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- PDB-1eaw: Crystal structure of the MTSP1 (matriptase)-BPTI (aprotinin) complex -

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Basic information

Entry
Database: PDB / ID: 1eaw
TitleCrystal structure of the MTSP1 (matriptase)-BPTI (aprotinin) complex
Components
  • PANCREATIC TRYPSIN INHIBITOR
  • SUPPRESSOR OF TUMORIGENICITY 14
KeywordsHYDROLASE/INHIBITOR / COMPLEX (SERINE PROTEASE INHIBITOR) / SERINE PROTEINASE / MATRIX DEGRADATION / INHIBITOR / GLYCOPROTE HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


matriptase / epithelial cell morphogenesis involved in placental branching / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / Formation of the cornified envelope / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity ...matriptase / epithelial cell morphogenesis involved in placental branching / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / Formation of the cornified envelope / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / keratinocyte differentiation / serine protease inhibitor complex / serine-type peptidase activity / neural tube closure / serine-type endopeptidase inhibitor activity / protein catabolic process / protease binding / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / plasma membrane
Similarity search - Function
Peptidase S1A, matripase / 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 ...Peptidase S1A, matripase / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pancreatic trypsin inhibitor / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsFriedrich, R. / Bode, W.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Catalytic Domain Structures of Mt-Sp1/Matriptase, a Matrix-Degrading Transmembrane Serine Proteinase.
Authors: Friedrich, R. / Fuentes-Prior, P. / Ong, E. / Coombs, G. / Hunter, M. / Oehler, R. / Pierson, D. / Gonzalez, R. / Huber, R. / Bode, W. / Madison, E.L.
History
DepositionJul 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 13, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "CA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" AND "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPPRESSOR OF TUMORIGENICITY 14
B: PANCREATIC TRYPSIN INHIBITOR
C: SUPPRESSOR OF TUMORIGENICITY 14
D: PANCREATIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)65,9834
Polymers65,9834
Non-polymers00
Water1,44180
1
A: SUPPRESSOR OF TUMORIGENICITY 14
B: PANCREATIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)32,9912
Polymers32,9912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SUPPRESSOR OF TUMORIGENICITY 14
D: PANCREATIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)32,9912
Polymers32,9912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.099, 54.233, 67.824
Angle α, β, γ (deg.)107.62, 96.86, 103.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SUPPRESSOR OF TUMORIGENICITY 14 / MATRIPTASE / MEMBRANE-TYPE SERINE PROTEASE 1 / MT-SP1


Mass: 26463.756 Da / Num. of mol.: 2 / Fragment: CATALYTIC RESIDUES 615-855
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: Q9Y5Y6, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein PANCREATIC TRYPSIN INHIBITOR / BBASIC PROTEASE INHIBITOR / BPI / BPTI / APROTININ


Mass: 6527.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00974
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: 4HTC
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MHEPES1reservoirpH6.5
220 %PEG40001reservoir
32 %1reservoirCsCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.93→12 Å / Num. obs: 12200 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: -0.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.4
Reflection shellResolution: 2.93→3.11 Å / % possible all: 93.1
Reflection
*PLUS
Lowest resolution: 12 Å / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
% possible obs: 93.1 % / Rmerge(I) obs: 0.343

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HTC

4htc


Resolution: 2.93→11.99 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 722936.73 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 984 8.1 %SHELLS
Rwork0.199 ---
obs0.199 12200 94.4 %-
Solvent computationSolvent model: MODEL
Displacement parametersBiso mean: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-
2--0 Å2-
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.93→11.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 0 80 4698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.93→3.11 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 152 7.6 %
Rwork0.3 1855 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SO4.PARSO4.TOP
X-RAY DIFFRACTION3BEN.PARSO4.PAR
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rwork: 0.3

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