Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.07 kDa 
• Atom Count: 5285 
• Modelled Residue Count: 652 
• Deposited Residue Count: 743 
• Unique protein chains: 1

3SNH

Crystal structure of nucleotide-free human dynamin1

• PDB DOI: 10.2210/pdb3SNH/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-06-29 Released: 2011-09-21 
• Deposition Author(s): Faelber, K., Daumke, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.331 
• R-Value Work: 0.288 
• R-Value Observed: 0.290 

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

• PubMed: 21927000 
• DOI: 10.1038/nature10369
• Primary Citation of Related Structures:  
  3SNH


• 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 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.

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Organizational Affiliation: 

Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynamin-1	A	743	Homo sapiens	Mutation(s): 6  Gene Names: DNM, DNM1 EC: 3.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q05193 (Homo sapiens) Explore Q05193  Go to UniProtKB:  Q05193
PHAROS:  Q05193

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.331 
• R-Value Work: 0.288 
• R-Value Observed: 0.290 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.056	α = 90
b = 201.993	β = 90
c = 59.016	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-29 
• Released Date: 2011-09-21 
Deposition Author(s): Faelber, K., Daumke, O.

Revision History  

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