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- PDB-5nx1: Combinatorial Engineering of Proteolytically Resistant APPI Varia... -

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Basic information

Entry
Database: PDB / ID: 5nx1
TitleCombinatorial Engineering of Proteolytically Resistant APPI Variants that Selectively Inhibit Human Kallikrein 6 for Cancer Therapy
Components
  • (Amyloid-beta A4 protein) x 3
  • Kallikrein-6
KeywordsHYDROLASE / Serine_protease / inhibitor / complex
Function / homology
Function and homology information


tissue regeneration / cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / hormone metabolic process / amyloid precursor protein metabolic process ...tissue regeneration / cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / hormone metabolic process / amyloid precursor protein metabolic process / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / regulation of neuron projection development / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / regulation of cell differentiation / TRAF6 mediated NF-kB activation / presynaptic active zone / protein autoprocessing / positive regulation of protein metabolic process / neuromuscular process controlling balance / collagen catabolic process / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / intercellular bridge / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / myelination / Mitochondrial protein degradation / response to interleukin-1 / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / protein maturation / axonogenesis / positive regulation of calcium-mediated signaling / dendritic shaft / platelet alpha granule lumen / secretory granule / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / learning / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / recycling endosome / positive regulation of interleukin-6 production
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / PH-like domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å
AuthorsShahar, A. / Sananes, A. / Radisky, E.S. / Papo, N.
CitationJournal: J.Biol.Chem. / Year: 2018
Title: A potent, proteolysis-resistant inhibitor of kallikrein-related peptidase 6 (KLK6) for cancer therapy, developed by combinatorial engineering.
Authors: Sananes, A. / Cohen, I. / Shahar, A. / Hockla, A. / De Vita, E. / Miller, A.K. / Radisky, E.S. / Papo, N.
History
DepositionMay 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallikrein-6
B: Amyloid-beta A4 protein
D: Amyloid-beta A4 protein
C: Amyloid-beta A4 protein


Theoretical massNumber of molelcules
Total (without water)42,8824
Polymers42,8824
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-24 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.543, 77.702, 92.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kallikrein-6 / Neurosin / Protease M / SP59 / Serine protease 18 / Serine protease 9 / Zyme


Mass: 24417.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK6, PRSS18, PRSS9 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#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: 2945.086 Da / Num. of mol.: 1 / Fragment: UNP residues 289-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P05067
#3: Protein 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: 6295.999 Da / Num. of mol.: 1 / Fragment: UNP residues 302-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P05067
#4: Protein 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: 9223.071 Da / Num. of mol.: 1 / Fragment: UNP residues 289-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P05067
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH 5.5, 25% Polyethylene Glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.853→47.262 Å / Num. obs: 36867 / % possible obs: 99.52 % / Redundancy: 2 % / Rpim(I) all: 0.031 / Net I/σ(I): 13.48
Reflection shellResolution: 1.853→1.92 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.08 / Num. unique all: 3528 / CC1/2: 0.574 / Rpim(I) all: 0.642 / % possible all: 96.37

