6W9N | pdb_00006w9n

Solution structure of the FYVE domain of ALFY


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

Validation slider image for 6W9N

This is version 1.3 of the entry. See complete history

Literature

A highly conserved glutamic acid in ALFY inhibits membrane binding to aid in aggregate clearance.

Reinhart, E.F.Litt, N.A.Katzenell, S.Pellegrini, M.Yamamoto, A.Ragusa, M.J.

(2021) Traffic 22: 23-37

  • DOI: https://doi.org/10.1111/tra.12771
  • Primary Citation Related Structures: 
    6W9N

  • PubMed Abstract: 

    Autophagy-linked FYVE protein (ALFY) is a large, multidomain protein involved in the degradation of protein aggregates by selective autophagy. The C-terminal FYVE domain of ALFY has been shown to bind phosphatidylinositol 3-phosphate (PI(3)P); however, ALFY only partially colocalizes with other FYVE domains in cells. Thus, we asked if the FYVE domain of ALFY has distinct membrane binding properties compared to other FYVE domains and whether these properties might affect its function in vivo. We found that the FYVE domain of ALFY binds weakly to PI(3)P containing membranes in vitro. This weak binding is the result of a highly conserved glutamic acid within the membrane insertion loop in the FYVE domain of ALFY that is not present in any other human FYVE domain. In addition, not only does this glutamic acid reduce binding to membranes in vitro and inhibits its targeting to membranes in vivo, but it is also important for the ability of ALFY to clear protein aggregates.


  • Organizational Affiliation
    • Department of Chemistry, Dartmouth College, Hanover, New Hampshire.

Macromolecule Content 

  • Total Structure Weight: 9.07 kDa 
  • Atom Count: 622 
  • Modeled Residue Count: 78 
  • Deposited Residue Count: 78 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat and FYVE domain-containing protein 378Homo sapiensMutation(s): 0 
Gene Names: WDFY3KIAA0993
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZQ1 (Homo sapiens)
Explore Q8IZQ1 
Go to UniProtKB:  Q8IZQ1
PHAROS:  Q8IZQ1
GTEx:  ENSG00000163625 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IZQ1
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM113132
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP35GM128662

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references