4TKN

Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structural Determinants for Binding of Sorting Nexin 17 (SNX17) to the Cytoplasmic Adaptor Protein Krev Interaction Trapped 1 (KRIT1).

Stiegler, A.L., Zhang, R., Liu, W., Boggon, T.J.

(2014) J Biol Chem 289: 25362-25373

  • DOI: 10.1074/jbc.M114.584011
  • Primary Citation of Related Structures:  
    4TKN

  • PubMed Abstract: 

    • Sorting nexin 17 (SNX17) is a member of the family of cytoplasmic sorting nexin adaptor proteins that regulate endosomal trafficking of cell surface proteins. SNX17 localizes to early endosomes where it directly binds NPX(Y/F) motifs in the cytoplasmic tails of its target receptors to mediate their rates of endocytic internalization, recycling, and/or degradation ...

    Sorting nexin 17 (SNX17) is a member of the family of cytoplasmic sorting nexin adaptor proteins that regulate endosomal trafficking of cell surface proteins. SNX17 localizes to early endosomes where it directly binds NPX(Y/F) motifs in the cytoplasmic tails of its target receptors to mediate their rates of endocytic internalization, recycling, and/or degradation. SNX17 has also been implicated in mediating cell signaling and can interact with cytoplasmic proteins. KRIT1 (Krev interaction trapped 1), a cytoplasmic adaptor protein associated with cerebral cavernous malformations, has previously been shown to interact with SNX17. Here, we demonstrate that SNX17 indeed binds directly to KRIT1 and map the binding to the second Asn-Pro-Xaa-Tyr/Phe (NPX(Y/F)) motif in KRIT1. We further characterize the interaction as being mediated by the FERM domain of SNX17. We present the co-crystal structure of SNX17-FERM with the KRIT1-NPXF2 peptide to 3.0 Å resolution and demonstrate that the interaction is highly similar in structure and binding affinity to that between SNX17 and P-selectin. We verify the molecular details of the interaction by site-directed mutagenesis and pulldown assay and thereby confirm that the major binding site for SNX17 is confined to the NPXF2 motif in KRIT1. Taken together, our results verify a direct interaction between SNX17 and KRIT1 and classify KRIT1 as a SNX17 binding partner.

    Organizational Affiliation: 

    From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520 titus.boggon@yale.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sorting nexin-17A, B, C286Homo sapiensMutation(s): 0 
Gene Names: SNX17, KIAA0064
UniProt & NIH Common Fund Data Resources
Find proteins for Q15036 (Homo sapiens)
Explore Q15036 
Go to UniProtKB:  Q15036
PHAROS:  Q15036
GTEx:  ENSG00000115234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15036
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Krev interaction trapped protein 1D, E, F19Homo sapiensMutation(s): 0 
Gene Names: KRIT1, CCM1
UniProt & NIH Common Fund Data Resources
Find proteins for O00522 (Homo sapiens)
Explore O00522 
Go to UniProtKB:  O00522
PHAROS:  O00522
GTEx:  ENSG00000001631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00522
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/5 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.924α = 90
b = 191.202β = 110.25
c = 46.593γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
Cootmodel building
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS085078

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence