6KOI

Crystal structure of SNX11-PXe domain in dimer form.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular Basis for PI(3,5)P2Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation.

Xu, T.Gan, Q.Wu, B.Yin, M.Xu, J.Shu, X.Liu, J.

(2020) J Mol Biol 432: 4750-4761

  • DOI: https://doi.org/10.1016/j.jmb.2020.06.010
  • Primary Citation of Related Structures:  
    6KOI, 6KOJ, 6KOK

  • PubMed Abstract: 

    Phosphatidylinositol 3,5-bisphosphate (PI(3,5)P 2 ) is an essential phosphoinositide required for endosome homeostasis and sorting for lysosomal degradation; however, the underlying mechanisms, especially in mammals, remain elusive or unexplored. Here we determined a structure of PI(3,5)P 2 bound to Sorting Nexin 11 (SNX11) with an opened PPII-C loop. We also obtained an SNX11 structure with its PPII-C in "closed" form that serves as a potential PI3P-binding model. In addition, our results reveal that SNX11 can interact with the V1D subunit of vacuolar H + -ATPase (V-ATPase), which provides a link between PI(3,5)P 2 and human V-ATPase and further evidence for their roles in the endosome homeostasis regulation. Lastly, a new apo-form structure of SNX11, combined with molecular dynamics (MD) studies, indicates that the α5 helix can unfold from the PX domain of SNX11 when targeting the membrane or interacting with its partner. Taken together, these findings identify a novel PI(3,5)P 2 effector, which will shed light on the PIs recognizing mechanism and the understanding of the downstream sorting events triggered by different PI binding.


  • Organizational Affiliation

    State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China. Electronic address: xu_tingting@gibh.ac.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-11
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
160Homo sapiensMutation(s): 0 
Gene Names: SNX11
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5W9 (Homo sapiens)
Explore Q9Y5W9 
Go to UniProtKB:  Q9Y5W9
PHAROS:  Q9Y5W9
GTEx:  ENSG00000002919 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5W9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.04α = 90
b = 190.434β = 90
c = 237.012γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China31570759

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description