3SNH

Crystal structure of nucleotide-free human dynamin1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.288 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of nucleotide-free dynamin.

Faelber, K.Posor, Y.Gao, S.Held, M.Roske, Y.Schulze, D.Haucke, V.Noe, F.Daumke, O.

(2011) Nature 477: 556-560

  • DOI: 10.1038/nature10369

  • PubMed Abstract: 
  • Dynamin is a mechanochemical GTPase that oligomerizes around the neck of clathrin-coated pits and catalyses vesicle scission in a GTP-hydrolysis-dependent manner. The molecular details of oligomerization and the mechanism of the mechanochemical coupl ...

    Dynamin is a mechanochemical GTPase that oligomerizes around the neck of clathrin-coated pits and catalyses vesicle scission in a GTP-hydrolysis-dependent manner. The molecular details of oligomerization and the mechanism of the mechanochemical coupling are currently unknown. Here we present the crystal structure of human dynamin 1 in the nucleotide-free state with a four-domain architecture comprising the GTPase domain, the bundle signalling element, the stalk and the pleckstrin homology domain. Dynamin 1 oligomerized in the crystals via the stalks, which assemble in a criss-cross fashion. The stalks further interact via conserved surfaces with the pleckstrin homology domain and the bundle signalling element of the neighbouring dynamin molecule. This intricate domain interaction rationalizes a number of disease-related mutations in dynamin 2 and suggests a structural model for the mechanochemical coupling that reconciles previous models of dynamin function.


    Organizational Affiliation

    Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. katja.faelber@mdc-berlin.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynamin-1
A
743Homo sapiensMutation(s): 6 
Gene Names: DNM1 (DNM)
EC: 3.6.5.5
Find proteins for Q05193 (Homo sapiens)
Go to Gene View: DNM1
Go to UniProtKB:  Q05193
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.288 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 155.056α = 90.00
b = 201.993β = 90.00
c = 59.016γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-26
    Type: Database references