3HS8 | pdb_00003hs8

Intersectin 1-peptide-AP2 alpha ear complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.235 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3HS8

This is version 1.3 of the entry. See complete history

Literature

Regulation of synaptic vesicle recycling by complex formation between intersectin 1 and the clathrin adaptor complex AP2.

Pechstein, A.Bacetic, J.Vahedi-Faridi, A.Gromova, K.Sundborger, A.Tomlin, N.Krainer, G.Vorontsova, O.Schafer, J.G.Owe, S.G.Cousin, M.A.Saenger, W.Shupliakov, O.Haucke, V.

(2010) Proc Natl Acad Sci U S A 107: 4206-4211

  • DOI: https://doi.org/10.1073/pnas.0911073107
  • Primary Citation Related Structures: 
    3HS8, 3HS9

  • PubMed Abstract: 

    Clathrin-mediated synaptic vesicle (SV) recycling involves the spatiotemporally controlled assembly of clathrin coat components at phosphatidylinositiol (4, 5)-bisphosphate [PI(4,5)P(2)]-enriched membrane sites within the periactive zone. Such spatiotemporal control is needed to coordinate SV cargo sorting with clathrin/AP2 recruitment and to restrain membrane fission and synaptojanin-mediated uncoating until membrane deformation and clathrin coat assembly are completed. The molecular events underlying these control mechanisms are unknown. Here we show that the endocytic SH3 domain-containing accessory protein intersectin 1 scaffolds the endocytic process by directly associating with the clathrin adaptor AP2. Acute perturbation of the intersectin 1-AP2 interaction in lamprey synapses in situ inhibits the onset of SV recycling. Structurally, complex formation can be attributed to the direct association of hydrophobic peptides within the intersectin 1 SH3A-B linker region with the "side sites" of the AP2 alpha- and beta-appendage domains. AP2 appendage association of the SH3A-B linker region inhibits binding of the inositol phosphatase synaptojanin 1 to intersectin 1. These data identify the intersectin-AP2 complex as an important regulator of clathrin-mediated SV recycling in synapses.


  • Organizational Affiliation
    • Institute of Chemistry and Biochemistry, Freie Universität and Charité Universitätsmedizin Berlin, 14195 Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 32.17 kDa 
  • Atom Count: 2,171 
  • Modeled Residue Count: 250 
  • Deposited Residue Count: 285 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adaptor protein complex AP-2, alpha 2 subunit273Mus musculusMutation(s): 0 
Gene Names: Ap2a2
UniProt & NIH Common Fund Data Resources
Find proteins for P17427 (Mus musculus)
Explore P17427 
Go to UniProtKB:  P17427
IMPC:  MGI:101920
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17427
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
peptide from Intersectin-1, residues 840-851B [auth P]12N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Z0R4 (Mus musculus)
Explore Q9Z0R4 
Go to UniProtKB:  Q9Z0R4
IMPC:  MGI:1338069
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z0R4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.484α = 90
b = 120.412β = 90
c = 32.22γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references