5H4Z

Crystal structure of S202G mutant of human SYT-5 C2A domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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This is version 1.3 of the entry. See complete history


Literature

Structural analysis of Ca(2+)-binding pocket of synaptotagmin 5 C2A domain

Qiu, X.Ge, J.Gao, Y.Teng, M.Niu, L.

(2017) Int J Biol Macromol 95: 946-953

  • DOI: https://doi.org/10.1016/j.ijbiomac.2016.10.083
  • Primary Citation of Related Structures:  
    5H4Y, 5H4Z

  • PubMed Abstract: 

    Synaptotagmins constitute a family of multifunctional integral membrane proteins found predominantly on vesicles in neural and endocrine tissues. 17 isoforms of synaptotagmin family in mammals have been identified, 7 isoforms among them are known to be able to bind Ca 2+ via their C2 domains. This study presents the crystal structure of the first C2 domain (C2A domain) of synaptotagmin 5 complexed with Ca 2+ at 1.90Å resolution. Comparison of the Ca 2+ -binding pocket of synaptotagmin 5 C2A domain with other synaptotagmin C2 domains demonstrated that a serine residue locating at Ca 2+ -binding loop probably responsible to the conformational variation of Ca 2+ -binding pocket, and thus impacts the Ca 2+ -binding mechanism of C2 domain, which is verified by structural analysis of the serine mutant and Ca 2+ -binding assays via isothermal titration calorimetry. Alteration of Ca 2+ -binding mechanism might be correlated with different Ca 2+ response rates of synaptotagmins, which is the basis of the functions of synaptotagmins in regulating various types of Ca 2+ -triggered vesicle-membrane fusion processes.


  • Organizational Affiliation

    Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, PR China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China; Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, PR China; Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptotagmin-5
A, B
150Homo sapiensMutation(s): 2 
Gene Names: SYT5
UniProt & NIH Common Fund Data Resources
Find proteins for O00445 (Homo sapiens)
Explore O00445 
Go to UniProtKB:  O00445
PHAROS:  O00445
GTEx:  ENSG00000129990 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00445
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.005α = 90
b = 118.656β = 90
c = 109.464γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Science Foundation of Zhejiang ProvinceChinaLQ14C050001
National Natural Science Foundation of ChinaChina31400683

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description