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- PDB-7jxn: Beta hairpin derived from Abeta17-36 with an F20Cha mutation -

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Basic information

Entry
Database: PDB / ID: 7jxn
TitleBeta hairpin derived from Abeta17-36 with an F20Cha mutation
ComponentsAmyloid-beta 17-36 peptide
KeywordsDE NOVO PROTEIN / amyloid / oligomer / Alzheimer's disease / beta-hairpin
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 precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKreutzer, A.G. / Haerianardakani, S. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Phenylalanine Mutation to Cyclohexylalanine Facilitates Triangular Trimer Formation by beta-Hairpins Derived from A beta.
Authors: Haerianardakani, S. / Kreutzer, A.G. / Salveson, P.J. / Samdin, T.D. / Guaglianone, G.E. / Nowick, J.S.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
D: Amyloid-beta 17-36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8887
Polymers8,7954
Non-polymers943
Water1,02757
1
A: Amyloid-beta 17-36 peptide
D: Amyloid-beta 17-36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4915
Polymers4,3972
Non-polymers943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amyloid-beta 17-36 peptide
C: Amyloid-beta 17-36 peptide


Theoretical massNumber of molelcules
Total (without water)4,3972
Polymers4,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.167, 37.167, 116.994
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-214-

HOH

31B-105-

HOH

41B-106-

HOH

51B-112-

HOH

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Components

#1: Protein/peptide
Amyloid-beta 17-36 peptide / APP / ABPP / APPI / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta A4 ...APP / ABPP / APPI / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta A4 protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 2198.625 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop
Details: Bis-Tris buffer, ammonium acetate, and methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 123.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2019
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.49
ReflectionResolution: 2→32.19 Å / Num. obs: 12449 / % possible obs: 99.9 % / Redundancy: 19.4 % / CC1/2: 1 / Rmerge(I) obs: 0.01302 / Rpim(I) all: 0.01302 / Rrim(I) all: 0.01841 / Net I/σ(I): 33.1
Reflection shellResolution: 2→2.072 Å / Redundancy: 19.5 % / Num. unique obs: 1258 / CC1/2: 0.987 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→32.19 Å / Cross valid method: THROUGHOUT / σ(F): 14.73 / Phase error: 33.22 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3012 1213 9.9 %
Rwork0.2766 11036 -
obs0.2827 12249 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 26.977 Å2 / Biso min: 5.77 Å2
Refinement stepCycle: final / Resolution: 2→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 3 57 676
Biso mean--21.81 24.51 -
Num. residues----84
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.080.30331440.31361226137089
2.08-2.170.34461340.33671227136190
2.18-2.290.3581300.32041220135090
2.29-2.430.35331380.29921220135890
2.43-2.620.27131300.28561227135790
2.62-2.880.27571290.30911235136491
2.88-3.30.30251340.27221209134390
3.3-4.150.30041420.25071233137590
4.16-32.190.25051320.25571239137190
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)
10.08520.02150.03220.013-0.02390.13-0.0626-0.0661-0.01150.01340.03030.0481-0.0075-0.0199-0.09430.0920.1045-0.04030.38650.42710.628120.190426.833634.9598
20.1185-0.18930.18622.87350.76210.7321-0.09770.0722-0.0772-0.16860.0464-0.17920.15410.04780.02370.2092-0.17080.1227-0.1831-0.07360.3985.246525.466841.9035
31.72280.7909-2.13314.7793-3.44744.8197-0.24020.1920.13-0.48220.15860.0780.4931-0.14010.00360.1707-0.0794-0.01670.16960.3270.284215.488523.065437.1622
43.6679-4.1398-0.48898.37741.08111.5555-0.3851-0.1053-0.450.85320.27250.3060.3732-0.01030.30010.2849-0.0866-0.04950.18270.13930.434913.332530.78682.632
53.7426-3.447-1.1315.3011.94213.31240.0707-0.0864-0.01150.3909-0.1960.41550.3055-0.05550.18110.0382-0.0232-0.01530.0899-0.01510.171117.674618.97876.8397
60.09790.0484-0.29721.0831-1.10051.7625-0.37820.51540.0778-0.32860.3229-0.5293-0.450.77760.20360.0091-0.2594-0.11750.2719-0.11330.670522.367728.374464.5631
70.51380.3272-0.16871.87080.86472.03690.00990.0070.1026-0.00430.11020.29280.0484-0.0804-0.10590.3443-0.05120.02250.0643-0.0580.389510.719517.392769.4052
82.77272.5759-3.4294.6327-2.19836.0062-0.2010.1383-0.3368-0.0738-0.0019-0.0871-0.1184-0.27940.26230.1092-0.0567-0.13770.1258-0.0930.268813.784620.814771.9012
90.0399-0.03080.06741.0398-0.10570.10590.0607-0.00530.01380.05370.02510.05020.026-0.09290.11180.1677-0.20940.24640.11320.05460.555813.216631.977352.6188
107.62360.9967-0.48764.7371-0.90153.54820.090.252-0.4622-0.0994-0.31890.37340.36420.07590.32710.04870.04870.0760.20540.04350.21149.973621.248146.906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )A1 - 7
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 17 )A8 - 17
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 20 )A18 - 20
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 7 )B1 - 7
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 20 )B8 - 20
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 7 )C1 - 7
7X-RAY DIFFRACTION7chain 'C' and (resid 8 through 12 )C8 - 12
8X-RAY DIFFRACTION8chain 'C' and (resid 13 through 20 )C13 - 20
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 8 )D1 - 8
10X-RAY DIFFRACTION10chain 'D' and (resid 9 through 20 )D9 - 20

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