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- PDB-4isl: Crystal Structure of the inactive Matriptase in complex with its ... -

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Basic information

Entry
Database: PDB / ID: 4isl
TitleCrystal Structure of the inactive Matriptase in complex with its inhibitor HAI-1
Components
  • Kunitz-type protease inhibitor 1
  • Suppressor of tumorigenicity 14 protein
Keywordshydrolase/hydrolase inhibitor / Beta barrel / Serine protease inhibitor / epithelium / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


positive regulation of glial cell differentiation / epithelium development / Signaling by MST1 / matriptase / epithelial cell morphogenesis involved in placental branching / negative regulation of neural precursor cell proliferation / MET Receptor Activation / branching involved in labyrinthine layer morphogenesis / Formation of the cornified envelope / placenta blood vessel development ...positive regulation of glial cell differentiation / epithelium development / Signaling by MST1 / matriptase / epithelial cell morphogenesis involved in placental branching / negative regulation of neural precursor cell proliferation / MET Receptor Activation / branching involved in labyrinthine layer morphogenesis / Formation of the cornified envelope / placenta blood vessel development / cellular response to BMP stimulus / epidermis development / keratinocyte differentiation / extracellular matrix organization / serine-type peptidase activity / neural tube closure / protein catabolic process / serine-type endopeptidase inhibitor activity / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / Peptidase S1A, matripase / MANSC domain profile. / K319L-like, PKD domain / SEA domain superfamily / SEA domain profile. / SEA domain ...MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / Peptidase S1A, matripase / MANSC domain profile. / K319L-like, PKD domain / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Pancreatic trypsin inhibitor Kunitz domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Factor Xa Inhibitor / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / 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. / 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 / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLUTATHIONE / TRIETHYLENE GLYCOL / Kunitz-type protease inhibitor 1 / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHuang, M.D. / Zhao, B.Y. / Yuan, C. / Li, R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal structures of matriptase in complex with its inhibitor hepatocyte growth factor activator inhibitor-1.
Authors: Zhao, B. / Yuan, C. / Li, R. / Qu, D. / Huang, M. / Ngo, J.C.
History
DepositionJan 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Kunitz-type protease inhibitor 1
A: Suppressor of tumorigenicity 14 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3328
Polymers33,4042
Non-polymers9286
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-8 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.934, 61.934, 178.997
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein Kunitz-type protease inhibitor 1 / Hepatocyte growth factor activator inhibitor type 1 / HAI-1


Mass: 6941.824 Da / Num. of mol.: 1 / Fragment: Kunitz domain I (unp residues 245-304)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAI1, SPINT1, UNQ223/PRO256 / Plasmid: PMT/BIP/V5-his-A / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: O43278
#2: Protein Suppressor of tumorigenicity 14 protein / Matriptase / Membrane-type serine protease 1 / MT-SP1 / Prostamin / Serine protease 14 / Serine ...Matriptase / Membrane-type serine protease 1 / MT-SP1 / Prostamin / Serine protease 14 / Serine protease TADG-15 / Tumor-associated differentially-expressed gene 15 protein


Mass: 26461.783 Da / Num. of mol.: 1 / Fragment: Serine protease domain (unp residues 615-855) / Mutation: N164Q, S805A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS14, SNC19, ST14, TADG15 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q9Y5Y6, matriptase

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Non-polymers , 5 types, 178 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, 20% (w/v) polyethylene glycol 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 29858 / % possible obs: 98.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.057 / Χ2: 2.247 / Net I/σ(I): 21.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.29-2.336.90.14912521.866183
2.33-2.377.70.14415291.85198.6
2.37-2.428.20.1414401.86198.6
2.42-2.478.20.12315031.93198.8
2.47-2.528.20.11915011.917198.7
2.52-2.588.20.11115291.942198.8
2.58-2.648.20.09914422.095198.8
2.64-2.728.20.09215192.095198.7
2.72-2.798.20.08415212.13199.1
2.79-2.898.10.07914752.167199.1
2.89-2.998.10.07215062.278199.1
2.99-3.118.10.06315232.339199.2
3.11-3.258.10.05915102.469199.2
3.25-3.428.10.05314772.453199.5
3.42-3.638.10.04915502.53199.4
3.63-3.928.10.04514942.547199.3
3.92-4.3180.04415022.743199.5
4.31-4.937.90.04415182.883199.6
4.93-6.217.80.04215382.577199.4
6.21-507.80.03615292.162198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P8G

3p8g


Resolution: 2.29→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.534 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 823 5.1 %RANDOM
Rwork0.1838 ---
obs0.1861 16250 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.75 Å2 / Biso mean: 21.6666 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 61 172 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212512
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9543395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4255303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3323.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66215379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4731519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211946
X-RAY DIFFRACTIONr_mcbond_it0.3891.51509
X-RAY DIFFRACTIONr_mcangle_it0.78822414
X-RAY DIFFRACTIONr_scbond_it1.20331003
X-RAY DIFFRACTIONr_scangle_it2.0614.5981
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 52 -
Rwork0.186 1056 -
all-1108 -
obs--95.03 %

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