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- PDB-6har: Crystal structure of Mesotrypsin in complex with APPI-M17C/I18F/F34C -

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Basic information

Entry
Database: PDB / ID: 6har
TitleCrystal structure of Mesotrypsin in complex with APPI-M17C/I18F/F34C
Components
  • Amyloid-beta A4 protein
  • PRSS3 protein
KeywordsPROTEIN FIBRIL / PRSS3 / Mesotrypsin / Serine protease / Kunitz type inhibitor / APPI
Function / homology
Function and homology information


transition metal ion binding / clathrin-coated pit / serine-type endopeptidase inhibitor activity / endocytosis / heparin binding / nervous system development / growth cone / perikaryon / membrane => GO:0016020 / early endosome ...transition metal ion binding / clathrin-coated pit / serine-type endopeptidase inhibitor activity / endocytosis / heparin binding / nervous system development / growth cone / perikaryon / membrane => GO:0016020 / early endosome / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Amyloid-beta precursor protein / 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, extracellular / Amyloidogenic glycoprotein, heparin-binding ...Amyloid-beta precursor protein / 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, 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 / Few Secondary Structures / Irregular / 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 / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ABPP / PRSS3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 Å
AuthorsShahar, A. / Cohen, I. / Radisky, E. / Papo, N.
Funding support1items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF)2015134
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Disulfide engineering of human Kunitz-type serine protease inhibitors enhances proteolytic stability and target affinity toward mesotrypsin.
Authors: Cohen, I. / Coban, M. / Shahar, A. / Sankaran, B. / Hockla, A. / Lacham, S. / Caulfield, T.R. / Radisky, E.S. / Papo, N.
History
DepositionAug 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRSS3 protein
E: Amyloid-beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4314
Polymers33,3282
Non-polymers1022
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-17 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.091, 82.781, 46.559
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PRSS3 protein /


Mass: 24257.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N2U3
#2: Protein Amyloid-beta A4 protein


Mass: 9070.899 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: H7C0V9
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.97 Å3/Da / Density % sol: 37.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.8, 16% PEG 20, 000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.497→46.47 Å / Num. obs: 40015 / % possible obs: 96.46 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.057 / Rrim(I) all: 0.068 / Net I/σ(I): 7.3
Reflection shellResolution: 1.497→1.551 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C67

5c67


Resolution: 1.497→46.466 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.45
RfactorNum. reflection% reflection
Rfree0.1928 2000 5 %
Rwork0.169 --
obs0.1703 40008 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.497→46.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 5 250 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052252
X-RAY DIFFRACTIONf_angle_d0.7933071
X-RAY DIFFRACTIONf_dihedral_angle_d6.0251259
X-RAY DIFFRACTIONf_chiral_restr0.088324
X-RAY DIFFRACTIONf_plane_restr0.005405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4973-1.53470.31771130.30462446X-RAY DIFFRACTION87
1.5347-1.57620.3571360.2732716X-RAY DIFFRACTION97
1.5762-1.62260.26171400.24912677X-RAY DIFFRACTION95
1.6226-1.6750.24421410.23082728X-RAY DIFFRACTION98
1.675-1.73480.25161310.20642704X-RAY DIFFRACTION96
1.7348-1.80430.22061350.20032703X-RAY DIFFRACTION95
1.8043-1.88640.21271490.18062737X-RAY DIFFRACTION98
1.8864-1.98590.21631540.16392749X-RAY DIFFRACTION98
1.9859-2.11030.20421550.15672762X-RAY DIFFRACTION99
2.1103-2.27320.19941440.162737X-RAY DIFFRACTION98
2.2732-2.5020.18831360.16142745X-RAY DIFFRACTION97
2.502-2.8640.19391420.15932789X-RAY DIFFRACTION99
2.864-3.60810.16481740.15872700X-RAY DIFFRACTION97
3.6081-46.4880.15261500.14142815X-RAY DIFFRACTION98
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)
11.0187-0.5314-1.29173.96994.34085.3911-0.0403-0.2562-0.08220.30080.1529-0.11540.37590.1339-0.13380.13460.0252-0.00340.12690.02360.157831.5656-12.9114-26.8682
22.1644-0.1549-0.11991.6733-0.12192.7534-0.0305-0.0617-0.09570.02640.0041-0.0554-0.0169-0.20220.02320.08630.00330.00480.11180.0010.128914.6964-7.1431-26.0413
31.9231-0.7946-0.35663.13870.71772.4639-0.1495-0.2879-0.09070.37420.1109-0.14030.3405-0.02490.01280.1278-0.02110.02580.11770.0160.118218.0489-11.2793-19.6181
44.80680.97460.82424.13391.59628.1236-0.10160.1347-0.1583-0.06880.03010.0949-0.0896-0.38610.05430.12810.0273-0.02560.1845-0.00060.1719.745-1.6529-41.9709
50.8254-0.3397-0.96150.63660.19453.18350.0055-0.08230.05230.067-0.0189-0.0245-0.16640.1409-0.00250.1023-0.0129-0.01190.0902-0.01220.145424.6255-0.9526-27.4889
61.85421.0134-0.70855.11580.80193.49040.0880.1502-0.35620.0939-0.0771-0.02340.4981-0.1661-0.06370.16820.0169-0.01020.1258-0.0120.237723.6807-21.9009-33.5517
71.6430.09261.33610.2535-0.62324.838-0.09650.17170.03960.04030.0319-0.037-0.2461-0.0320.05480.12980.00950.01440.1282-0.00360.152624.89-5.2741-47.2858
81.112-0.0014-0.27242.0349-0.21312.83830.00310.0554-0.02530.02550.0318-0.11730.02540.0931-0.03280.07610.0037-0.00420.12-0.00690.158525.5036-7.7466-39.2783
93.55020.28940.0717.4433-0.77241.927-0.06650.2425-0.1161-0.36150.10520.19140.4523-0.2317-0.00150.2043-0.0281-0.00980.202-0.04350.166423.7775-15.3779-48.9829
102.4048-0.8975-1.2463.46571.07873.14330.105-0.04540.28060.0419-0.07720.0554-0.4333-0.1132-0.01290.11580.0131-0.01150.08090.00080.148216.77835.7159-34.003
113.04323.61340.16845.040.27290.0167-0.05280.1927-0.1002-0.16750.07020.0966-0.0130.1391-0.01050.14360.0171-0.02080.1332-0.03180.20418.6123-22.9917-41.478
121.04470.7739-0.14444.47151.84771.7362-0.10040.0362-0.00430.08850.10980.43090.14190.0832-0.04060.17450.0174-0.01140.17430.00620.25044.3293-26.3363-39.2061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 140 )
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 215 )
9X-RAY DIFFRACTION9chain 'A' and (resid 216 through 225 )
10X-RAY DIFFRACTION10chain 'A' and (resid 226 through 246 )
11X-RAY DIFFRACTION11chain 'E' and (resid 3 through 24 )
12X-RAY DIFFRACTION12chain 'E' and (resid 25 through 56 )

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