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- PDB-5oqv: Near-atomic resolution fibril structure of complete amyloid-beta(... -

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Basic information

Entry
Database: PDB / ID: 5oqv
TitleNear-atomic resolution fibril structure of complete amyloid-beta(1-42) by cryo-EM
ComponentsAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid / fibril / aggregation / Alzheimer's disease / Protein fibril
Function / homologyRIP-mediated NFkB activation via ZBP1 / Proteinase inhibitor I2, Kunitz, conserved site / The NLRP3 inflammasome / Amyloidogenic glycoprotein, copper-binding domain superfamily / G alpha (q) signalling events / Amyloidogenic glycoprotein, heparin-binding domain superfamily / G alpha (i) signalling events / E2 domain superfamily / Amyloid beta A4 protein / Lysosome Vesicle Biogenesis ...RIP-mediated NFkB activation via ZBP1 / Proteinase inhibitor I2, Kunitz, conserved site / The NLRP3 inflammasome / Amyloidogenic glycoprotein, copper-binding domain superfamily / G alpha (q) signalling events / Amyloidogenic glycoprotein, heparin-binding domain superfamily / G alpha (i) signalling events / E2 domain superfamily / Amyloid beta A4 protein / Lysosome Vesicle Biogenesis / Amyloidogenic glycoprotein, E2 domain / Amyloidogenic glycoprotein, intracellular domain, conserved site / Pancreatic trypsin inhibitor Kunitz domain superfamily / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / Amyloidogenic glycoprotein, extracellular domain conserved site / Formyl peptide receptors bind formyl peptides and many other ligands / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, heparin-binding / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Amyloidogenic glycoprotein, amyloid-beta peptide / Pancreatic trypsin inhibitor Kunitz domain / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein / Advanced glycosylation endproduct receptor signaling / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / PH-like domain superfamily / Copper-binding of amyloid precursor, CuBD / Platelet degranulation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Pancreatic trypsin inhibitor (Kunitz) family profile. / ECM proteoglycans / Amyloidogenic glycoprotein intracellular domain signature. / Amyloid fiber formation / Amyloidogenic glycoprotein extracellular domain signature. / Pancreatic trypsin inhibitor (Kunitz) family signature. / E2 domain of amyloid precursor protein / TRAF6 mediated NF-kB activation / Post-translational protein phosphorylation / beta-amyloid precursor protein C-terminus / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Beta-amyloid peptide (beta-APP) / Amyloid A4 N-terminal heparin-binding / Kunitz/Bovine pancreatic trypsin inhibitor domain / Amyloidogenic glycoprotein, copper-binding / positive regulation of cellular response to tunicamycin / positive regulation of G-protein coupled receptor internalization / positive regulation of protein import / regulation of acetylcholine-gated cation channel activity / amylin binding / positive regulation of cellular response to thapsigargin / positive regulation of 1-phosphatidylinositol-3-kinase activity / heparan sulfate binding / receptor activator activity / positive regulation of response to endoplasmic reticulum stress / regulation of response to calcium ion / acetylcholine receptor activator activity / regulation of dendritic spine maintenance / endosome to plasma membrane transport vesicle / collateral sprouting in absence of injury / cellular response to norepinephrine stimulus / lipoprotein particle / positive regulation of oxidative stress-induced neuron death / synaptic growth at neuromuscular junction / microglia development / growth cone lamellipodium / regulation of synapse structure or activity / negative regulation of mitochondrion organization / mating behavior / regulation of amyloid fibril formation / astrocyte projection / smooth endoplasmic reticulum calcium ion homeostasis / protein trimerization / regulation of epidermal growth factor-activated receptor activity / growth cone filopodium / regulation of spontaneous synaptic transmission / axo-dendritic transport / cellular process / tumor necrosis factor production / axon midline choice point recognition / astrocyte activation involved in immune response / positive regulation of astrocyte activation / intermediate-density lipoprotein particle / positive regulation of amyloid fibril formation / suckling behavior / PTB domain binding / go:0030816: / modulation of excitatory postsynaptic potential / positive regulation of microglial cell activation / neuron remodeling / amyloid-beta complex / acetylcholine receptor binding / positive regulation of G-protein coupled receptor protein signaling pathway / main axon / activation of MAPKKK activity / positive regulation of amyloid-beta formation / ciliary rootlet / positive regulation of cell activation / high-density lipoprotein particle / lipoprotein metabolic process / peptidase activator activity
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4 Å resolution
AuthorsGremer, L. / Schoelzel, D. / Schenk, C. / Reinartz, E. / Labahn, J. / Ravelli, R. / Tusche, M. / Lopez-Iglesias, C. / Hoyer, W. / Heise, H. / Willbold, D. / Schroeder, G.F.
CitationJournal: Science / Year: 2017
Title: Fibril structure of amyloid-β(1-42) by cryo-electron microscopy.
Authors: Lothar Gremer / Daniel Schölzel / Carla Schenk / Elke Reinartz / Jörg Labahn / Raimond B G Ravelli / Markus Tusche / Carmen Lopez-Iglesias / Wolfgang Hoyer / Henrike Heise / Dieter Willbold / Gunnar F Schröder
Abstract: Amyloids are implicated in neurodegenerative diseases. Fibrillar aggregates of the amyloid-β protein (Aβ) are the main component of the senile plaques found in brains of Alzheimer's disease ...Amyloids are implicated in neurodegenerative diseases. Fibrillar aggregates of the amyloid-β protein (Aβ) are the main component of the senile plaques found in brains of Alzheimer's disease patients. We present the structure of an Aβ(1-42) fibril composed of two intertwined protofilaments determined by cryo-electron microscopy (cryo-EM) to 4.0-angstrom resolution, complemented by solid-state nuclear magnetic resonance experiments. The backbone of all 42 residues and nearly all side chains are well resolved in the EM density map, including the entire N terminus, which is part of the cross-β structure resulting in an overall "LS"-shaped topology of individual subunits. The dimer interface protects the hydrophobic C termini from the solvent. The characteristic staggering of the nonplanar subunits results in markedly different fibril ends, termed "groove" and "ridge," leading to different binding pathways on both fibril ends, which has implications for fibril growth.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 14, 2017 / Release: Sep 13, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 13, 2017Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.2Sep 27, 2017Structure modelStructure summarystruct_keywords_struct_keywords.text
1.3Oct 18, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

