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- PDB-8owe: Lipidic amyloid-beta(1-40) fibril - polymorph L2-L3 -

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Basic information

Entry
Database: PDB / ID: 8owe
TitleLipidic amyloid-beta(1-40) fibril - polymorph L2-L3
ComponentsAmyloid-beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid-beta / fibril / lipids
Function / homology
Function and homology information


Golgi-associated vesicle / clathrin-coated pit / serine-type endopeptidase inhibitor activity / endocytosis / heparin binding / growth cone / perikaryon / early endosome / cell surface / endoplasmic reticulum ...Golgi-associated vesicle / clathrin-coated pit / serine-type endopeptidase inhibitor activity / endocytosis / heparin binding / growth cone / perikaryon / early endosome / cell surface / endoplasmic reticulum / extracellular region / metal ion binding / 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: 3.75 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 27, 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
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"
d_6ens_1(chain "F" and resid 4 through 40)
d_7ens_1(chain "G" and resid 4 through 40)
d_8ens_1(chain "H" and resid 4 through 40)
d_9ens_1(chain "I" and resid 4 through 40)
d_10ens_1(chain "J" and resid 4 through 40)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PHEVALA1 - 37
d_21ens_1PHEVALB1 - 37
d_31ens_1PHEVALC1 - 37
d_41ens_1PHEVALD1 - 37
d_51ens_1PHEVALE1 - 37
d_61ens_1PHEVALF4 - 40
d_71ens_1PHEVALG4 - 40
d_81ens_1PHEVALH4 - 40
d_91ens_1PHEVALI4 - 40
d_101ens_1PHEVALJ4 - 40

NCS oper:
IDCodeMatrixVector
1given(0.999567698096, 0.0294009680526, 1.87397994437E-7), (-0.0294009680528, 0.999567698095, 1.33926245217E-6), (-1.47941369357E-7, -1.34419316891E-6, 0.999999999999)-3.80212446688, 3.91544340793, 4.65015967439
2given(0.998271294566, 0.058774334918, -1.91375070882E-7), (-0.058774334918, 0.998271294566, 3.56802398716E-7), (2.12015063439E-7, -3.4493764996E-7, 1)-7.4871729577, 7.94098356988, 9.3000102919
3given(0.996111947447, 0.0880964707245, -5.28165318744E-8), (-0.0880964707245, 0.996111947447, 1.90178098711E-7), (6.93651977283E-8, -1.84785726215E-7, 1)-11.0523286716, 12.0729150289, 13.9500095118
4given(0.993091244, 0.117344710531, -6.84063640165E-7), (-0.117344710531, 0.993091244, -4.27442766967E-8), (6.74321796611E-7, 1.22720216759E-7, 1)-14.4945919169, 16.3082725318, 18.599904759
5given(0.455152678024, 0.878631152702, 0.14437221751), (-0.825988160377, 0.477186744066, -0.300060610886), (-0.332535108831, 0.0173236482635, 0.942931753949)-23.4791742699, 254.139550049, 49.0210210746
6given(0.43067262017, 0.892280176628, 0.13548867345), (-0.839012251568, 0.451149634977, -0.304175029512), (-0.332535014629, 0.0173231999769, 0.942931795406)-19.7995050731, 258.635334212, 53.6710483568
7given(0.405820902692, 0.905157427519, 0.126488838819), (-0.851310550711, 0.424723401502, -0.30802658727), (-0.332535323216, 0.0173223446656, 0.942931702293)-15.9893945047, 263.020765481, 58.3211890062
8given(0.380617158714, 0.917253095879, 0.117376899743), (-0.862873747607, 0.397927948994, -0.311612328223), (-0.33253492175, 0.0173235536248, 0.942931821664)-12.051554412, 267.292705655, 62.9709965001
9given(0.355085626312, 0.928554636424, 0.108168780901), (-0.873689923282, 0.370791437524, -0.314927972423), (-0.332535886698, 0.0173204224443, 0.942931538885)-7.99064694608, 271.446487679, 67.6214815091

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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 L2-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 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: -1.69 ° / Axial rise/subunit: 4.65 Å / Axial symmetry: C1
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13034 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.72 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01383000
ELECTRON MICROSCOPYf_angle_d2.46534020
ELECTRON MICROSCOPYf_chiral_restr0.1703425
ELECTRON MICROSCOPYf_plane_restr0.0277525
ELECTRON MICROSCOPYf_dihedral_angle_d22.52071020
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.00057792683083
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000416273797662
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000569129444607
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000574121172222
ens_1d_6AELECTRON MICROSCOPYNCS constraints4.18554118546
ens_1d_7AELECTRON MICROSCOPYNCS constraints4.18553927891
ens_1d_8AELECTRON MICROSCOPYNCS constraints4.18552525089
ens_1d_9AELECTRON MICROSCOPYNCS constraints4.18553375762
ens_1d_10AELECTRON MICROSCOPYNCS constraints4.18553669987

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