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- EMDB-61783: Wild-type native PMEL amyloid - polymorph 2 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61783
TitleWild-type native PMEL amyloid - polymorph 2
Map dataWild-type native PMEL amyloid, polymorph 2
Sample
  • Cell: Wild-type native PMEL amyloid extracted from melanoma cell line
    • Protein or peptide: M-alpha
Keywordsmelanosome / melanoma / pigment / melanin / amyloid / glaucoma / STRUCTURAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.79 Å
AuthorsOda T / Yanagisawa H
Funding support Japan, France, 2 items
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, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61783.png

Downloads & links

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Map

FileDownload / File: emd_61783.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWild-type native PMEL amyloid, polymorph 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 90 pix.
= 79.056 Å		0.88 Å/pix.
x 90 pix.
= 79.056 Å		0.88 Å/pix.
x 90 pix.
= 79.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8784 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.21767081 - 0.5420842
Average (Standard dev.)0.006340041 (±0.05039604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 79.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61783_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_61783_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_61783_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wild-type native PMEL amyloid extracted from melanoma cell line

EntireName: Wild-type native PMEL amyloid extracted from melanoma cell line
Components
  • Cell: Wild-type native PMEL amyloid extracted from melanoma cell line
    • Protein or peptide: M-alpha

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Supramolecule #1: Wild-type native PMEL amyloid extracted from melanoma cell line

SupramoleculeName: Wild-type native PMEL amyloid extracted from melanoma cell line
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: M-alpha

MacromoleculeName: M-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.611115 KDa
SequenceString:
YVWKTWGQYW QVLGGPVSGL SIGTGRAMLG THT

UniProtKB: Melanocyte protein PMEL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 4.4 / Component - Concentration: 150.0 mM / Component - Formula: CH3COONa / Component - Name: Sodium acetate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 5.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 352878
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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