6N5Z

Crystal structure of the SNX5 PX domain in complex with the Sema4C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins.

Simonetti, B.Paul, B.Chaudhari, K.Weeratunga, S.Steinberg, F.Gorla, M.Heesom, K.J.Bashaw, G.J.Collins, B.M.Cullen, P.J.

(2019) Nat Cell Biol 21: 1219-1233

  • DOI: https://doi.org/10.1038/s41556-019-0393-3
  • Primary Citation of Related Structures:  
    6N5X, 6N5Y, 6N5Z

  • PubMed Abstract: 

    Protein trafficking requires coat complexes that couple recognition of sorting motifs in transmembrane cargoes with biogenesis of transport carriers. The mechanisms of cargo transport through the endosomal network are poorly understood. Here, we identify a sorting motif for endosomal recycling of cargoes, including the cation-independent mannose-6-phosphate receptor and semaphorin 4C, by the membrane tubulating BAR domain-containing sorting nexins SNX5 and SNX6. Crystal structures establish that this motif folds into a β-hairpin, which binds a site in the SNX5/SNX6 phox homology domains. Over sixty cargoes share this motif and require SNX5/SNX6 for their recycling. These include cargoes involved in neuronal migration and a Drosophila snx6 mutant displays defects in axonal guidance. These studies identify a sorting motif and provide molecular insight into an evolutionary conserved coat complex, the 'Endosomal SNX-BAR sorting complex for promoting exit 1' (ESCPE-1), which couples sorting motif recognition to the BAR-domain-mediated biogenesis of cargo-enriched tubulo-vesicular transport carriers.


  • Organizational Affiliation

    Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-5,Semaphorin-4C
A, B
179Homo sapiensMutation(s): 0 
Gene Names: SNX5SEMA4CKIAA1739SEMAIUNQ5855/PRO34487
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5X3 (Homo sapiens)
Explore Q9Y5X3 
Go to UniProtKB:  Q9Y5X3
PHAROS:  Q9Y5X3
GTEx:  ENSG00000089006 
Find proteins for Q9C0C4 (Homo sapiens)
Explore Q9C0C4 
Go to UniProtKB:  Q9C0C4
PHAROS:  Q9C0C4
GTEx:  ENSG00000168758 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9Y5X3Q9C0C4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.52α = 90
b = 87.698β = 90
c = 100.487γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references