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- PDB-9jsu: Wild-type native PMEL amyloid - polymorph 2 -

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Basic information

Entry
Database: PDB / ID: 9jsu
TitleWild-type native PMEL amyloid - polymorph 2
ComponentsM-alpha
KeywordsSTRUCTURAL PROTEIN / melanosome / melanoma / pigment / melanin / amyloid / glaucoma
Function / homology
Function and homology information


cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body membrane / Regulation of MITF-M-dependent genes involved in pigmentation / melanosome / endoplasmic reticulum membrane ...cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body membrane / Regulation of MITF-M-dependent genes involved in pigmentation / melanosome / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Immunoglobulin-like fold
Similarity search - Domain/homology
Melanocyte protein PMEL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.79 Å
AuthorsOda, T. / Yanagisawa, H.
Funding support Japan, France, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24H02285 Japan
Human Frontier Science Program (HFSP)RGP006/2023 France
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM of wild-type and mutant PMEL amyloid cores reveals structural mechanism of pigment dispersion syndrome.
Authors: Haruaki Yanagisawa / Harumi Arai / Tony Wang / Hideyuki Miyazawa / Masahide Kikkawa / Toshiyuki Oda /
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 ...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.
History
DepositionOct 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M-alpha
B: M-alpha
C: M-alpha
D: M-alpha
E: M-alpha
F: M-alpha
G: M-alpha
H: M-alpha


Theoretical massNumber of molelcules
Total (without water)28,8898
Polymers28,8898
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
M-alpha / 95 kDa melanocyte-specific secreted glycoprotein / P26 / Secreted melanoma-associated ME20 antigen ...95 kDa melanocyte-specific secreted glycoprotein / P26 / Secreted melanoma-associated ME20 antigen / ME20-S / ME20S


Mass: 3611.115 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HMV-II / References: UniProt: P40967
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Wild-type native PMEL amyloid extracted from melanoma cell line
Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Organelle: Melanosome
Buffer solutionpH: 4.4
Buffer componentConc.: 150 mM / Name: Sodium acetate / Formula: CH3COONa
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 5.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 352878 / Symmetry type: POINT

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