3ZVR

Crystal structure of Dynamin

• PDB DOI: https://doi.org/10.2210/pdb3ZVR/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-07-27 Released: 2011-09-21 
• Deposition Author(s): Ford, M.G.J., Jenni, S., Nunnari, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Models: experimental

Literature

The Crystal Structure of Dynamin

Ford, M.G.J., Jenni, S., Nunnari, J.

(2011) Nature 477: 561

• PubMed: 21927001 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.08 kDa 
• Atom Count: 5,460 
• Modelled Residue Count: 669 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DYNAMIN-1	A	772	Rattus norvegicus	Mutation(s): 1  EC: 3.6.5.5
UniProt
Find proteins for P21575 (Rattus norvegicus) Explore P21575  Go to UniProtKB:  P21575

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	B [auth A], C [auth A], D [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.45	α = 90
b = 191.61	β = 90
c = 60.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Ford, M.G.J., Jenni, S., Nunnari, J.

Revision History  

• 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
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description