Biological Assembly 1  

 3D View: Structure | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 70.84 kDa 
• Atom Count: 4797 
• Modelled Residue Count: 585 
• Deposited Residue Count: 622 
• Unique protein chains: 1

1AUV

STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN

• DOI: 10.2210/pdb1AUV/pdb

• Classification: TRANSFERASE
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-09-02 Released: 1998-03-18 
• Deposition Author(s): Esser, L., Wang, C., Deisenhofer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.255 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Synapsin I is structurally similar to ATP-utilizing enzymes.

Esser, L., Wang, C.R., Hosaka, M., Smagula, C.S., Sudhof, T.C., Deisenhofer, J.

(1998) EMBO J 17: 977-984

• PubMed: 9463376 
• DOI: 10.1093/emboj/17.4.977
• Primary Citation of Related Structures:  
  1AUV, 1AUX


• PubMed Abstract: 
  

Synapsins are abundant synaptic vesicle proteins with an essential regulatory function in the nerve terminal. We determined the crystal structure of a fragment (synC) consisting of residues 110-420 of bovine synapsin I; synC coincides with the large middle domain (C-domain), the most conserved domain of synapsins. SynC molecules are folded into compact domains and form closely associated dimers. SynC monomers are strikingly similar in structure to a family of ATP-utilizing enzymes, which includes glutathione synthetase and D-alanine:D-alanine ligase. SynC binds ATP in a Ca2+-dependent manner. The crystal structure of synC in complex with ATPgammaS and Ca2+ explains the preference of synC for Ca2+ over Mg2+. Our results suggest that synapsins may also be ATP-utilizing enzymes.

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Related Citations: 

• Identification, Expression, and Crystallization of the Protease-Resistant Conserved Domain of Synapsin I
  Wang, C.R., Esser, L., Smagula, C.S., Sudhof, T.C., Deisenhofer, J.
  (1997) Protein Sci 6: 2264

• Synapsins: Mosaics of Shared and Individual Domains in a Family of Synaptic Vesicle Phosphoproteins
  Sudhof, T.C., Czernik, A.J., Kao, H.T., Takei, K., Johnston, P.A., Horiuchi, A., Kanazir, S.D., Wagner, M.A., Perin, M.S., De Camilli, P., Greengard, P.
  (1989) Science 245: 1474

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Organizational Affiliation: 

Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235-9050, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPSIN IA	A, B	311	Bos taurus	Mutation(s): 10  Gene Names: SYN1
UniProt
Find proteins for P17599 (Bos taurus) Explore P17599  Go to UniProtKB:  P17599

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.255 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.4	α = 90
b = 76.4	β = 90
c = 180.94	γ = 120

Software Package:

Software Name	Purpose
MLPHARE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-09-02 
• Released Date: 1998-03-18 
Deposition Author(s): Esser, L., Wang, C., Deisenhofer, J.

Revision History  

• Version 1.0: 1998-03-18
  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 1.3: 2012-02-15
  Changes: Structure summary