8UF4 | pdb_00008uf4

Crystal structure of wildtype dystroglycan proteolytic domain (juxtamembrane domain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.275 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of proteolytic cleavage regulation by the extracellular matrix receptor dystroglycan.

Anderson, M.J.M.Hayward, A.N.Smiley, A.T.Shi, K.Pawlak, M.R.Aird, E.J.Grant, E.Greenberg, L.Aihara, H.Evans 3rd, R.L.Ulens, C.Gordon, W.R.

(2024) Structure 32: 1984-1996.e5

  • DOI: https://doi.org/10.1016/j.str.2024.08.019
  • Primary Citation of Related Structures:  
    8UF4

  • PubMed Abstract: 

    The dystrophin-glycoprotein-complex (DGC), anchored by the transmembrane protein dystroglycan, functions to mechanically link the extracellular matrix and actin cytoskeleton. Breaking this connection is associated with diseases such as muscular dystrophy, yet cleavage of dystroglycan by matrix-metalloproteinases (MMPs) remains an understudied mechanism to disrupt the DGC. We determined the crystal structure of the membrane-adjacent domain (amino acids 491-722) of E. coli expressed human dystroglycan to understand MMP cleavage regulation. The structural model includes tandem immunoglobulin-like (IGL) and sperm/enterokinase/agrin-like (SEAL) domains, which support proteolysis in diverse receptors to facilitate mechanotransduction, membrane protection, and viral entry. The structure reveals a C-terminal extension that buries the MMP site by packing into a hydrophobic pocket, a unique mechanism of MMP cleavage regulation. We further demonstrate structure-guided and disease-associated mutations disrupt proteolytic regulation using a cell-surface proteolysis assay. Thus disrupted proteolysis is a potentially relevant mechanism for "breaking" the DGC link to contribute to disease pathogenesis.


  • Organizational Affiliation
    • Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
a-dystroglycan
A, C
163Homo sapiensMutation(s): 0 
Gene Names: DAG1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14118 (Homo sapiens)
Explore Q14118 
Go to UniProtKB:  Q14118
PHAROS:  Q14118
GTEx:  ENSG00000173402 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14118
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-dystroglycan
B, D
95Homo sapiensMutation(s): 0 
Gene Names: DAG1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14118 (Homo sapiens)
Explore Q14118 
Go to UniProtKB:  Q14118
PHAROS:  Q14118
GTEx:  ENSG00000173402 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14118
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.275 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.945α = 90
b = 86.577β = 90
c = 128γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R35GM119483
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R35GM118047

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary
  • Version 1.2: 2025-03-26
    Changes: Database references