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- PDB-9lip: The cryo-EM structure of the native PMEL fibril lamella -

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Basic information

Entry
Database: PDB / ID: 9lip
TitleThe cryo-EM structure of the native PMEL fibril lamella
Components
  • (M-alpha) x 3
  • M-beta
KeywordsPROTEIN FIBRIL / PMEL
Function / homology
Function and homology information


cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome organization / melanosome membrane / 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 organization / melanosome membrane / 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: 3.48 Å
AuthorsMa, B.Y. / Yao, Y.X. / Dong, H. / Li, D. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Atomic structure and in situ visualization of native PMEL lamellae in melanosomes.
Authors: Boyuan Ma / Yuxuan Yao / Hui Dong / Linli Yang / Danni Li / Qinyue Zhao / Bo Sun / Yong Chen / Cong Liu / Dan Li /
Abstract: Melanin synthesis within melanosomes critically depends on the fibrillar architecture formed by the pigment cell-specific protein PMEL. Although PMEL fibrils have historically been classified as ...Melanin synthesis within melanosomes critically depends on the fibrillar architecture formed by the pigment cell-specific protein PMEL. Although PMEL fibrils have historically been classified as functional amyloids, their native supramolecular organization in situ and detailed molecular architecture have remained unresolved. In this study, we combine in situ cryo-electron tomography (cryo-ET) and cryo-electron microscopy (cryo-EM) to elucidate the native structural organization of PMEL fibrils within human melanosomes from both patient melanoma tissues and melanocyte cell lines. We demonstrate that PMEL does not form conventional isolated amyloid fibrils, but rather assembles into highly organized lamellar sheets consisting of laterally aligned fibrils interconnected by flexible linker regions. Cryo-EM structures reveal a distinctive butterfly-shaped fibril unit composed of multiple structured domains, including both the proteolytically cleaved Mα and Mβ fragments of PMEL, which assemble into a amyloid-like β-sheet arrangement. Notably, we identify intrinsically disordered regions critical for lamellar assembly and curvature and verify key glycosylation modifications in the structure. This architecture distinguishes PMEL fibrils from canonical amyloids and elucidates the molecular basis underlying melanosome integrity and pigmentation. Moreover, our work provides molecular insights relevant for pigmentation disorders and PMEL-associated diseases, including melanoma.
History
DepositionJan 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Q: M-alpha
R: M-alpha
S: M-alpha
T: M-beta
U: M-alpha
V: M-alpha
W: M-alpha
X: M-beta
A: M-alpha
B: M-alpha
C: M-alpha
D: M-beta
E: M-alpha
F: M-alpha
G: M-alpha
H: M-beta
I: M-alpha
J: M-alpha
K: M-alpha
L: M-beta
M: M-alpha
N: M-alpha
O: M-alpha
P: M-beta
g: M-alpha
h: M-alpha
i: M-alpha
j: M-beta
k: M-alpha
l: M-alpha
m: M-alpha
n: M-beta
Y: M-alpha
Z: M-alpha
a: M-alpha
b: M-beta
c: M-alpha
d: M-alpha
e: M-alpha
f: M-beta
o: M-alpha
p: M-alpha
q: M-alpha
r: M-beta
s: M-alpha
t: M-alpha
u: M-alpha
v: M-beta


Theoretical massNumber of molelcules
Total (without water)240,66848
Polymers240,66848
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: 2389.683 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40967
#2: Protein
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: 8272.350 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40967
#3: Protein
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: 7429.333 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40967
#4: Protein/peptide
M-beta


Mass: 1964.267 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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: PMEL / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 382507 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417400
ELECTRON MICROSCOPYf_angle_d0.65423772
ELECTRON MICROSCOPYf_dihedral_angle_d15.0939948
ELECTRON MICROSCOPYf_chiral_restr0.0482784
ELECTRON MICROSCOPYf_plane_restr0.0052952

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