5H4Y

Crystal structure of human synaptotagmin 5 C2A domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.ijbiomac.2016.10.083
  • Primary Citation of Related Structures:  

  • 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 ...

    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 Ca2+ via their C2 domains. This study presents the crystal structure of the first C2 domain (C2A domain) of synaptotagmin 5 complexed with Ca2+ at 1.90Å resolution. Comparison of the Ca2+-binding pocket of synaptotagmin 5 C2A domain with other synaptotagmin C2 domains demonstrated that a serine residue locating at Ca2+-binding loop probably responsible to the conformational variation of Ca2+-binding pocket, and thus impacts the Ca2+-binding mechanism of C2 domain, which is verified by structural analysis of the serine mutant and Ca2+-binding assays via isothermal titration calorimetry. Alteration of Ca2+-binding mechanism might be correlated with different Ca2+ response rates of synaptotagmins, which is the basis of the functions of synaptotagmins in regulating various types of Ca2+-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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Synaptotagmin-5
A
150Homo sapiensMutation(s): 1 
Gene Names: SYT5
Find proteins for O00445 (Homo sapiens)
Go to Gene View: SYT5
Go to UniProtKB:  O00445
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 93.966α = 90.00
b = 93.966β = 90.00
c = 28.052γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2012CB917200
National Natural Science Foundation of ChinaChina31170726
National Natural Science Foundation of ChinaChina31370732

Revision History 

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Database references