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- PDB-8z9v: Amyloid beta and TTR -

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Basic information

Entry
Database: PDB / ID: 8z9v
TitleAmyloid beta and TTR
Components
  • Amyloid-beta protein 42
  • Transthyretin
KeywordsSTRUCTURAL PROTEIN / Amyloid beta / TTR
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / regulation of synapse structure or activity / positive regulation of synaptic transmission, cholinergic / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / PTB domain binding / astrocyte projection / Golgi-associated vesicle / neuron remodeling / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Defective visual phototransduction due to STRA6 loss of function / regulation of multicellular organism growth / dendrite development / nuclear envelope lumen / The canonical retinoid cycle in rods (twilight vision) / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / purine nucleobase metabolic process / hormone binding / negative regulation of long-term synaptic potentiation / signaling receptor activator activity / transition metal ion binding / Non-integrin membrane-ECM interactions / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / intracellular copper ion homeostasis / modulation of excitatory postsynaptic potential / Notch signaling pathway / main axon / ECM proteoglycans / molecular sequestering activity / response to insulin-like growth factor stimulus / positive regulation of T cell migration / regulation of presynapse assembly / extracellular matrix organization / swimming behavior / neuronal dense core vesicle / adult locomotory behavior / regulation of long-term neuronal synaptic plasticity / Purinergic signaling in leishmaniasis infection / Retinoid metabolism and transport / positive regulation of chemokine production / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / axonogenesis / cellular response to manganese ion / retinoid metabolic process / neuron projection maintenance / clathrin-coated pit / cellular response to cAMP / visual learning / astrocyte activation / synaptic cleft / regulation of neuron apoptotic process / positive regulation of glycolytic process / Mitochondrial protein degradation / platelet alpha granule lumen / ionotropic glutamate receptor signaling pathway / response to interleukin-1 / learning / locomotory behavior / cellular response to copper ion / endosome lumen / trans-Golgi network membrane / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / central nervous system development / dendritic shaft / protein serine/threonine kinase binding / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / microglial cell activation / cellular response to nerve growth factor stimulus / hormone activity / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / endocytosis / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of JNK cascade / recycling endosome / Golgi lumen / response to lead ion
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, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...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, heparin-binding / Amyloid A4 N-terminal heparin-binding / 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, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Transthyretin, conserved site / Transthyretin signature 2. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / PH-like domain superfamily
Similarity search - Domain/homology
Transthyretin / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.84 Å
AuthorsLee, H.N. / Han, C.W. / Jang, S.B. / Jeong, M.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Amyloid beta and TTR
Authors: Lee, H.N. / Han, C.W. / Jang, S.B. / Jeong, M.S.
History
DepositionApr 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
e: Amyloid-beta protein 42
b: Transthyretin
A: Transthyretin


Theoretical massNumber of molelcules
Total (without water)31,4253
Polymers31,4253
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Amyloid-beta protein 42 / Abeta42 / Beta-APP42


Mass: 3762.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05067
#2: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13831.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The complex of Amyloid beta and TTR / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.82
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93330 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00662273
ELECTRON MICROSCOPYf_angle_d1.16363092
ELECTRON MICROSCOPYf_chiral_restr0.0635347
ELECTRON MICROSCOPYf_plane_restr0.0083399
ELECTRON MICROSCOPYf_dihedral_angle_d14.42991337

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