Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.72 kDa 
• Atom Count: 6039 
• Residue Count: 682 
• Unique protein chains: 1

2X2E

Dynamin GTPase dimer, long axis form

• DOI: 10.2210/pdb2X2E/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-01-12 Released: 2010-04-28 
• Deposition Author(s): Chappie, J.S., Acharya, S., Leonard, M., Schmid, S.L., Dyda, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

G Domain Dimerization Controls Dynamin'S Assembly-Stimulated Gtpase Activity.

Chappie, J.S., Acharya, S., Leonard, M., Schmid, S.L., Dyda, F.

(2010) Nature 465: 435

• PubMed: 20428113 
• DOI: 10.1038/nature09032
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Dynamin is an atypical GTPase that catalyses membrane fission during clathrin-mediated endocytosis. The mechanisms of dynamin's basal and assembly-stimulated GTP hydrolysis are unknown, though both are indirectly influenced by the GTPase effector domain (GED). Here we present the 2.0 A resolution crystal structure of a human dynamin 1-derived minimal GTPase-GED fusion protein, which was dimeric in the presence of the transition state mimic GDP.AlF(4)(-).The structure reveals dynamin's catalytic machinery and explains how assembly-stimulated GTP hydrolysis is achieved through G domain dimerization. A sodium ion present in the active site suggests that dynamin uses a cation to compensate for the developing negative charge in the transition state in the absence of an arginine finger. Structural comparison to the rat dynamin G domain reveals key conformational changes that promote G domain dimerization and stimulated hydrolysis. The structure of the GTPase-GED fusion protein dimer provides insight into the mechanisms underlying dynamin-catalysed membrane fission.

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Organizational Affiliation: 

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DYNAMIN-1	A, D	353	Homo sapiens	Mutation(s): 1  Gene Names: DNM1, DNM EC: 3.6.5.5
Find proteins for Q05193 (Homo sapiens) Explore Q05193  Go to UniProtKB:  Q05193
NIH Common Fund Data Resources
PHAROS  Q05193 GTEx  ENSG00000106976

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	A, D	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ALF	A, D	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG	A, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	A, D	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.61	α = 90
b = 81.02	β = 90
c = 181.54	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SHARPD	phasing
DM	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-12 
• Released Date: 2010-04-28 
Deposition Author(s): Chappie, J.S., Acharya, S., Leonard, M., Schmid, S.L., Dyda, F.

Revision History 

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-08-31
  Changes: Database references, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other