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- EMDB-39869: Amyloid beta and TTR -

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Basic information

Entry
Database: EMDB / ID: EMD-39869
TitleAmyloid beta and TTR
Map data
Sample
  • Complex: The complex of Amyloid beta and TTR
    • Protein or peptide: Amyloid-beta protein 42
    • Protein or peptide: Transthyretin
KeywordsAmyloid beta / TTR / STRUCTURAL PROTEIN
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / hippocampal neuron apoptotic process ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / hippocampal neuron apoptotic process / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of synapse structure or activity / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / astrocyte projection / Lysosome Vesicle Biogenesis / Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / The canonical retinoid cycle in rods (twilight vision) / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / purine nucleobase metabolic process / hormone binding / negative regulation of long-term synaptic potentiation / signaling receptor activator activity / Non-integrin membrane-ECM interactions / Advanced glycosylation endproduct receptor signaling / molecular sequestering activity / transition metal ion binding / phototransduction, visible light / main axon / The NLRP3 inflammasome / modulation of excitatory postsynaptic potential / regulation of multicellular organism growth / intracellular copper ion homeostasis / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / response to insulin-like growth factor stimulus / retinoid metabolic process / Retinoid metabolism and transport / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / Notch signaling pathway / cellular response to manganese ion / swimming behavior / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / astrocyte activation / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / Mitochondrial protein degradation / response to interleukin-1 / axonogenesis / protein serine/threonine kinase binding / platelet alpha granule lumen / regulation of neuron apoptotic process / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / dendritic shaft / trans-Golgi network membrane / endosome lumen / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / adult locomotory behavior / learning / Post-translational protein phosphorylation / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nerve growth factor stimulus / hormone activity / TAK1-dependent IKK and NF-kappa-B activation / recycling endosome / synapse organization / regulation of long-term neuronal synaptic plasticity / visual learning / positive regulation of JNK cascade / response to lead ion / Golgi lumen / positive regulation of interleukin-6 production / cognition
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / 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 ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / 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 / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Transthyretin / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.84 Å
AuthorsLee HN / Han CW / Jang SB / Jeong MS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Amyloid beta and TTR
Authors: Lee HN / Han CW / Jang SB / Jeong MS
History
DepositionApr 23, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39869.png

Downloads & links

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Map

FileDownload / File: emd_39869.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 262.05 Å		0.66 Å/pix.
x 400 pix.
= 262.05 Å		0.66 Å/pix.
x 400 pix.
= 262.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65513 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0278
Minimum - Maximum-0.18462503 - 0.30316448
Average (Standard dev.)-0.00007357829 (±0.009919316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-199-199-199
Dimensions400400400
Spacing400400400
CellA=B=C: 262.05002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39869_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39869_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of Amyloid beta and TTR

EntireName: The complex of Amyloid beta and TTR
Components
  • Complex: The complex of Amyloid beta and TTR
    • Protein or peptide: Amyloid-beta protein 42
    • Protein or peptide: Transthyretin

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Supramolecule #1: The complex of Amyloid beta and TTR

SupramoleculeName: The complex of Amyloid beta and TTR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Amyloid-beta protein 42

MacromoleculeName: Amyloid-beta protein 42 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.762293 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DSGYEVHHQK LVFFAEDVGS NKGAIIGLMV GGVVIA

UniProtKB: Amyloid-beta precursor protein

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Macromolecule #2: Transthyretin

MacromoleculeName: Transthyretin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.831412 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPTGTGESKR PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPFHE HAEVVFTAND SGPRRYTIAA LLSPYSYSTT AVVTNPKE

UniProtKB: Transthyretin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.82
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2trh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93330
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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