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- PDB-9jst: Wild-type native PMEL amyloid - polymorph 1 -

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Basic information

Entry
Database: PDB / ID: 9jst
TitleWild-type native PMEL amyloid - polymorph 1
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 / Golgi apparatus / endoplasmic reticulum / 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: To Be Published
Title: Cryo-EM of PMEL Amyloids Reveals Pathogenic Mechanism of G175S in Pigment Dispersion Syndrome.
Authors: Yanagisawa, H. / Oda, T.
History
DepositionOct 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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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)30,7478
Polymers30,7478
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: 3843.394 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HMV-II / Tissue: Vagina melanoma / 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: 286491 / Symmetry type: POINT

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