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 7RFQ | pdb_00007rfq

STRUCTURE OF BACTERIAL SYLF DOMAIN CONTAINING PROTEIN, BETA CELL EXPANSION FACTOR A (BEFA)

  • Classification: SIGNALING PROTEIN
  • Organism(s): Aeromonas veronii
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-07-14 Released: 2022-07-20 
  • Deposition Author(s): Sweeney, E.G.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.155 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.131 (Depositor) 
  • R-Value Observed: 
    0.132 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7RFQ

This is version 1.3 of the entry. See complete history. 

Literature

BefA, a microbiota-secreted membrane disrupter, disseminates to the pancreas and increases beta cell mass.

Hill, J.H., Massaquoi, M.S., Sweeney, E.G., Wall, E.S., Jahl, P., Bell, R., Kallio, K., Derrick, D., Murtaugh, L.C., Parthasarathy, R., Remington, S.J., Round, J.L., Guillemin, K.

(2022) Cell Metab 34: 1779-1791.e9

  • DOI: https://doi.org/10.1016/j.cmet.2022.09.001
  • Primary Citation Related Structures: 
    7RFQ

  • PubMed Abstract: 

    Microbiome dysbiosis is a feature of diabetes, but how microbial products influence insulin production is poorly understood. We report the mechanism of BefA, a microbiome-derived protein that increases proliferation of insulin-producing β cells during development in gnotobiotic zebrafish and mice. BefA disseminates systemically by multiple anatomic routes to act directly on pancreatic islets. We detail BefA's atomic structure, containing a lipid-binding SYLF domain, and demonstrate that it permeabilizes synthetic liposomes and bacterial membranes. A BefA mutant impaired in membrane disruption fails to expand β cells, whereas the pore-forming host defense protein, Reg3, stimulates β cell proliferation. Our work demonstrates that membrane permeabilization by microbiome-derived and host defense proteins is necessary and sufficient for β cell expansion during pancreas development, potentially connecting microbiome composition with diabetes risk.


  • Organizational Affiliation: 
    • Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA; Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112, USA.

Macromolecule Content 

  • Total Structure Weight: 30.22 kDa 
  • Atom Count: 2,068 
  • Modeled Residue Count: 223 
  • Deposited Residue Count: 270 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA CELL EXPANSION FACTOR A (BEFA)270Aeromonas veroniiMutation(s): 0 
Gene Names: AMS64_07270
UniProt
Find proteins for A0A2S3XLU2 (Aeromonas veronii)
Explore A0A2S3XLU2 
Go to UniProtKB:  A0A2S3XLU2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S3XLU2
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.155 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.131 (Depositor) 
  • R-Value Observed: 0.132 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.67α = 90
b = 64.55β = 113.26
c = 42.63γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2022-11-09
    Changes: Database references
  • Version 1.3: 2024-05-22
    Changes: Data collection