5JP2 | pdb_00005jp2

Fcho1 Mu homology domain (Danio Rerio) with bound Eps15 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.234 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5JP2

This is version 1.3 of the entry. See complete history

Literature

Transient Fcho1/2Eps15/RAP-2 Nanoclusters Prime the AP-2 Clathrin Adaptor for Cargo Binding.

Ma, L.Umasankar, P.K.Wrobel, A.G.Lymar, A.McCoy, A.J.Holkar, S.S.Jha, A.Pradhan-Sundd, T.Watkins, S.C.Owen, D.J.Traub, L.M.

(2016) Dev Cell 37: 428-443

  • DOI: https://doi.org/10.1016/j.devcel.2016.05.003
  • Primary Citation Related Structures: 
    5JP2

  • PubMed Abstract: 

    Clathrin-coated vesicles form by rapid assembly of discrete coat constituents into a cargo-sorting lattice. How the sequential phases of coat construction are choreographed is unclear, but transient protein-protein interactions mediated by short interaction motifs are pivotal. We show that arrayed Asp-Pro-Phe (DPF) motifs within the early-arriving endocytic pioneers Eps15/R are differentially decoded by other endocytic pioneers Fcho1/2 and AP-2. The structure of an Eps15/R⋅Fcho1 μ-homology domain complex reveals a spacing-dependent DPF triad, bound in a mechanistically distinct way from the mode of single DPF binding to AP-2. Using cells lacking FCHO1/2 and with Eps15 sequestered from the plasma membrane, we establish that without these two endocytic pioneers, AP-2 assemblies are fleeting and endocytosis stalls. Thus, distinct DPF-based codes within the unstructured Eps15/R C terminus direct the assembly of temporary Fcho1/2⋅Eps15/R⋅AP-2 ternary complexes to facilitate conformational activation of AP-2 by the Fcho1/2 interdomain linker to promote AP-2 cargo engagement.


  • Organizational Affiliation
    • Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA.

Macromolecule Content 

  • Total Structure Weight: 68.22 kDa 
  • Atom Count: 4,596 
  • Modeled Residue Count: 578 
  • Deposited Residue Count: 626 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor substrate 15A [auth E],
C [auth F]
27Homo sapiensMutation(s): 0 
Gene Names: EPS15AF1P
UniProt & NIH Common Fund Data Resources
Find proteins for P42566 (Homo sapiens)
Explore P42566 
Go to UniProtKB:  P42566
PHAROS:  P42566
GTEx:  ENSG00000085832 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42566
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
F-BAR domain only protein 1B [auth A],
D [auth B]
286Danio rerioMutation(s): 0 
Gene Names: fcho1
UniProt
Find proteins for A0A0R4IA99 (Danio rerio)
Explore A0A0R4IA99 
Go to UniProtKB:  A0A0R4IA99
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R4IA99
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.234 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 239.778α = 90
b = 239.778β = 90
c = 44.091γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom090909Z

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2026-02-11
    Changes: Data collection