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- EMDB-56480: Medin fibril generated from the heterotypic interaction of Abeta4... -

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Basic information

Entry
Database: EMDB / ID: EMD-56480
TitleMedin fibril generated from the heterotypic interaction of Abeta40 and Medin.
Map data
Sample
  • Complex: In vitro assembled Medin, resulting from the co-aggregation of recombinantly purified Amyloid Beta 40 peptide with synthetically produced Medin.
    • Protein or peptide: Lactadherin
KeywordsMedin / Amyloid / Aggregation / MFGE8 / Neurodegeneration / PROTEIN FIBRIL
Function / homology
Function and homology information


acrosomal membrane / apoptotic cell clearance / phosphatidylserine binding / single fertilization / Post-translational protein phosphorylation / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / extracellular matrix / angiogenesis ...acrosomal membrane / apoptotic cell clearance / phosphatidylserine binding / single fertilization / Post-translational protein phosphorylation / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / extracellular matrix / angiogenesis / cell adhesion / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / : / extracellular exosome / extracellular region / membrane
Similarity search - Function
: / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. ...: / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsPradhan B / Kumar ST / Wagner J / Gallardo R / Zorzini V / Orlando G / Vleeschouwer MD / Madine J / Louros N / Neher J ...Pradhan B / Kumar ST / Wagner J / Gallardo R / Zorzini V / Orlando G / Vleeschouwer MD / Madine J / Louros N / Neher J / Schymkowitz J / Rousseau F
Funding support Belgium, United States, 3 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0C3522N Belgium
Research Foundation - Flanders (FWO)12AWB24N Belgium
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG079234 United States
CitationJournal: To Be Published
Title: Medin drives Abeta40 to adopt Abeta42-like fibril polymorphs in vitro
Authors: Pradhan B / Kumar ST / Wagner J / Gallardo R / Zorzini V / Orlando G / Vleeschouwer MD / Madine J / Louros N / Neher J / Schymkowitz J / Rousseau F
History
DepositionJan 26, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56480.png

Downloads & links

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Map

FileDownload / File: emd_56480.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.21427773 - 0.45433888
Average (Standard dev.)0.00020580474 (±0.021691058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_56480_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56480_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In vitro assembled Medin, resulting from the co-aggregation of re...

EntireName: In vitro assembled Medin, resulting from the co-aggregation of recombinantly purified Amyloid Beta 40 peptide with synthetically produced Medin.
Components
  • Complex: In vitro assembled Medin, resulting from the co-aggregation of recombinantly purified Amyloid Beta 40 peptide with synthetically produced Medin.
    • Protein or peptide: Lactadherin

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Supramolecule #1: In vitro assembled Medin, resulting from the co-aggregation of re...

SupramoleculeName: In vitro assembled Medin, resulting from the co-aggregation of recombinantly purified Amyloid Beta 40 peptide with synthetically produced Medin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Lactadherin

MacromoleculeName: Lactadherin / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.434945 KDa
SequenceString:
RLDKQGNFNA WVAGSYGNDQ WLQVDLGSSK EVTGIITQGA RNFGSVQFVA

UniProtKB: Lactadherin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 2.67 sec. / Average electron dose: 1.313326186 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.804 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.008 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 47541
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9u02:
Medin fibril generated from the heterotypic interaction of Abeta40 and Medin.

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