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- PDB-5onq: Alzheimer's Amyloid-Beta Peptide Fragment 29-40 in Complex with C... -

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Basic information

Entry
Database: PDB / ID: 5onq
TitleAlzheimer's Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd-substituted Thermolysin
Components
  • Amyloid-beta A4 protein
  • Thermolysin
KeywordsHYDROLASE / peptidase / protein-peptide complex / amyloid-beta peptide
Function / homology
Function and homology information


thermolysin / 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 ...thermolysin / 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 / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / 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 / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / 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 / negative regulation of neuron differentiation / ECM proteoglycans / intracellular copper ion homeostasis / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / 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 / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / response to interleukin-1 / cholesterol metabolic process / positive regulation of mitotic cell cycle / extracellular matrix organization / adult locomotory behavior / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / learning / dendritic shaft / positive regulation of long-term synaptic potentiation / central nervous system development / locomotory behavior / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / serine-type endopeptidase inhibitor activity / visual learning / neuromuscular junction / recycling endosome / metalloendopeptidase activity / cognition / Golgi lumen / positive regulation of inflammatory response / neuron cellular homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / cellular response to amyloid-beta / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction
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. / 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 / Neutral Protease Domain 2 / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / Neutral Protease; domain 2 / 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
: / Amyloid-beta precursor protein / Thermolysin
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.17 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_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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)35,3588
Polymers34,7902
Non-polymers5686
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-52 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.488, 93.488, 129.558
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-769-

HOH

21A-798-

HOH

31A-872-

HOH

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Components

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

#1: Protein Thermolysin / Neutral protease


Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P43133, 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: 429.512 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, 399 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#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.: 393 / 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: 2.35 Å3/Da / Density % sol: 47.64 % / Mosaicity: 0.05 °
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: 1.17→46.74 Å / Num. obs: 111781 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 10.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.027 / Rrim(I) all: 0.083 / Net I/σ(I): 14.6 / Num. measured all: 994505
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
1.17-1.218.10.86786021106250.7340.3160.9262.198
4.53-46.748.30.0321806521700.9990.0120.03451.898.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.25data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementStarting model: pdbid 1kei

1kei


Resolution: 1.17→43.97 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1716 5700 5.11 %
Rwork0.1625 105910 -
obs0.1629 111610 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.93 Å2 / Biso mean: 14.6381 Å2 / Biso min: 6.64 Å2
Refinement stepCycle: final / Resolution: 1.17→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 9 393 2856
Biso mean--26.13 25.33 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052577
X-RAY DIFFRACTIONf_angle_d0.8223518
X-RAY DIFFRACTIONf_chiral_restr0.083376
X-RAY DIFFRACTIONf_plane_restr0.005464
X-RAY DIFFRACTIONf_dihedral_angle_d4.821866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.17-1.18330.24951890.2563386357596
1.1833-1.19720.21261740.23153429360398
1.1972-1.21180.26141850.22153466365199
1.2118-1.22720.26791770.25953439361699
1.2272-1.24330.24572090.2263453366299
1.2433-1.26030.22361810.2423449363099
1.2603-1.27840.2491770.23683494367199
1.2784-1.29740.23021940.202934983692100
1.2974-1.31770.21991640.196335113675100
1.3177-1.33930.17822040.17434763680100
1.3393-1.36240.19952100.18513484369499
1.3624-1.38720.2011940.19853413360798
1.3872-1.41390.17431950.163435303725100
1.4139-1.44270.17491890.171235073696100
1.4427-1.47410.22771950.179434963691100
1.4741-1.50840.16621860.160135443730100
1.5084-1.54610.17921950.15423495369099
1.5461-1.58790.17592140.143535093723100
1.5879-1.63470.14171930.138835343727100
1.6347-1.68740.15991850.139335423727100
1.6874-1.74770.15661770.140535563733100
1.7477-1.81770.1351680.140336043772100
1.8177-1.90040.16011810.142935623743100
1.9004-2.00060.15621890.14263542373199
2.0006-2.1260.14151920.14236013793100
2.126-2.29010.15311810.14535863767100
2.2901-2.52060.15581870.155536233810100
2.5206-2.88520.1591970.16123622381999
2.8852-3.63480.17742100.158136873897100
3.6348-44.00070.16322080.16153872408099
Refinement TLS params.Method: refined / Origin x: 11.54 Å / Origin y: 30.8993 Å / Origin z: -2.4989 Å
111213212223313233
T0.0642 Å20.0075 Å20.019 Å2-0.0824 Å2-0.0017 Å2--0.0778 Å2
L1.105 °20.1669 °20.4655 °2-0.3307 °20.0671 °2--0.4392 °2
S0.0184 Å °-0.0164 Å °-0.0182 Å °0.0291 Å °-0.0235 Å °0.0538 Å °0.0227 Å °-0.0447 Å °0.0033 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 316
2X-RAY DIFFRACTION1ALLA401 - 893
3X-RAY DIFFRACTION1ALLB29 - 33
4X-RAY DIFFRACTION1ALLB101
5X-RAY DIFFRACTION1ALLC1 - 3

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