5D3Q

Dynamin 1 GTPase-BSE fusion dimer complexed with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the GTPase domain and the bundle signalling element of dynamin in the GDP state.

Anand, R.Eschenburg, S.Reubold, T.F.

(2016) Biochem.Biophys.Res.Commun. 469: 76-80

  • DOI: 10.1016/j.bbrc.2015.11.074

  • PubMed Abstract: 
  • Dynamin is the prototype of a family of large multi-domain GTPases. The 100 kDa protein is a key player in clathrin-mediated endocytosis, where it cleaves off vesicles from membranes using the energy from GTP hydrolysis. We have solved the high resol ...

    Dynamin is the prototype of a family of large multi-domain GTPases. The 100 kDa protein is a key player in clathrin-mediated endocytosis, where it cleaves off vesicles from membranes using the energy from GTP hydrolysis. We have solved the high resolution crystal structure of a fusion protein of the GTPase domain and the bundle signalling element (BSE) of dynamin 1 liganded with GDP. The structure provides a hitherto missing snapshot of the GDP state of the hydrolytic cycle of dynamin and reveals how the switch I region moves away from the active site after GTP hydrolysis and release of inorganic phosphate. Comparing our structure of the GDP state with the known structures of the GTP state, the transition state and the nucleotide-free state of dynamin 1 we describe the structural changes through the hydrolytic cycle.


    Organizational Affiliation

    Hannover Medical School, Institute for Biophysical Chemistry, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.,Hannover Medical School, Institute for Biophysical Chemistry, Carl-Neuberg-Str. 1, 30625 Hannover, Germany. Electronic address: Reubold.Thomas@mh-hannover.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynamin-1,Dynamin-1
A, B
345Homo sapiensMutation(s): 0 
Gene Names: DNM1 (DNM)
EC: 3.6.5.5
Find proteins for Q05193 (Homo sapiens)
Go to Gene View: DNM1
Go to UniProtKB:  Q05193
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.220α = 99.40
b = 49.960β = 87.18
c = 82.520γ = 105.18
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2017-03-22
    Type: Data collection