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- PDB-6oiz: Amyloid-Beta (20-34) wild type -

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Basic information

Entry
Database: PDB / ID: 6oiz
TitleAmyloid-Beta (20-34) wild type
ComponentsAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / protofilament / 2 sub 1 screw symmetry
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity ...regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / : / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Mitochondrial protein degradation / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / positive regulation of mitotic cell cycle / response to interleukin-1 / adult locomotory behavior / extracellular matrix organization / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / neuron cellular homeostasis / Golgi lumen / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / endocytosis / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle
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. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 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 A4 protein / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / AB INITIO PHASING / cryo EM / Resolution: 1.1 Å
Model detailsProtofilament structure of Amyloid-beta 20-34 with the age-associated post-translational ...Protofilament structure of Amyloid-beta 20-34 with the age-associated post-translational modification of aspartate isomerization at position 23
AuthorsSawaya, M.R. / Warmack, R.A. / Zee, C.T. / Gonen, T. / Clarke, S.G. / Eisenberg, D.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)5T32GM008496 United States
National Science Foundation (NSF, United States)MCB-1714569 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM-007185 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2019
Title: Structure of amyloid-β (20-34) with Alzheimer's-associated isomerization at Asp23 reveals a distinct protofilament interface.
Authors: Rebeccah A Warmack / David R Boyer / Chih-Te Zee / Logan S Richards / Michael R Sawaya / Duilio Cascio / Tamir Gonen / David S Eisenberg / Steven G Clarke /
Abstract: Amyloid-β (Aβ) harbors numerous posttranslational modifications (PTMs) that may affect Alzheimer's disease (AD) pathogenesis. Here we present the 1.1 Å resolution MicroED structure of an Aβ 20- ...Amyloid-β (Aβ) harbors numerous posttranslational modifications (PTMs) that may affect Alzheimer's disease (AD) pathogenesis. Here we present the 1.1 Å resolution MicroED structure of an Aβ 20-34 fibril with and without the disease-associated PTM, L-isoaspartate, at position 23 (L-isoAsp23). Both wild-type and L-isoAsp23 protofilaments adopt β-helix-like folds with tightly packed cores, resembling the cores of full-length fibrillar Aβ structures, and both self-associate through two distinct interfaces. One of these is a unique Aβ interface strengthened by the isoaspartyl modification. Powder diffraction patterns suggest a similar structure may be adopted by protofilaments of an analogous segment containing the heritable Iowa mutation, Asp23Asn. Consistent with its early onset phenotype in patients, Asp23Asn accelerates aggregation of Aβ 20-34, as does the L-isoAsp23 modification. These structures suggest that the enhanced amyloidogenicity of the modified Aβ segments may also reduce the concentration required to achieve nucleation and therefore help spur the pathogenesis of AD.
History
DepositionApr 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 7, 2022Group: Data collection / Database references / Category: database_2 / em_diffraction_shell
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_diffraction_shell.em_diffraction_stats_id / _em_diffraction_shell.id
Revision 1.3May 15, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)1,4921
Polymers1,4921
Non-polymers00
Water1267
1
A: Amyloid beta A4 protein
x 5


Theoretical massNumber of molelcules
Total (without water)7,4585
Polymers7,4585
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
Unit cell
Length a, b, c (Å)33.170, 4.780, 30.330
Angle α, β, γ (deg.)90.000, 111.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Amyloid beta A4 protein


Mass: 1491.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: L7XCZ9, UniProt: P05067*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: crystal of amyloid-beta residues 20-34 wild type / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 6.21 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
EM crystal formationInstrument: Varioscan plate reader / Atmosphere: air / Details: shaken at 1200 rpm / Temperature: 310 K / Time: 30 HOUR
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1water1
250 mMtris base1
3150 mMNaCl1
41 %dimethylsulfoxide1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample is a crystal.
Specimen supportDetails: 30 seconds on each side / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Chamber temperature: 100 K
CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 18.21 %

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Data collection

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K
Image recordingAverage exposure time: 3 sec. / Electron dose: 0.01 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Num. of diffraction images: 404 / Num. of grids imaged: 2
Image scansWidth: 2048 / Height: 2048
EM diffractionCamera length: 1050 mm
EM diffraction shellResolution: 1→1.05 Å / Fourier space coverage: 41.2 % / Multiplicity: 3.09 / Num. of structure factors: 315 / Phase residual: 0.1 °
EM diffraction statsFourier space coverage: 85.2 % / High resolution: 1.1 Å / Num. of intensities measured: 23638 / Num. of structure factors: 3546 / Phase error: 22.7 ° / Phase residual: 0.1 ° / Phase error rejection criteria: 0.1 / Rmerge: 0.189 / Rsym: 0.189
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: FEI TALOS ARCTICA / Wavelength: 0.0251 Å
DetectorType: FEI CETA (4k x 4k) / Detector: CMOS DETECTOR / Date: Mar 21, 2019
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1.1→7.737 Å / Num. obs: 3546 / % possible obs: 85.2 % / Redundancy: 6.666 % / Biso Wilson estimate: 10.09 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.189 / Rrim(I) all: 0.204 / Χ2: 0.739 / Net I/σ(I): 5.41 / Num. measured all: 23638
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.136.1410.4593.2815663122550.8280.49881.7
1.13-1.167.1730.4693.5319443032710.8640.50389.4
1.16-1.198.1340.4893.8121312992620.8580.52287.6
1.19-1.235.1850.4093.4610942432110.830.45486.8
1.23-1.274.9950.3154.210342442070.8740.3584.8
1.27-1.315.2020.3084.2610822382080.8890.33887.4
1.31-1.365.6510.3464.1811982442120.8760.38186.9
1.36-1.425.860.394.1112542442140.8480.4387.7
1.42-1.487.1860.3155.2615812502200.8960.3488
1.48-1.569.0750.316.3419242442120.8980.3386.9
1.56-1.648.6010.2437.0416172131880.9290.25888.3
1.64-1.745.9470.2395.999041831520.9060.26283.1
1.74-1.866.1260.2286.439251811510.9470.2583.4
1.86-2.016.8250.1997.4210921891600.970.21684.7
2.01-2.27.2430.1798.0210721751480.9780.19384.6
2.2-2.468.8260.1738.9613151691490.9770.18488.2
2.46-2.845.2710.157.55506126960.960.16776.2
2.84-3.485.2910.1267.825451241030.990.14183.1
3.48-4.927.5840.1259.97661181010.9820.13285.6
4.92-7.7373.3850.1336.878861260.9820.15542.6

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHENIXdev_3360refinement
PDB_EXTRACT3.25data extraction
SHELXDphasing
EM software
IDNameVersionCategory
6Coot0.8.9.1model fitting
13PHENIXdev 3360model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 111.1 ° / ∠γ: 90 ° / A: 33.17 Å / B: 4.78 Å / C: 30.33 Å / Space group name: P21 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: maximum liklihood
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→7.737 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2126 352 9.93 %
Rwork0.1944 --
obs0.1963 3544 85.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 34.51 Å2 / Biso mean: 8.141 Å2 / Biso min: 2.2 Å2
Refinement stepCycle: final / Resolution: 1.1→7.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms105 0 0 7 112
Biso mean---20.78 -
Num. residues----15
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.25860.2691140.21261027114186
1.2586-1.58350.24261190.21781088120787
1.5835-7.73690.1851190.17911077119684

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