  • DOI: https://doi.org/10.1038/s41467-019-09355-y
  • Primary Citation of Related Structures:  
    5WOE, 6ECM, 6EDX, 6EE0, 6MBI

  • PubMed Abstract: 

    Phox homology (PX) domains are membrane interacting domains that bind to phosphatidylinositol phospholipids or phosphoinositides, markers of organelle identity in the endocytic system. Although many PX domains bind the canonical endosome-enriched lipid PtdIns3P, others interact with alternative phosphoinositides, and a precise understanding of how these specificities arise has remained elusive. Here we systematically screen all human PX domains for their phospholipid preferences using liposome binding assays, biolayer interferometry and isothermal titration calorimetry. These analyses define four distinct classes of human PX domains that either bind specifically to PtdIns3P, non-specifically to various di- and tri-phosphorylated phosphoinositides, bind both PtdIns3P and other phosphoinositides, or associate with none of the lipids tested. A comprehensive evaluation of PX domain structures reveals two distinct binding sites that explain these specificities, providing a basis for defining and predicting the functional membrane interactions of the entire PX domain protein family.


  • Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-15128Homo sapiensMutation(s): 0 
Gene Names: SNX15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRS6 (Homo sapiens)
Explore Q9NRS6 
Go to UniProtKB:  Q9NRS6
PHAROS:  Q9NRS6
GTEx:  ENSG00000110025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRS6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.250 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.498α = 90
b = 54.498β = 90
c = 83.58γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP160101743
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1099114
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1136021

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description