3ZVR

Crystal structure of Dynamin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Crystal Structure of Dynamin

Ford, M.G.J.Jenni, S.Nunnari, J.

(2011) Nature 477: 561

  • DOI: 10.1038/nature10441
  • Primary Citation of Related Structures:  
    3ZVR

  • PubMed Abstract: 
  • Dynamin-related proteins (DRPs) are multi-domain GTPases that function via oligomerization and GTP-dependent conformational changes to play central roles in regulating membrane structure across phylogenetic kingdoms. How DRPs harness self-assembly and GTP-dependent conformational changes to remodel membranes is not understood ...

    Dynamin-related proteins (DRPs) are multi-domain GTPases that function via oligomerization and GTP-dependent conformational changes to play central roles in regulating membrane structure across phylogenetic kingdoms. How DRPs harness self-assembly and GTP-dependent conformational changes to remodel membranes is not understood. Here we present the crystal structure of an assembly-deficient mammalian endocytic DRP, dynamin 1, lacking the proline-rich domain, in its nucleotide-free state. The dynamin 1 monomer is an extended structure with the GTPase domain and bundle signalling element positioned on top of a long helical stalk with the pleckstrin homology domain flexibly attached on its opposing end. Dynamin 1 dimer and higher order dimer multimers form via interfaces located in the stalk. Analysis of these interfaces provides insight into DRP family member specificity and regulation and provides a framework for understanding the biogenesis of higher order DRP structures and the mechanism of DRP-mediated membrane scission events.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DYNAMIN-1A772Rattus norvegicusMutation(s): 1 
Gene Names: Dnm1Dnm
EC: 3.6.5.5
Find proteins for P21575 (Rattus norvegicus)
Explore P21575 
Go to UniProtKB:  P21575
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.45α = 90
b = 191.61β = 90
c = 60.52γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Atomic model, Database references, Derived calculations, Other
  • Version 1.2: 2011-10-12
    Changes: Database references, Other