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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
DescriptorAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid / fibril / aggregation / Alzheimer's disease
Specimen sourceHomo sapiens / human
MethodElectron microscopy (4 Å resolution / Filament / Helical)
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.
CitationScience, 2017

Science, 2017 StrPapers
Fibril structure of amyloid-ß(1-42) by cryoelectron microscopy.
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

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

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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: Polypeptide(L)
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 / References: UniProt: P05067

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

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Sample preparation

ComponentName: Beta-amyloid protein 42 fibrils / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Escherichia coli
Buffer solutionDetails: in water / pH: 2
Buffer component
IDConc.UnitsNameBuffer 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 FIELD / 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
IDNameVersionCategoryImaging IDDetailsImage processing IDFitting ID
2EPU1.8.0.1533IMAGE ACQUISITION1
4SPARX4.0CTF CORRECTIONsxcter1
9SPARX4.0INITIAL EULER ASSIGNMENTsxhelicon1
10SPARX4.0FINAL EULER ASSIGNMENTsxheliconlocal.py1
12SPARX4.0RECONSTRUCTION1
13PHENIX1.11.1MODEL REFINEMENT1
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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