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- EMDB-0619: Amyloid Beta KLVFFAENVGS 16-26 D23N Iowa mutation -

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Basic information

Entry
Database: EMDB / ID: EMD-0619
TitleAmyloid Beta KLVFFAENVGS 16-26 D23N Iowa mutation
Map dataAmyloid Beta KLVFFAENVGS 16-26 D23N Iowa mutation
Sample
  • Complex: Fibrils of Amyloid Beta segment 16-26
    • Protein or peptide: Amyloid-beta precursor protein
Keywordsamyloid / PROTEIN FIBRIL
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 / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / 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 / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / transition metal ion binding / main axon / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / ECM proteoglycans / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / axonogenesis / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / response to interleukin-1 / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / adult locomotory behavior / positive regulation of interleukin-1 beta production / endosome lumen / dendritic shaft / positive regulation of long-term synaptic potentiation / trans-Golgi network membrane / TAK1-dependent IKK and NF-kappa-B activation / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity / positive regulation of non-canonical NF-kappaB signal transduction / regulation of long-term neuronal synaptic plasticity / synapse organization / cellular response to nerve growth factor stimulus / visual learning / recycling endosome / positive regulation of interleukin-6 production / response to lead ion / Golgi lumen / cognition / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / cellular response to amyloid-beta / neuron projection development / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of gene expression / regulation of translation / early endosome membrane / perikaryon / G alpha (i) signalling events / G alpha (q) signalling events / dendritic spine
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 / 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 crystallography / cryo EM / Resolution: 1.402 Å
AuthorsGriner SL / Sawaya MR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 AG029430 United States
CitationJournal: Elife / Year: 2019
Title: Structure based inhibitors of Amyloid Beta core suggest a common interface with Tau.
Authors: Griner SL / Seidler P / Bowler J / Murray KA / Yang TP / Sahay S / Sawaya MR / Cascio D / Rodriguez JA / Philipp S / Sosna J / Glabe CG / Gonen T / Eisenberg DS
History
DepositionFeb 28, 2019-
Header (metadata) releaseMar 20, 2019-
Map releaseOct 30, 2019-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6o4j
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0619.png

Downloads & links

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Map

FileDownload / File: emd_0619.map.gz / Format: CCP4 / Size: 304.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAmyloid Beta KLVFFAENVGS 16-26 D23N Iowa mutation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.35 Å/pix.
x 36 pix.
= 12.76 Å		0.39 Å/pix.
x 30 pix.
= 11.67 Å		0.36 Å/pix.
x 72 pix.
= 51.91 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.389 Å / Y: 0.36049 Å / Z: 0.35444 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7 / Movie #1: 0.7
Minimum - Maximum-1.8594286 - 3.3643832
Average (Standard dev.)0.000000000266055 (±0.47364908)
SymmetrySpace group: 4
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions307236
Spacing3014436
CellA: 11.67 Å / B: 51.91 Å / C: 12.76 Å
α: 90.0 ° / β: 114.18 ° / γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.3890.360486111111110.35444444444444
M x/y/z3014436
origin x/y/z0.0000.0000.000
length x/y/z11.67051.91012.760
α/β/γ90.000114.18090.000
start NX/NY/NZ000
NX/NY/NZ307236
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS723036
D min/max/mean-1.8593.3640.000

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Supplemental data

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Sample components

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Entire : Fibrils of Amyloid Beta segment 16-26

EntireName: Fibrils of Amyloid Beta segment 16-26
Components
  • Complex: Fibrils of Amyloid Beta segment 16-26
    • Protein or peptide: Amyloid-beta precursor protein

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Supramolecule #1: Fibrils of Amyloid Beta segment 16-26

SupramoleculeName: Fibrils of Amyloid Beta segment 16-26 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Amyloid-beta precursor protein

MacromoleculeName: Amyloid-beta precursor protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.235432 KDa
SequenceString:
(ACE)KLVFFAENV GS(NH2)

UniProtKB: Amyloid-beta precursor protein

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

Concentration7.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMMgCl2magnesium formate
10.0 %C2H6OSDMSO
100.0 mMC4H11NO3Tris Base
15.0 %C3H8Oisopropanol
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Detailsnanocrystals
Crystal formationInstrument: microcentrifuge tube / Atmosphere: air / Temperature: 310.0 K / Time: 4.0 DAY

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number diffraction images: 1331 / Average electron dose: 0.03 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1840 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.402 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystallography statisticsNumber intensities measured: 47598 / Number structure factors: 2355 / Fourier space coverage: 85.4 / R sym: 0.24 / R merge: 0.24 / Overall phase error: 0 / Overall phase residual: 0.01 / Phase error rejection criteria: 0 / High resolution: 1.4 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.4 Å / Shell - Low resolution: 1.44 Å / Shell - Number structure factors: 163 / Shell - Phase residual: 0.01 / Shell - Fourier space coverage: 78 / Shell - Multiplicity: 12.1

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Atomic model buiding 1

Initial modelPDB ID:

2y2a


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: OTHER / Target criteria: Maximum likelihood
Output model

PDB-6o4j:
Amyloid Beta KLVFFAENVGS 16-26 D23N Iowa mutation

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