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Structure viewerMolecule:
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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


Theoretical massNumber of molelcules
Total (without water)40,6819
Polyers40,6819
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)29420
ΔGint (kcal/M)-125
Surface area (Å2)15810
MethodPISA

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Components

#1: Protein/peptide
Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid precursor protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 4520.087 Da / Num. of mol.: 9 / Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05067

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Beta-amyloid protein 42 fibrilsAmyloid beta / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionDetails: in water / pH: 2
Buffer component
IDConc.NameBuffer ID
130 % (v/v)acetonitrile1
20.1 % (v/v)trifluoroacetic acid1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: UltrAuFoil R 1.2/1.3 Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: 2.5 microL sample was applied to the grid, blotted for 2.5 s before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 110000 / Cs: 2.7 mm
Image recordingAverage exposure time: 2 sec. / Electron dose: 24 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2026

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Processing

EM software
IDNameVersionCategoryDetails
2EPU1.8.0.1533image acquisition
4SPARX4.0CTF correctionsxcter
9SPARX4.0initial Euler assignmentsxhelicon
10SPARX4.0final Euler assignmentsxheliconlocal.py
12SPARX4.03D reconstruction
13PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -179.275 deg. / Axial rise/subunit: 2.335 Å / Axial symmetry: C1
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 127765
Details: For the even/odd test, the fibrils were split after the final reconstruction (no gold-standard). These two half sets were then refined further independently for another 12 iterations.
Number of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL / Target criteria: Cross-correlation coefficient

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