6N5X

Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121 - Form 1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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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: 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 ...

    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: 

    School of Biochemistry, University of Bristol, Bristol, UK. pete.cullen@bristol.ac.uk.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sorting nexin-5,Cation-independent mannose-6-phosphate receptorA182Homo sapiensMutation(s): 0 
Gene Names: SNX5, IGF2R, MPRI
UniProt & NIH Common Fund Data Resources
Find proteins for P11717 (Homo sapiens)
Explore P11717 
Go to UniProtKB:  P11717
PHAROS:  P11717
Find proteins for Q9Y5X3 (Homo sapiens)
Explore Q9Y5X3 
Go to UniProtKB:  Q9Y5X3
PHAROS:  Q9Y5X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP11717Q9Y5X3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JEF
Query on JEF
Download Ideal Coordinates CCD File 
C [auth A]O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500)
C30 H63 N O10
ICCXIDTYQFYPNV-RUMGZKRTSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.653α = 90
b = 64.73β = 90
c = 69.251γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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