1D2N

D2 DOMAIN OF N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb1D2N/pdb

• Classification: HEXAMERIZATION DOMAIN
• Organism(s): Cricetulus griseus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-06-30 Released: 1998-10-14 
• Deposition Author(s): Lenzen, C.U., Steinmann, D., Whiteheart, S.W., Weis, W.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.223 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein.

Lenzen, C.U., Steinmann, D., Whiteheart, S.W., Weis, W.I.

(1998) Cell 94: 525-536

• PubMed: 9727495 
• DOI: https://doi.org/10.1016/s0092-8674(00)81593-7
• Primary Citation of Related Structures:  
  1D2N


• PubMed Abstract: 
  

  N-ethylmaleimide-sensitive fusion protein (NSF) is a cytosolic ATPase required for many intracellular vesicle fusion reactions. NSF consists of an amino-terminal region that interacts with other components of the vesicle trafficking machinery, followed by two homologous ATP-binding cassettes, designated D1 and D2, that possess essential ATPase and hexamerization activities, respectively. The crystal structure of D2 bound to Mg2+-AMPPNP has been determined at 1.75 A resolution. The structure consists of a nucleotide-binding and a helical domain, and it is unexpectedly similar to the first two domains of the clamp-loading subunit delta' of E. coli DNA polymerase III. The structure suggests several regions responsible for coupling of ATP hydrolysis to structural changes in full-length NSF.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, California 94305, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 31.16 kDa 
• Atom Count: 2,262 
• Modelled Residue Count: 246 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN	A	272	Cricetulus griseus	Mutation(s): 0  EC: 3.6.4.6
UniProt
Find proteins for P18708 (Cricetulus griseus) Explore P18708  Go to UniProtKB:  P18708

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.223 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.33	α = 90
b = 116.33	β = 90
c = 40.24	γ = 120

Software Package:

Software Name	Purpose
DM	model building
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Lenzen, C.U., Steinmann, D., Whiteheart, S.W., Weis, W.I.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2024-02-07
  Changes: Atomic model, Data collection, Database references, Derived calculations