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- PDB-8ovm: Lipidic amyloid-beta(1-40) fibril - polymorph L2 -

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Basic information

Entry
Database: PDB / ID: 8ovm
TitleLipidic amyloid-beta(1-40) fibril - polymorph L2
ComponentsAmyloid-beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid-beta / fibril / lipids
Function / homology
Function and homology information


signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft ...signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular region / nucleus / plasma membrane
Similarity search - Function
Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain ...Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta A4 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsFrieg, B. / Han, M. / Giller, K. / Dienemann, C. / Riedel, D. / Becker, S. / Andreas, L.B. / Griesinger, C. / Schroeder, G.F.
Funding support Germany, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
Helmholtz Association Germany
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of lipidic fibrils of amyloid-β (1-40).
Authors: Benedikt Frieg / Mookyoung Han / Karin Giller / Christian Dienemann / Dietmar Riedel / Stefan Becker / Loren B Andreas / Christian Griesinger / Gunnar F Schröder /
Abstract: Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques ...Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques revealed a high amount of amyloid-β (Aβ) fibrils and a high concentration of lipids, suggesting that fibril-lipid interactions may also be relevant for the pathogenesis of AD. Therefore, we grew Aβ40 fibrils in the presence of lipid vesicles and determined their structure by cryo-electron microscopy (cryo-EM) to high resolution. The fold of the major polymorph is similar to the structure of brain-seeded fibrils reported previously. The majority of the lipids are bound to the fibrils, as we show by cryo-EM and NMR spectroscopy. This apparent lipid extraction from vesicles observed here in vitro provides structural insights into potentially disease-relevant fibril-lipid interactions.
History
DepositionApr 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 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: Amyloid-beta A4 protein
B: Amyloid-beta A4 protein
C: Amyloid-beta A4 protein
D: Amyloid-beta A4 protein
E: Amyloid-beta A4 protein


Theoretical massNumber of molelcules
Total (without water)21,6795
Polymers21,6795
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGVALA1 - 36
d_21ens_1ARGVALB1 - 36
d_31ens_1ARGVALC1 - 36
d_41ens_1ARGVALD1 - 36
d_51ens_1ARGVALE1 - 36

NCS oper:
IDCodeMatrixVector
1given(0.999219754962, 0.0394923893897, 0.000482155169666), (-0.0394924060539, 0.999219870316, 2.50865488273E-5), (-0.000480788298351, -4.41084429136E-5, 0.999999883449)-4.99258891674, 5.13050986119, 4.74332732916
2given(0.996999340405, 0.0773755640406, -0.00231026419938), (-0.0773732788283, 0.997001627969, 0.00106280340413), (0.00238557218067, -0.000880861576829, 0.999996766559)-9.20306682944, 10.1763076997, 9.14425178591
3given(0.993004427528, 0.118075998656, 0.000515219837685), (-0.118076007573, 0.993004560041, -1.31835454518E-5), (-0.00051317230854, -4.77437824521E-5, 0.999999867187)-14.2236385947, 15.9460923219, 14.099481169
4given(0.987580396639, 0.157113692071, 0.000497933681677), (-0.157113691874, 0.987580521398, -3.97558239266E-5), (-0.000497995789251, -3.89701266746E-5, 0.999999875241)-18.5072718534, 21.6197257844, 18.7734125794

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Components

#1: Protein/peptide
Amyloid-beta A4 protein


Mass: 4335.852 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4DM00

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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: The L2 amyloid-beta(1-40) fibril in complex with lipids
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 6.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -2.26 ° / Axial rise/subunit: 4.67 Å / Axial symmetry: C1
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83126 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 94.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00671385
ELECTRON MICROSCOPYf_angle_d0.98831855
ELECTRON MICROSCOPYf_chiral_restr0.0897200
ELECTRON MICROSCOPYf_plane_restr0.002240
ELECTRON MICROSCOPYf_dihedral_angle_d11.0014475
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000705239263288
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000559000667689
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000709921620895
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000745801785948

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