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- EMDB-31428: Cryo-EM structure of the fibril formed by disaccharide-modified a... -

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Basic information

Entry
Database: EMDB / ID: EMD-31428
TitleCryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42)
Map data
Sample
  • Organelle or cellular component: Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42)
    • Protein or peptide: Amyloid-beta A4 protein
  • Ligand: ACETIC ACID
Keywordsamyloid fibril / PROTEIN FIBRIL
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsXia WC / Sun YP / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: O-Glycosylation Induces Amyloid-beta To Form New Fibril Polymorphs Vulnerable for Degradation
Authors: Liu D / Wei Q / Xia W / He C / Zhang Q / Huang L / Wang X / Sun Y / Ma Y / Zhang X / Wang Y / Shi X / Liu C / Dong S
History
DepositionJun 10, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31428.png

Downloads & links

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Map

FileDownload / File: emd_31428.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 208 pix.
= 220.48 Å		1.06 Å/pix.
x 208 pix.
= 220.48 Å		1.06 Å/pix.
x 208 pix.
= 220.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0211
Minimum - Maximum-0.054166462 - 0.10085359
Average (Standard dev.)0.0002648145 (±0.0031887398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 220.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the fibril formed by disaccharide-modified a...

EntireName: Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42)
Components
  • Organelle or cellular component: Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42)
    • Protein or peptide: Amyloid-beta A4 protein
  • Ligand: ACETIC ACID

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Supramolecule #1: Cryo-EM structure of the fibril formed by disaccharide-modified a...

SupramoleculeName: Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42)
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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Macromolecule #1: Amyloid-beta A4 protein

MacromoleculeName: Amyloid-beta A4 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.90044 KDa
SequenceString:
HDSGYEVHHQ KLVFFAEDVG SNKGAIIGLM VGGVVIA

UniProtKB: Amyloid-beta A4 protein

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Macromolecule #3: ACETIC ACID

MacromoleculeName: ACETIC ACID / type: ligand / ID: 3 / Number of copies: 6 / Formula: ACY
Molecular weightTheoretical: 60.052 Da
Chemical component information

ChemComp-ACY:
ACETIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.324 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92523
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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