9DKZ | pdb_00009dkz

In situ microED structure of the Eosinophil major basic protein-1

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-09-10 Released: 2024-09-25 
  • Deposition Author(s): Yang, J.E., Bingman, C.A., Mitchell, J., Mosher, D., Wright, E.R.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.311 (Depositor), 0.343 (DCC) 
  • R-Value Work: 
    0.268 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 
    0.273 (Depositor) 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

In situ crystalline structure of the human eosinophil major basic protein-1.

Yang, J.E.Mitchell, J.M.Bingman, C.A.Mosher, D.F.Wright, E.R.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.10.09.617336
  • Primary Citation of Related Structures:  
    9DKZ

  • PubMed Abstract: 

    Eosinophils are white blood cells that participate in innate immune responses and have an essential role in the pathogenesis of inflammatory and neoplastic disorders. Upon activation, eosinophils release cytotoxic proteins such as major basic protein-1 (MBP-1) from cytoplasmic secretory granules (SGr) wherein MBP-1 is stored as nanocrystals. How the MBP-1 nanocrystalline core is formed, stabilized, and subsequently mobilized remains unknown. Here, we report the in-situ structure of crystalline MBP-1 within SGrs of human eosinophils. The structure reveals a mechanism for intragranular crystal packing and stabilization of MBP-1 via a structurally conserved loop region that is associated with calcium-dependent carbohydrate binding in other C-type lectin (CTL) proteins. Single-cell and single-SGr profiling correlating real-space three-dimensional information from cellular montage cryo-electron tomography (cryo-ET) and microcrystal electron diffraction (MicroED) data obtained from non-activated and IL33-activated eosinophils revealed activation-dependent crystal expansion and extrusion of expanded crystals from SGr. These results suggest that MBP-1 crystals play a dynamic role in the release of SGr contents. Collectively, this research demonstrates the importance of in-situ macromolecular structure determination.


  • Organizational Affiliation
    • Department of Biochemistry, University of Wisconsin, Madison, WI USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bone marrow proteoglycan116Homo sapiensMutation(s): 0 
Gene Names: PRG2MBP
UniProt & NIH Common Fund Data Resources
Find proteins for P13727 (Homo sapiens)
Explore P13727 
Go to UniProtKB:  P13727
PHAROS:  P13727
GTEx:  ENSG00000186652 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13727
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.20 Å
  • R-Value Free:  0.311 (Depositor), 0.343 (DCC) 
  • R-Value Work:  0.268 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 0.273 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.24α = 90
b = 57.87β = 90
c = 59.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX1.21.1-5286
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM114561
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM139168
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesP01 HL088594
Department of Energy (DOE, United States)United StatesDE-SC0023013
Department of Energy (DOE, United States)United StatesDE-SC0018409

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary
  • Version 1.2: 2024-11-13
    Changes: Database references