1PX2 | pdb_00001px2

Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP (Form 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.240 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Tetramerization and ATP binding by a protein comprising the A, B, and C domains of rat synapsin I.

Brautigam, C.A.Chelliah, Y.Deisenhofer, J.

(2004) J Biological Chem 279: 11948-11956

  • DOI: https://doi.org/10.1074/jbc.M312015200
  • Primary Citation Related Structures: 
    1PK8, 1PX2

  • PubMed Abstract: 

    Synapsins are multidomain proteins that are critical for regulating neurotransmitter release in vertebrates. In the present study, two crystal structures of the C domain of rat synapsin I (rSynI-C) in complex with Ca(2+) and ATP reveal that this protein can form a tetramer and that a flexible loop (the "multifunctional loop") contacts bound ATP. Further experiments were carried out on a protein comprising the A, B, and C domains of rat synapsin I (rSynI-ABC). An ATP-stabilized tetramer of rSynI-ABC is observed during velocity sedimentation and size-exclusion chromatographic experiments. These hydrodynamic results also indicate that the A and B domains exist in an extended conformation. Calorimetric measurements of ATP binding to wild-type and mutant rSynI-ABC demonstrate that the multifunctional loop and a cross-tetramer contact are important for ATP binding. The evidence supports a view of synapsin I as an ATP-utilizing, tetrameric protein made up of monomers that have a flexible, extended N terminus.


  • Organizational Affiliation
    • Howard Hughes Medical Institute and the Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9050, USA.

Macromolecule Content 

  • Total Structure Weight: 92.17 kDa 
  • Atom Count: 5,139 
  • Modeled Residue Count: 588 
  • Deposited Residue Count: 844 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Synapsin I
A, B
422Rattus norvegicusMutation(s): 0 
Gene Names: SYN1
UniProt
Find proteins for P09951 (Rattus norvegicus)
Explore P09951 
Go to UniProtKB:  P09951
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09951
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.240 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96α = 90
b = 96β = 90
c = 305.8γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-03-13
    Changes: Source and taxonomy, Structure summary