6SER | pdb_00006ser

Crystal structure of human STARD10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6SER

This is version 1.2 of the entry. See complete history

Literature

The type 2 diabetes gene product STARD10 is a phosphoinositide-binding protein that controls insulin secretory granule biogenesis.

Carrat, G.R.Haythorne, E.Tomas, A.Haataja, L.Muller, A.Arvan, P.Piunti, A.Cheng, K.Huang, M.Pullen, T.J.Georgiadou, E.Stylianides, T.Amirruddin, N.S.Salem, V.Distaso, W.Cakebread, A.Heesom, K.J.Lewis, P.A.Hodson, D.J.Briant, L.J.Fung, A.C.H.Sessions, R.B.Alpy, F.Kong, A.P.S.Benke, P.I.Torta, F.Teo, A.K.K.Leclerc, I.Solimena, M.Wigley, D.B.Rutter, G.A.

(2020) Mol Metab 40: 101015-101015

  • DOI: https://doi.org/10.1016/j.molmet.2020.101015
  • Primary Citation Related Structures: 
    6SER

  • PubMed Abstract: 

    Risk alleles for type 2 diabetes at the STARD10 locus are associated with lowered STARD10 expression in the β-cell, impaired glucose-induced insulin secretion, and decreased circulating proinsulin:insulin ratios. Although likely to serve as a mediator of intracellular lipid transfer, the identity of the transported lipids and thus the pathways through which STARD10 regulates β-cell function are not understood. The aim of this study was to identify the lipids transported and affected by STARD10 in the β-cell and the role of the protein in controlling proinsulin processing and insulin granule biogenesis and maturation. We used isolated islets from mice deleted selectively in the β-cell for Stard10 (βStard10KO) and performed electron microscopy, pulse-chase, RNA sequencing, and lipidomic analyses. Proteomic analysis of STARD10 binding partners was executed in the INS1 (832/13) cell line. X-ray crystallography followed by molecular docking and lipid overlay assay was performed on purified STARD10 protein. βStard10KO islets had a sharply altered dense core granule appearance, with a dramatic increase in the number of "rod-like" dense cores. Correspondingly, basal secretion of proinsulin was increased versus wild-type islets. The solution of the crystal structure of STARD10 to 2.3 Å resolution revealed a binding pocket capable of accommodating polyphosphoinositides, and STARD10 was shown to bind to inositides phosphorylated at the 3' position. Lipidomic analysis of βStard10KO islets demonstrated changes in phosphatidylinositol levels, and the inositol lipid kinase PIP4K2C was identified as a STARD10 binding partner. Also consistent with roles for STARD10 in phosphoinositide signalling, the phosphoinositide-binding proteins Pirt and Synaptotagmin 1 were amongst the differentially expressed genes in βStard10KO islets. Our data indicate that STARD10 binds to, and may transport, phosphatidylinositides, influencing membrane lipid composition, insulin granule biosynthesis, and insulin processing.


  • Organizational Affiliation
    • Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK.

Macromolecule Content 

  • Total Structure Weight: 34.06 kDa 
  • Atom Count: 2,120 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 291 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
START domain-containing protein 10291Homo sapiensMutation(s): 0 
Gene Names: STARD10SDCCAG28CGI-52
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y365 (Homo sapiens)
Explore Q9Y365 
Go to UniProtKB:  Q9Y365
GTEx:  ENSG00000214530 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y365
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE

Query on PGE



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.336α = 90
b = 101.199β = 90
c = 125.75γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N009258/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2026-08-12
    Changes: Database references, Structure summary