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- PDB-9wtw: Amyloid-beta 40 Flemish (A21G) mutant Filaments from Human Brain -

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Basic information

Entry
Database: PDB / ID: 9wtw
TitleAmyloid-beta 40 Flemish (A21G) mutant Filaments from Human Brain
ComponentsAmyloid-beta protein 40
KeywordsPROTEIN FIBRIL / Amyloid-beta / Alzheimer's disease / Neurodegeneration / Protein aggregation
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 / 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 / Golgi-associated vesicle / PTB domain binding / astrocyte projection / neuron remodeling / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / dendrite development / regulation of multicellular organism growth / nuclear envelope lumen / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / transition metal ion binding / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / modulation of excitatory postsynaptic potential / intracellular copper ion homeostasis / Notch signaling pathway / main axon / ECM proteoglycans / response to insulin-like growth factor stimulus / positive regulation of T cell migration / regulation of presynapse assembly / neuronal dense core vesicle / swimming behavior / adult locomotory behavior / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of calcium-mediated signaling / extracellular matrix organization / positive regulation of mitotic cell cycle / axonogenesis / cellular response to manganese ion / neuron projection maintenance / clathrin-coated pit / astrocyte activation / regulation of neuron apoptotic process / Mitochondrial protein degradation / positive regulation of glycolytic process / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / learning / response to interleukin-1 / cellular response to cAMP / cellular response to copper ion / endosome lumen / trans-Golgi network membrane / locomotory behavior / positive regulation of interleukin-1 beta production / dendritic shaft / central nervous system development / positive regulation of long-term synaptic potentiation / protein serine/threonine kinase binding / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / microglial cell activation / cellular response to nerve growth factor stimulus / visual learning / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / synapse organization / positive regulation of interleukin-6 production / recycling endosome / positive regulation of JNK cascade / response to lead ion / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / endocytosis / neuron projection development / positive regulation of inflammatory response / calcium ion transport / positive regulation of tumor necrosis factor production / regulation of translation / regulation of gene expression / Platelet degranulation / heparin binding
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. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsGuillen-Poza, P.A. / Yang, Y. / Hervas, R.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Other government Hong Kong
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2026
Title: Distinct amyloid-beta filament fold in individuals with APP Flemish mutation
Authors: Khaki, P.S.S. / Guillen-Poza, P.A. / Wong, C. / Robinson, A.C. / Ng, R.C.-L. / Yang, Y. / Hervas, R.
History
DepositionSep 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Amyloid-beta protein 40
J: Amyloid-beta protein 40
I: Amyloid-beta protein 40
H: Amyloid-beta protein 40
G: Amyloid-beta protein 40
A: Amyloid-beta protein 40
D: Amyloid-beta protein 40
C: Amyloid-beta protein 40
F: Amyloid-beta protein 40
E: Amyloid-beta protein 40


Theoretical massNumber of molelcules
Total (without water)43,21810
Polymers43,21810
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Amyloid-beta protein 40 / Abeta40 / Beta-APP40


Mass: 4321.826 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05067
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Amyloid-beta 40 (A21G) Flemish filaments extracted from human brain with Alzheimer's disease
Type: TISSUE / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.817 ° / Axial rise/subunit: 4.882 Å / Axial symmetry: C2
3D reconstructionResolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38206 / Symmetry type: HELICAL
RefinementResolution: 1.98→1.98 Å / Cor.coef. Fo:Fc: 0.821 / SU B: 4.481 / SU ML: 0.104 / ESU R: 0.066
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.3557 --
obs0.3557 85783 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 54.546 Å2
Refinement stepCycle: 1 / Total: 602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.012606
ELECTRON MICROSCOPYr_bond_other_d00.016560
ELECTRON MICROSCOPYr_angle_refined_deg1.4671.795812
ELECTRON MICROSCOPYr_angle_other_deg0.5761.7471284
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.074576
ELECTRON MICROSCOPYr_dihedral_angle_2_deg1.6352
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.2331096
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.080.284
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.02720
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02144
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it4.4714.496310
ELECTRON MICROSCOPYr_mcbond_other4.4554.491310
ELECTRON MICROSCOPYr_mcangle_it7.0218.043384
ELECTRON MICROSCOPYr_mcangle_other7.0458.056385
ELECTRON MICROSCOPYr_scbond_it9.9016.419296
ELECTRON MICROSCOPYr_scbond_other9.8856.427297
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other16.29111.012429
ELECTRON MICROSCOPYr_long_range_B_refined20.12646.58510
ELECTRON MICROSCOPYr_long_range_B_other20.04846.63509
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.714 6367 -
obs--100 %

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