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- PDB-7u4p: Covalently stabilized triangular trimer composed of Abeta17-36 be... -

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Basic information

Entry
Database: PDB / ID: 7u4p
TitleCovalently stabilized triangular trimer composed of Abeta17-36 beta-hairpins
ComponentsAmyloid-beta 17-36 peptide
KeywordsDE NOVO PROTEIN / Abeta oligomer / beta-hairpin / trimer / dodecamer / Alzheimer's disease
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 / regulation of synapse structure or activity / 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 / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / 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 / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / 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 / positive regulation of protein metabolic process / dendrite development / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / main axon / transition metal ion binding / 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 / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / axonogenesis / response to interleukin-1 / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / adult locomotory behavior / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / dendritic shaft / 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 / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / cellular response to nerve growth factor stimulus / visual learning / recycling endosome / response to lead ion / positive regulation of interleukin-6 production / 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 / G alpha (i) signalling events / perikaryon / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsKreutzer, A.G. / Haerianardakani, S. / Nowick, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1RF1AG062296-01 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)1RF1AG072587-01 United States
CitationJournal: Acs Cent.Sci. / Year: 2024
Title: Antibodies Raised Against an A beta Oligomer Mimic Recognize Pathological Features in Alzheimer's Disease and Associated Amyloid-Disease Brain Tissue.
Authors: Kreutzer, A.G. / Parrocha, C.M.T. / Haerianardakani, S. / Guaglianone, G. / Nguyen, J.T. / Diab, M.N. / Yong, W. / Perez-Rosendahl, M. / Head, E. / Nowick, J.S.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid-beta 17-36 peptide
B: Amyloid-beta 17-36 peptide
C: Amyloid-beta 17-36 peptide


Theoretical massNumber of molelcules
Total (without water)6,6443
Polymers6,6443
Non-polymers00
Water45025
1
A: Amyloid-beta 17-36 peptide
B: Amyloid-beta 17-36 peptide
C: Amyloid-beta 17-36 peptide

A: Amyloid-beta 17-36 peptide
B: Amyloid-beta 17-36 peptide
C: Amyloid-beta 17-36 peptide

A: Amyloid-beta 17-36 peptide
B: Amyloid-beta 17-36 peptide
C: Amyloid-beta 17-36 peptide

A: Amyloid-beta 17-36 peptide
B: Amyloid-beta 17-36 peptide
C: Amyloid-beta 17-36 peptide


Theoretical massNumber of molelcules
Total (without water)26,57612
Polymers26,57612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+5/31
crystal symmetry operation10_666-y+1,-x+1,-z+5/31
Buried area10630 Å2
ΔGint-48 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.054, 62.054, 47.839
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-103-

HOH

21B-109-

HOH

31C-101-

HOH

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Components

#1: Protein/peptide Amyloid-beta 17-36 peptide / Amyloid-beta protein 40 / Abeta40 / Beta-APP40


Mass: 2214.628 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris at pH 8.3, 0.2 M MgCl2, 2.8 M 1,6-hexanediol

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 21, 2019
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.803→31.03 Å / Num. obs: 5373 / % possible obs: 99.74 % / Redundancy: 36.2 % / CC1/2: 1 / Rmerge(I) obs: 0.0643 / Net I/σ(I): 39.93
Reflection shellResolution: 1.803→1.868 Å / Rmerge(I) obs: 0.9299 / Num. unique obs: 522 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JXO

7jxo


Resolution: 1.803→31.03 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 960 10.1 %
Rwork0.2051 8545 -
obs0.2092 5373 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.39 Å2 / Biso mean: 62.0242 Å2 / Biso min: 23.61 Å2
Refinement stepCycle: final / Resolution: 1.803→31.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms459 0 0 25 484
Biso mean---59.71 -
Num. residues----63
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.803-1.90.30851330.28071230
1.9-2.020.27531380.23261212
2.02-2.170.26361310.22731228
2.17-2.390.26181440.24221210
2.39-2.740.29871320.24751208
2.74-3.450.21521450.19861228
3.45-31.030.23561370.17841229
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6764-5.45246.32266.8632-8.15089.5415-0.3295-0.39670.11080.16190.37680.4569-0.0740.0866-0.15690.30660.05550.07040.37830.05580.31457.66628.60350.304
26.8387-3.79252.90965.9419-5.74545.6383-0.0354-0.13020.47161.08840.02850.1839-1.1147-0.097-0.2140.47730.01810.02510.3751-0.0580.38696.25339.61348.167
37.9416-2.7826-1.7074.59486.4989.82820.1909-0.1567-0.50040.3012-0.13290.57350.76670.0941-0.03520.31950.0016-0.00740.24920.0270.34152.9224.52142.391
46.6834-1.4151-2.99453.1433.15064.99380.43890.6122-2.5543-0.7185-0.26130.65520.1453-1.4559-0.01340.46150.0047-0.08230.4902-0.07360.60121.08717.36332.934
51.89051.14291.93357.3794-0.11182.487-1.3116-0.2785-0.43660.01260.56450.0504-1.93070.46150.73210.3276-0.052-0.01910.48030.08170.41298.55719.91349.098
63.08-3.112-2.52227.4735-0.5354.31760.2982-1.7993-1.94471.41420.0656-0.89531.52150.2326-0.31390.54170.0076-0.12660.5940.3190.542115.26615.72554.047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:8 )A1 - 8
2X-RAY DIFFRACTION2( CHAIN A AND ( RESID 9:19 OR RESID 20:20 ) )A9 - 19
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 9:19 OR RESID 20:20 ) )A20
4X-RAY DIFFRACTION3( CHAIN B AND RESID 1:8 )B1 - 8
5X-RAY DIFFRACTION4( CHAIN B AND ( RESID 9:19 OR RESID 20:20 ) )B9 - 19
6X-RAY DIFFRACTION4( CHAIN B AND ( RESID 9:19 OR RESID 20:20 ) )B20
7X-RAY DIFFRACTION5( CHAIN C AND RESID 3:8 )C3 - 8
8X-RAY DIFFRACTION6( CHAIN C AND RESID 9:21 )C9 - 21

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