1AUX

STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH CALCIUM ATP-GAMMA-S BOUND

• PDB DOI: https://doi.org/10.2210/pdb1AUX/pdb

• Classification: TRANSFERASE
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-09-06 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: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

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: https://doi.org/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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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 70.93 kDa 
• Atom Count: 4,752 
• Modelled Residue Count: 584 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPSIN IA	A, B	311	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P17599 (Bos taurus) Explore P17599  Go to UniProtKB:  P17599

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	D [auth A], F [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.16	α = 90
b = 76.16	β = 90
c = 182.33	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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: Non-polymer description
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Other, Refinement description