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- PDB-8owk: Lipidic amyloid-beta(1-40) fibril - polymorph L3-L3 -

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Basic information

Entry
Database: PDB / ID: 8owk
TitleLipidic amyloid-beta(1-40) fibril - polymorph L3-L3
ComponentsAmyloid-beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid-beta / fibril / lipids
Function / homology
Function and homology information


Golgi-associated vesicle / clathrin-coated pit / heparin binding / growth cone / perikaryon / early endosome / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular region / nucleus
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. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / Amyloidogenic glycoprotein, extracellular ...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. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 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: 3.86 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 28, 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
F: Amyloid-beta A4 protein
G: Amyloid-beta A4 protein
H: Amyloid-beta A4 protein
I: Amyloid-beta A4 protein
J: Amyloid-beta A4 protein


Theoretical massNumber of molelcules
Total (without water)43,35910
Polymers43,35910
Non-polymers00
Water0
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"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 1 - 40 / Label seq-ID: 1 - 40

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(0.998664836275, -0.0516503695439, 0.0008855016183), (0.0516511699528, 0.998664776315, -0.000906195127801), (-0.000837513962336, 0.000950722403519, 0.999999197348)6.86338043625, -6.56798142458, -9.41078017904
2given(0.999674986881, -0.0254703803375, -0.0010864300547), (0.0254715056332, 0.99967501296, 0.00103482568852), (0.00105971957514, -0.00106216236586, 0.999998874402)3.56289751346, -3.41145246398, -4.64183410761
3given(0.999644508301, 0.0265555921789, -0.00237855980976), (-0.0265527991023, 0.999646694106, 0.00119825829047), (0.00240953990904, -0.00113467489881, 0.999996453309)-3.08691823984, 3.40322758001, 4.52341333407
4given(0.998481813929, 0.0550759247537, -0.000842476316536), (-0.0550758042671, 0.99848216227, 0.000165570016805), (0.000850316495983, -0.000118918590002, 0.99999963141)-6.9606907534, 7.43454746073, 9.23011761861
5given(-0.999999838758, -0.000567826267192, 7.54145736073E-6), (0.000567821965384, -0.999999682731, -0.000558673355847), (7.85868437429E-6, -0.00055866898356, 0.999999843914)262.558469941, 262.480303713, 0.0814281240388
6given(-0.998664836275, 0.0516503695439, -0.000885501617696), (-0.0516511699529, -0.998664776315, 0.000906195127375), (-0.000837513961756, 0.000950722403063, 0.999999197348)255.636619564, 269.067981425, -9.41078017904
7given(-0.999674986881, 0.0254703803375, 0.00108643005485), (-0.0254715056332, -0.99967501296, -0.00103482568864), (0.00105971957529, -0.00106216236597, 0.999998874402)258.937102487, 265.911452464, -4.64183410761
8given(-0.999644508301, -0.0265555921789, 0.00237855980976), (0.0265527991023, -0.999646694106, -0.00119825829049), (0.00240953990904, -0.00113467489883, 0.999996453309)265.58691824, 259.09677242, 4.52341333407
9given(-0.998481813929, -0.0550759247538, 0.000842476315722), (0.0550758042673, -0.99848216227, -0.00016557001609), (0.00085031649513, -0.000118918589333, 0.99999963141)269.460690754, 255.065452539, 9.23011761861

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Components

#1: Protein/peptide
Amyloid-beta A4 protein


Mass: 4335.852 Da / Num. of mol.: 10
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 L3-L3 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 FIELDBright-field microscopy / 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: -1.52 ° / Axial rise/subunit: 4.65 Å / Axial symmetry: C2
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19050 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 124.93 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01263110
ELECTRON MICROSCOPYf_angle_d3.09044170
ELECTRON MICROSCOPYf_chiral_restr0.1211440
ELECTRON MICROSCOPYf_plane_restr0.008550
ELECTRON MICROSCOPYf_dihedral_angle_d7.40181060
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000725889544555
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000733323704118
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.00070616852473
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000704878349196
ens_1d_6AELECTRON MICROSCOPYNCS constraints0.0007298158405
ens_1d_7AELECTRON MICROSCOPYNCS constraints0.000725889544555
ens_1d_8AELECTRON MICROSCOPYNCS constraints0.00073332370412
ens_1d_9AELECTRON MICROSCOPYNCS constraints0.000706168524732
ens_1d_10AELECTRON MICROSCOPYNCS constraints0.000704878349195

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