9JSX | pdb_00009jsx

G175S PMEL CAF amyloid - in vitro polymerized


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.79 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9JSX

This is version 1.1 of the entry. See complete history

Literature

Cryo-EM of wild-type and mutant PMEL amyloid cores reveals structural mechanism of pigment dispersion syndrome.

Yanagisawa, H.Arai, H.Wang, T.Miyazawa, H.Kikkawa, M.Oda, T.

(2025) Nat Commun 16: 5411-5411

  • DOI: https://doi.org/10.1038/s41467-025-61233-y
  • Primary Citation Related Structures: 
    9JST, 9JSU, 9JSV, 9JSW, 9JSX

  • PubMed Abstract: 

    PMEL amyloids serve as essential scaffolds for melanin deposition in melanosomes, playing a crucial role in pigmentation. Despite their importance, the high-resolution structure of PMEL amyloids has remained unresolved. Using cryo-electron microscopy, we determine near-atomic resolution structures of wild-type PMEL amyloid core, revealing two distinct polymorphic forms with structural features. We further investigate the pathogenic G175S mutation associated with pigment dispersion syndrome (PDS). Structural analysis reveales that G175S introduces an additional hydrogen bond, stabilizing an alternative fibril conformation. In vitro, the G175S mutant exhibits a fourfold increase in polymerization efficiency compared to the wild type. In cells, G175S expression resultes in a twofold increase in intracellular amyloid content and a ~70% increase in extracellular amyloids, without altering melanosome morphology or number. These results indicate that the G175S mutation enhances amyloidogenesis within melanosomes, elevating amyloid load and potentially contributing to PDS pathophysiology. This study provides molecular insights into PMEL amyloid formation, highlighting its structural diversity and dysregulation in pigmentation disorders.


  • Organizational Affiliation
    • Department of Cell Biology and Anatomy, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 30.29 kDa 
  • Atom Count: 2,144 
  • Modeled Residue Count: 272 
  • Deposited Residue Count: 272 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
M-alpha34Homo sapiensMutation(s): 1 
Gene Names: PMELD12S53EPMEL17SILV
UniProt & NIH Common Fund Data Resources
Find proteins for P40967 (Homo sapiens)
Explore P40967 
Go to UniProtKB:  P40967
PHAROS:  P40967
GTEx:  ENSG00000185664 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40967
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.79 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan24H02285
Human Frontier Science Program (HFSP)FranceRGP006/2023

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references