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- PDB-9u02: Medin fibril generated from the heterotypic interaction of Abeta4... -

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Basic information

Entry
Database: PDB / ID: 9u02
TitleMedin fibril generated from the heterotypic interaction of Abeta40 and Medin.
ComponentsLactadherin
KeywordsPROTEIN FIBRIL / Medin / Amyloid / Aggregation / MFGE8 / Neurodegeneration
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsPradhan, B. / Kumar, S.T. / Wagner, J. / Gallardo, R. / Zorzini, V. / Orlando, G. / Vleeschouwer, M.D. / Madine, J. / Louros, N. / Neher, J. ...Pradhan, B. / Kumar, S.T. / Wagner, J. / Gallardo, R. / Zorzini, V. / Orlando, G. / Vleeschouwer, M.D. / Madine, J. / Louros, N. / Neher, J. / Schymkowitz, J. / Rousseau, F.
Funding support Belgium, United States, 3items
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, S.T. / Wagner, J. / Gallardo, R. / Zorzini, V. / Orlando, G. / Vleeschouwer, M.D. / Madine, J. / Louros, N. / Neher, J. / Schymkowitz, J. / Rousseau, F.
History
DepositionJan 26, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data 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
A: Lactadherin
B: Lactadherin
F: Lactadherin
G: Lactadherin
C: Lactadherin
H: Lactadherin
D: Lactadherin
I: Lactadherin
E: Lactadherin
J: Lactadherin


Theoretical massNumber of molelcules
Total (without water)54,34910
Polymers54,34910
Non-polymers00
Water00
1


  • Idetical with deposited unit in distinct coordinate
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
point symmetry operation1_555x,y,z1

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Components

#1: Protein/peptide
Lactadherin / Breast epithelial antigen BA46 / HMFG / MFGM / Milk fat globule-EGF factor 8 / MFG-E8 / SED1


Mass: 5434.945 Da / Num. of mol.: 10 / Source method: obtained synthetically / Details: MFGE8 / Source: (synth.) Homo sapiens (human) / References: UniProt: Q08431
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: In vitro assembled Medin, resulting from the co-aggregation of recombinantly purified Amyloid Beta 40 peptide with synthetically produced Medin.
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 298 K

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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 magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.67 sec. / Electron dose: 1.313326186 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPUimage acquisition
4cryoSPARC4.7CTF correction
7Cootmodel fitting
12cryoSPARC4.7.13D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.008 ° / Axial rise/subunit: 4.804 Å / Axial symmetry: C1
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47541 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033910
ELECTRON MICROSCOPYf_angle_d0.4535280
ELECTRON MICROSCOPYf_dihedral_angle_d4.229520
ELECTRON MICROSCOPYf_chiral_restr0.066550
ELECTRON MICROSCOPYf_plane_restr0.002700

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