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- PDB-5jbt: Mesotrypsin in complex with cleaved amyloid precursor like protei... -

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Basic information

Entry
Database: PDB / ID: 5jbt
TitleMesotrypsin in complex with cleaved amyloid precursor like protein 2 inhibitor (APLP2)
Components
  • (Amyloid-like protein ...) x 2
  • PRSS3 protein
KeywordsHydrolase/Hydrolase inhibitor / inhibitor protease serine / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / negative regulation of peptidase activity / platelet alpha granule membrane / antimicrobial humoral response / Alpha-defensins / zymogen activation / Antimicrobial peptides / transition metal ion binding / endothelial cell migration / trypsin ...Uptake of dietary cobalamins into enterocytes / negative regulation of peptidase activity / platelet alpha granule membrane / antimicrobial humoral response / Alpha-defensins / zymogen activation / Antimicrobial peptides / transition metal ion binding / endothelial cell migration / trypsin / digestion / serine-type peptidase activity / axonogenesis / central nervous system development / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / tertiary granule lumen / heparin binding / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / plasma membrane
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. / 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. ...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. / 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 / Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / PH-like domain superfamily / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Trypsin-3 / Amyloid beta precursor like protein 2 / PRSS3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKayode, O. / Wang, R. / Pendlebury, D. / Soares, A. / Radisky, E.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA154387 United States
CitationJournal: J. Biol. Chem. / Year: 2016
Title: An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis.
Authors: Kayode, O. / Wang, R. / Pendlebury, D.F. / Cohen, I. / Henin, R.D. / Hockla, A. / Soares, A.S. / Papo, N. / Caulfield, T.R. / Radisky, E.S.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Refinement description
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRSS3 protein
X: Amyloid-like protein 2
Y: Amyloid-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2995
Polymers30,1633
Non-polymers1362
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-52 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.956, 54.539, 56.632
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11Y-206-

HOH

21Y-210-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PRSS3 protein /


Mass: 24257.457 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS3 / Organ: pancreas / Plasmid: pTRAP-T7-wtHu3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N2U3, UniProt: P35030*PLUS

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Amyloid-like protein ... , 2 types, 2 molecules XY

#2: Protein/peptide Amyloid-like protein 2 / APLP-2 / APPH / Amyloid protein homolog / CDEI box-binding protein / CDEBP


Mass: 1482.747 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLP2, APPL2 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / References: UniProt: Q06481
#3: Protein/peptide Amyloid-like protein 2 / APLP-2 / APPH / Amyloid protein homolog / CDEI box-binding protein / CDEBP


Mass: 4423.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLP2, APPL2 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / References: UniProt: Q06481

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Non-polymers , 3 types, 261 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate 0.1 M Sodium Cacodylate Trihydrate 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.398→50 Å / Num. obs: 57667 / % possible obs: 99.8 % / Redundancy: 12.8 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.2
Reflection shellResolution: 1.398→1.42 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 6.76 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L33

3l33


Resolution: 1.4→36.51 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2078 / WRfactor Rwork: 0.1678 / FOM work R set: 0.8946 / SU B: 1.508 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0597 / SU Rfree: 0.0576 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 3082 5.1 %RANDOM
Rwork0.1629 ---
obs0.1647 57667 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.36 Å2 / Biso mean: 19.638 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.4→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 6 261 2363
Biso mean--31.95 30.32 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192180
X-RAY DIFFRACTIONr_bond_other_d0.0010.022022
X-RAY DIFFRACTIONr_angle_refined_deg2.1561.9492968
X-RAY DIFFRACTIONr_angle_other_deg2.3033.0074643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4635281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38924.19493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45315349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3421512
X-RAY DIFFRACTIONr_chiral_restr0.1470.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212522
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02504
X-RAY DIFFRACTIONr_rigid_bond_restr7.10434202
X-RAY DIFFRACTIONr_sphericity_free31.238585
X-RAY DIFFRACTIONr_sphericity_bonded12.90854322
LS refinement shellResolution: 1.398→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 218 -
Rwork0.227 4067 -
all-4285 -
obs--95.35 %

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