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AAP & 1LO6

1aap

1lo6


Resolution: 1.853→47.262 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.78
RfactorNum. reflection% reflection
Rfree0.2255 1848 5.01 %
Rwork0.1839 --
obs0.186 36853 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.853→47.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 0 195 2731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062646
X-RAY DIFFRACTIONf_angle_d0.8723602
X-RAY DIFFRACTIONf_dihedral_angle_d10.9072040
X-RAY DIFFRACTIONf_chiral_restr0.054374
X-RAY DIFFRACTIONf_plane_restr0.005475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.853-1.90270.34971230.3604248894
1.9027-1.95870.34231450.31012677100
1.9587-2.02190.30771290.26712659100
2.0219-2.09420.28111380.23982690100
2.0942-2.1780.26751410.21882658100
2.178-2.27710.24641490.20382692100
2.2771-2.39720.2561520.19542658100
2.3972-2.54740.22751320.18532697100
2.5474-2.7440.22451450.18892703100
2.744-3.02010.23131530.18812706100
3.0201-3.4570.22751390.18222728100
3.457-4.3550.16761490.13862753100
4.3550.2121530.15852896100
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)
12.3288-0.3744-0.49862.5395-0.16564.0502-0.07370.0328-0.1134-0.0946-0.07140.12260.1186-0.17040.16130.32140.00990.00580.1953-0.03730.1947-1.085353.037-35.2911
23.63550.9283.5693.6123.62337.99110.22240.4303-0.3075-0.3820.299-0.51980.34230.9106-0.38410.44870.04920.06870.31360.00190.35039.283153.7206-38.3311
36.62545.07830.02167.37350.91496.4687-0.15810.5505-0.0223-0.72130.08410.1820.3903-0.37960.07290.40390.1512-0.00490.2463-0.00390.27150.306150.7208-42.8447
45.1322-0.38131.15053.53750.96494.75570.10220.06540.13340.0029-0.0901-0.206-0.20060.18370.02830.29150.01050.00580.10750.0420.1993.690461.9102-36.5542
54.42070.1773-0.61272.7381-1.19610.71930.1303-0.25320.34650.08-0.02850.7004-0.7254-0.3937-0.04310.67070.0377-0.00080.3539-0.08350.2858-7.178265.6401-24.414
67.0683-1.64113.39953.4279-3.2484.07050.1638-0.1244-0.73790.3147-0.14080.32081.27710.3084-0.05540.55410.00010.11690.2112-0.00040.3528-0.909142.5144-27.6651
77.61522.93712.87947.83494.59378.388-0.0961-1.2390.970.4549-0.52630.5131-0.4821-0.54280.57340.57850.08470.00960.3696-0.08410.2769-2.759960.4638-15.6764
88.7222.6309-1.68643.2343-0.20038.6534-0.0203-0.2050.49830.78610.169-0.1887-1.00180.5024-0.11560.54270.0258-0.07760.2498-0.07510.31496.3164.2536-16.8814
93.63491.0739-5.15897.444-1.72327.4709-0.2195-0.20350.07160.76020.14180.34070.5323-0.33870.1960.47750.03160.0450.32610.01150.2512-1.967151.371-19.6542
103.2822-0.38361.06242.1197-0.97655.7433-0.3245-0.34720.06470.64110.0552-0.0671-0.089-0.03880.19760.37590.04840.00140.2279-0.02810.1742-0.232357.4921-21.0385
112.62320.5057-0.75896.7872-0.1132.9735-0.00820.1450.37750.05310.0033-0.2013-1.1077-0.134-0.06480.48980.0213-0.03830.2241-0.0040.3534.114369.5276-32.207
126.94942.9097-1.34646.9361-1.93526.8782-0.2480.03520.1048-0.46390.1446-0.13220.01420.19460.11330.3113-0.0008-0.03330.1836-0.00990.1628-15.660271.626-38.9758
138.8209-3.17110.92781.908-2.31625.9845-0.07020.34550.5517-0.3564-0.3247-0.4668-0.83280.49810.38760.7175-0.122-0.12340.38620.03870.3703-12.865979.4773-45.2557
147.5373-7.31914.27468.7872-4.13848.4006-0.42980.14430.49580.5222-0.1411-0.79880.10210.53440.53060.3217-0.0120.00760.27470.08320.302217.140445.6099-20.3335
158.9389-6.33911.89977.9768-1.0113.86960.5130.4277-0.4828-0.4868-0.5263-0.19330.91730.6861-0.05440.48310.1408-0.00890.34730.02920.334319.232938.5087-25.831
169.1365-4.5188-5.89523.62932.63235.0560.48030.64860.6994-1.2049-0.946-1.0984-0.39250.63490.250.39750.0530.09830.42910.17260.47321.394347.2015-24.9084
172.1791.2161-1.89922.17792.42239.95370.00890.548-0.3319-1.2295-0.7365-0.46510.93930.94540.75850.70860.28950.1330.92180.21760.591928.298838.8116-29.2013
186.7943.9272-0.35293.91182.68195.30770.0999-0.43730.3284-0.3959-0.33110.7018-0.2424-0.20730.16420.4056-0.0041-0.06220.3426-0.05080.2492-21.670372.2944-34.8604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 140 )
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 171 )
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 184 )
9X-RAY DIFFRACTION9chain 'A' and (resid 185 through 197 )
10X-RAY DIFFRACTION10chain 'A' and (resid 198 through 226 )
11X-RAY DIFFRACTION11chain 'A' and (resid 227 through 245 )
12X-RAY DIFFRACTION12chain 'D' and (resid 16 through 47 )
13X-RAY DIFFRACTION13chain 'D' and (resid 48 through 57 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 17 )
15X-RAY DIFFRACTION15chain 'C' and (resid 18 through 35 )
16X-RAY DIFFRACTION16chain 'C' and (resid 36 through 47 )
17X-RAY DIFFRACTION17chain 'C' and (resid 48 through 56 )
18X-RAY DIFFRACTION18chain 'B' and (resid 3 through 15 )

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