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- PDB-5onr: Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Th... -

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Basic information

Entry
Database: PDB / ID: 5onr
TitleAlzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin
Components
  • Amyloid-beta A4 protein
  • Thermolysin
KeywordsHYDROLASE / peptidase / protein-peptide complex / amyloid-beta peptide
Function / homology
Function and homology information


thermolysin / 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 / axo-dendritic transport / regulation of Wnt signaling pathway ...thermolysin / 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 / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / 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 / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / transition metal ion binding / main axon / regulation of multicellular organism growth / intracellular copper ion homeostasis / ECM proteoglycans / regulation of presynapse assembly / 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 / positive regulation of mitotic cell cycle / axonogenesis / 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 / positive regulation of interleukin-1 beta production / adult locomotory behavior / 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 / recycling endosome / visual learning / metalloendopeptidase activity / 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 translation / regulation of gene expression / early endosome membrane / G alpha (i) signalling events / perikaryon
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / 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 / Neutral Protease Domain 2 / Neutral Protease; domain 2 / 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 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / PH-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Thermolysin / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsLeite, J.P. / Gales, L.
CitationJournal: FEBS Lett. / Year: 2019
Title: Alzheimer's A beta1-40peptide degradation by thermolysin: evidence of inhibition by a C-terminal A beta product.
Authors: Leite, J.P. / Gales, L.
History
DepositionAug 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermolysin
B: Amyloid-beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9668
Polymers34,6622
Non-polymers3046
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-91 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.696, 92.696, 129.368
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-729-

HOH

21A-827-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin
#2: Protein/peptide Amyloid-beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta precursor protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 301.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067*PLUS

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Non-polymers , 4 types, 375 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.86 % / Mosaicity: 0.26 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 6
Details: 50 mM MES: 45% DMSO: 0.7-0.9 M NaCl: 0-0.4 M CdCl2: reservoir solution containing 30-40% ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97264 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 7, 2016
Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97264 Å / Relative weight: 1
ReflectionResolution: 1.39→46.35 Å / Num. obs: 66070 / % possible obs: 99.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 15.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.028 / Rrim(I) all: 0.092 / Net I/σ(I): 12.7 / Num. measured all: 647249 / Scaling rejects: 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.39-1.448.21.2245278264070.6390.4471.3071.799.9
5.38-46.35100.0421270112700.9990.0130.04536.797.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.25data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1kei

1kei


Resolution: 1.39→50.368 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 3410 5.19 %
Rwork0.1787 62334 -
obs0.1797 65744 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.6 Å2 / Biso mean: 19.2183 Å2 / Biso min: 10.07 Å2
Refinement stepCycle: final / Resolution: 1.39→50.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 9 369 2817
Biso mean--30.13 31.88 -
Num. residues----319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052521
X-RAY DIFFRACTIONf_angle_d0.7553438
X-RAY DIFFRACTIONf_chiral_restr0.078369
X-RAY DIFFRACTIONf_plane_restr0.005453
X-RAY DIFFRACTIONf_dihedral_angle_d2.7971353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.39-1.40990.31231520.288525642716100
1.4099-1.43090.3161530.284125642717100
1.4309-1.45330.26111300.279925882718100
1.4533-1.47710.30521410.290625632704100
1.4771-1.50260.24391360.241825782714100
1.5026-1.52990.27811380.242725852723100
1.5299-1.55930.25681410.22862572271399
1.5593-1.59120.24061600.207825622722100
1.5912-1.62580.24611350.191626122747100
1.6258-1.66360.21991260.188625932719100
1.6636-1.70520.21981490.177925692718100
1.7052-1.75130.20551280.173526312759100
1.7513-1.80280.17731430.16772561270499
1.8028-1.8610.18291470.17232577272499
1.861-1.92750.32641240.2582434255893
1.9275-2.00470.18481350.167726132748100
2.0047-2.0960.18241450.160526192764100
2.096-2.20650.17541260.155326402766100
2.2065-2.34470.2291320.20462486261894
2.3447-2.52570.14421480.16132631277999
2.5257-2.77990.19791530.163326392792100
2.7799-3.18210.20011570.157226812838100
3.1821-4.00880.15141310.15492680281198
4.0088-50.4010.18341800.16112792297297
Refinement TLS params.Method: refined / Origin x: 11.5377 Å / Origin y: 30.2289 Å / Origin z: -2.7047 Å
111213212223313233
T0.1228 Å20.0125 Å20.0283 Å2-0.1455 Å20.0007 Å2--0.1193 Å2
L1.1217 °20.1553 °20.4969 °2-0.394 °20.1081 °2--0.5302 °2
S0.0191 Å °-0.0142 Å °-0.0436 Å °0.0265 Å °-0.0344 Å °0.0642 Å °0.0285 Å °-0.0457 Å °0.0159 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 316
2X-RAY DIFFRACTION1ALLA401 - 869
3X-RAY DIFFRACTION1ALLB31 - 33

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