2X3V | pdb_00002x3v

Structure of The F-BAR Domain of Mouse Syndapin I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2X3V

This is version 1.2 of the entry. See complete history

Literature

Molecular Basis for SH3 Domain Regulation of F-Bar-Mediated Membrane Deformation.

Rao, Y.Ma, Q.Vahedi-Faridi, A.Sundborger, A.Pechstein, A.Puchkov, D.Luo, L.Shupliakov, O.Saenger, W.Haucke, V.

(2010) Proc Natl Acad Sci U S A 107: 8213

  • DOI: https://doi.org/10.1073/pnas.1003478107
  • Primary Citation Related Structures: 
    2X3V, 2X3W, 2X3X

  • PubMed Abstract: 

    Members of the Bin/amphiphysin/Rvs (BAR) domain protein superfamily are involved in membrane remodeling in various cellular pathways ranging from endocytic vesicle and T-tubule formation to cell migration and neuromorphogenesis. Membrane curvature induction and stabilization are encoded within the BAR or Fer-CIP4 homology-BAR (F-BAR) domains, alpha-helical coiled coils that dimerize into membrane-binding modules. BAR/F-BAR domain proteins often contain an SH3 domain, which recruits binding partners such as the oligomeric membrane-fissioning GTPase dynamin. How precisely BAR/F-BAR domain-mediated membrane deformation is regulated at the cellular level is unknown. Here we present the crystal structures of full-length syndapin 1 and its F-BAR domain. Our data show that syndapin 1 F-BAR-mediated membrane deformation is subject to autoinhibition by its SH3 domain. Release from the clamped conformation is driven by association of syndapin 1 SH3 with the proline-rich domain of dynamin 1, thereby unlocking its potent membrane-bending activity. We hypothesize that this mechanism might be commonly used to regulate BAR/F-BAR domain-induced membrane deformation and to potentially couple this process to dynamin-mediated fission. Our data thus suggest a structure-based model for SH3-mediated regulation of BAR/F-BAR domain function.


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

Macromolecule Content 

  • Total Structure Weight: 118.05 kDa 
  • Atom Count: 7,419 
  • Modeled Residue Count: 874 
  • Deposited Residue Count: 1,011 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
A, B, C
337Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q61644 (Mus musculus)
Explore Q61644 
Go to UniProtKB:  Q61644
IMPC:  MGI:1345181
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61644
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.06α = 90
b = 153.49β = 90
c = 213.29γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
XPREPphasing
SHELXDphasing
SHELXEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Other