7A1R | pdb_00007a1r

Crystal structure of the C2B domain of Trypanosoma brucei extended synaptotagmin (E-Syt)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.191 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7A1R

This is version 1.1 of the entry. See complete history

Literature

Structural studies of the shortest extended synaptotagmin with only two C2 domains from Trypanosoma brucei .

Stepinac, E.Landrein, N.Skwarzynska, D.Wojcik, P.Lesigang, J.Lucic, I.He, C.Y.Bonhivers, M.Robinson, D.R.Dong, G.

(2021) iScience 24: 102422-102422

  • DOI: https://doi.org/10.1016/j.isci.2021.102422
  • Primary Citation Related Structures: 
    7A1R

  • PubMed Abstract: 

    Extended synaptotagmins (E-Syts) localize at membrane contact sites between the endoplasmic reticulum (ER) and the plasma membrane to mediate inter-membrane lipid transfer and control plasma membrane lipid homeostasis. All known E-Syts contain an N-terminal transmembrane (TM) hairpin, a central synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain, and three or five C2 domains at their C termini. Here we report an uncharacterized E-Syt from the protist parasite Trypanosoma brucei , namely, TbE-Syt. TbE-Syt contains only two C2 domains (C2A and C2B), making it the shortest E-Syt known by now. We determined a 1.5-Å-resolution crystal structure of TbE-Syt-C2B and revealed that it binds lipids via both Ca 2+ - and PI(4,5)P 2 -dependent means. In contrast, TbE-Syt-C2A lacks the Ca 2+ -binding site but may still interact with lipids via a basic surface patch. Our studies suggest a mechanism for how TbE-Syt tethers the ER membrane tightly to the plasma membrane to transfer lipids between the two organelles.


  • Organizational Affiliation
    • Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria.

Macromolecule Content 

  • Total Structure Weight: 30.97 kDa 
  • Atom Count: 2,355 
  • Modeled Residue Count: 242 
  • Deposited Residue Count: 272 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Synaptotagmin
A, B
136Trypanosoma brucei equiperdumMutation(s): 0 
Gene Names: DPX39_100143600
Membrane Entity: Yes 
UniProt
Find proteins for Q388M5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q388M5 
Go to UniProtKB:  Q388M5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ388M5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT

Query on ACT



Download:Ideal Coordinates CCD File
L [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
J [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
M [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.191 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.908α = 90
b = 57.532β = 90
c = 84.57γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2021-06-02 
  • Deposition Author(s): Dong, G.

Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP28231-B28
Austrian Science FundAustriaP24383-B21

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references