8FRR | pdb_00008frr

Wild-type myocilin olfactomedin domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.155 (Depositor), 0.156 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.140 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming beta-propeller.

Saccuzzo, E.G.Mebrat, M.D.Scelsi, H.F.Kim, M.Ma, M.T.Su, X.Hill, S.E.Rheaume, E.Li, R.Torres, M.P.Gumbart, J.C.Van Horn, W.D.Lieberman, R.L.

(2024) Nat Commun 15: 155-155

  • DOI: https://doi.org/10.1038/s41467-023-44479-2
  • Primary Citation Related Structures: 
    8FRR

  • PubMed Abstract: 

    Studies of folded-to-misfolded transitions using model protein systems reveal a range of unfolding needed for exposure of amyloid-prone regions for subsequent fibrillization. Here, we probe the relationship between unfolding and aggregation for glaucoma-associated myocilin. Mutations within the olfactomedin domain of myocilin (OLF) cause a gain-of-function, namely cytotoxic intracellular aggregation, which hastens disease progression. Aggregation by wild-type OLF (OLF WT ) competes with its chemical unfolding, but only below the threshold where OLF loses tertiary structure. Representative moderate (OLF D380A ) and severe (OLF I499F ) disease variants aggregate differently, with rates comparable to OLF WT in initial stages of unfolding, and variants adopt distinct partially folded structures seen along the OLF WT urea-unfolding pathway. Whether initiated with mutation or chemical perturbation, unfolding propagates outward to the propeller surface. In sum, for this large protein prone to amyloid formation, the requirement for a conformational change to promote amyloid fibrillization leads to direct competition between unfolding and aggregation.


  • Organizational Affiliation
    • School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA.

Macromolecule Content 

  • Total Structure Weight: 29.41 kDa 
  • Atom Count: 2,544 
  • Modeled Residue Count: 259 
  • Deposited Residue Count: 259 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myocilin, C-terminal fragment259Homo sapiensMutation(s): 0 
Gene Names: MYOCGLC1ATIGR
UniProt & NIH Common Fund Data Resources
Find proteins for Q99972 (Homo sapiens)
Explore Q99972 
Go to UniProtKB:  Q99972
PHAROS:  Q99972
GTEx:  ENSG00000034971 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99972
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.155 (Depositor), 0.156 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.140 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.468α = 90
b = 50.527β = 96.25
c = 50.873γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United States10R01EY021205

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Structure summary