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- PDB-7qe8: Human cationic trypsin (TRY1) complexed with serine protease inhi... -

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Basic information

Entry
Database: PDB / ID: 7qe8
TitleHuman cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 (SPINK1)
Components
  • Serine protease inhibitor Kazal-type 1
  • Trypsin-1
KeywordsHYDROLASE / TRY1 / SPINK1 / serine protease / protease-inhibitor complex / catalytic triad
Function / homology
Function and homology information


negative regulation of nitric oxide mediated signal transduction / Uptake of dietary cobalamins into enterocytes / negative regulation of calcium ion import / regulation of acrosome reaction / regulation of store-operated calcium entry / Developmental Lineage of Pancreatic Acinar Cells / endopeptidase inhibitor activity / sperm capacitation / Activation of Matrix Metalloproteinases / nitric oxide mediated signal transduction ...negative regulation of nitric oxide mediated signal transduction / Uptake of dietary cobalamins into enterocytes / negative regulation of calcium ion import / regulation of acrosome reaction / regulation of store-operated calcium entry / Developmental Lineage of Pancreatic Acinar Cells / endopeptidase inhibitor activity / sperm capacitation / Activation of Matrix Metalloproteinases / nitric oxide mediated signal transduction / extracellular matrix disassembly / trypsin / digestion / serine-type endopeptidase inhibitor activity / : / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / : / 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 / 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
Serine protease inhibitor Kazal-type 1 / Serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNagel, F. / Palm, G.J. / Delcea, M. / Lammers, M.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)637877European Union
European Union (EU)ESF/14-BM-A55-0047/16European Union
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structural and Biophysical Insights into SPINK1 Bound to Human Cationic Trypsin.
Authors: Nagel, F. / Palm, G.J. / Geist, N. / McDonnell, T.C.R. / Susemihl, A. / Girbardt, B. / Mayerle, J. / Lerch, M.M. / Lammers, M. / Delcea, M.
History
DepositionDec 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin-1
B: Trypsin-1
C: Serine protease inhibitor Kazal-type 1
D: Serine protease inhibitor Kazal-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0397
Polymers60,7514
Non-polymers2883
Water181
1
A: Trypsin-1
D: Serine protease inhibitor Kazal-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4713
Polymers30,3752
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-29 kcal/mol
Surface area12380 Å2
MethodPISA
2
B: Trypsin-1
C: Serine protease inhibitor Kazal-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5674
Polymers30,3752
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-42 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.626, 77.626, 187.349
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Trypsin-1 / Beta-trypsin / Cationic trypsinogen / Serine protease 1 / Trypsin I


Mass: 24121.201 Da / Num. of mol.: 2 / Mutation: S200A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / References: UniProt: P07477, trypsin
#2: Protein Serine protease inhibitor Kazal-type 1 / Pancreatic secretory trypsin inhibitor / Tumor-associated trypsin inhibitor / TATI


Mass: 6254.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPINK1, PSTI / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / References: UniProt: P00995
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1 ul protein solution (20 mg/mL in 20 mM HEPES, pH 7.4, 150 mM NaCl) + 1 ul well solution (15% PEG 4000, 0.3 M AS), cryo 15% PEG 4000, 0.3 M AS, 8% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2021 / Details: DCM Si(111)
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 15112 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 19.1 % / Biso Wilson estimate: 85.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.17 / Rsym value: 0.166 / Net I/σ(I): 16.32
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 19.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2371 / CC1/2: 0.55 / Rrim(I) all: 2.721 / Rsym value: 2.651 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSVERSION Feb 5, 2021data reduction
XDSVERSION Feb 5, 2021data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TRN_A, 1CGI_I

Resolution: 2.9→45.75 Å / SU ML: 0.399 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 1509 9.99 %
Rwork0.2229 13589 -
obs0.225 15098 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.14 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 15 1 4230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054320
X-RAY DIFFRACTIONf_angle_d1.61885863
X-RAY DIFFRACTIONf_chiral_restr0.0829637
X-RAY DIFFRACTIONf_plane_restr0.01774
X-RAY DIFFRACTIONf_dihedral_angle_d17.5387602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.37421330.36571191X-RAY DIFFRACTION97.64
2.99-3.10.37771330.33421199X-RAY DIFFRACTION100
3.1-3.230.34031370.33551221X-RAY DIFFRACTION100
3.23-3.370.33331390.28761219X-RAY DIFFRACTION100
3.37-3.550.28231360.26471220X-RAY DIFFRACTION100
3.55-3.770.25511300.24251211X-RAY DIFFRACTION99.85
3.77-4.060.26161380.22791239X-RAY DIFFRACTION100
4.06-4.470.24561360.19431226X-RAY DIFFRACTION100
4.47-5.120.22061400.19291250X-RAY DIFFRACTION99.93
5.12-6.440.23361350.2191280X-RAY DIFFRACTION100
6.45-45.750.1891520.18371333X-RAY DIFFRACTION99.46
Refinement TLS params.Method: refined / Origin x: 2.85751608147 Å / Origin y: -22.8467911327 Å / Origin z: 11.6924138972 Å
111213212223313233
T0.873217124037 Å2-0.276353378849 Å2-0.25945411626 Å2-0.677371276093 Å20.157093655712 Å2--0.747447550667 Å2
L2.8252442398 °21.05267376098 °2-0.805705452881 °2-0.942758312526 °2-0.125428332687 °2--1.81850265099 °2
S-0.146797497796 Å °0.434560241109 Å °0.174205071999 Å °-0.253055227166 Å °0.204870874383 Å °0.267925616763 Å °0.0936002007952 Å °-0.466005147323 Å °-0.0428801158663 Å °
Refinement TLS groupSelection details: all

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