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- PDB-3gym: Structure of Prostasin in Complex with Aprotinin -

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Basic information

Entry
Database: PDB / ID: 3gym
TitleStructure of Prostasin in Complex with Aprotinin
Components
  • Pancreatic trypsin inhibitor
  • ProstasinPRSS8
KeywordsHYDROLASE/INHIBITOR / Prostasin / hCAP1 / channel Activating / Aprotinin / inhibition / Disulfide bond / Pharmaceutical / Protease inhibitor / Secreted / Serine protease inhibitor / Cell membrane / Glycoprotein / Hydrolase / Membrane / Protease / Serine protease / Transmembrane / Zymogen / HYDROLASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / Formation of the cornified envelope / sulfate binding / positive regulation of sodium ion transport / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / Formation of the cornified envelope / sulfate binding / positive regulation of sodium ion transport / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine protease inhibitor complex / serine-type peptidase activity / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Prostasin
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSpraggon, G. / Hornsby, M. / Shipway, A. / Harris, J.L. / Lesley, S.A.
CitationJournal: Protein Sci. / Year: 2009
Title: Active site conformational changes of prostasin provide a new mechanism of protease regulation by divalent cations.
Authors: Spraggon, G. / Hornsby, M. / Shipway, A. / Tully, D.C. / Bursulaya, B. / Danahay, H. / Harris, J.L. / Lesley, S.A.
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: 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: Prostasin
I: Pancreatic trypsin inhibitor
B: Prostasin
J: Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)69,5084
Polymers69,5084
Non-polymers00
Water0
1
A: Prostasin
I: Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7542
Polymers34,7542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4 kcal/mol
Surface area13340 Å2
MethodPISA
2
B: Prostasin
J: Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7542
Polymers34,7542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-4 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.659, 127.335, 134.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12I
22J

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 45:285 )A45 - 285
211chain B and (resseq 45:285 )B45 - 285
112chain I and (resseq 2:55 )I2 - 55
212chain J and (resseq 2:55 )J2 - 55

NCS ensembles :
ID
1
2

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Components

#1: Protein Prostasin / PRSS8 / Serine protease 8 / Prostasin light chain / Prostasin heavy chain


Mass: 28226.553 Da / Num. of mol.: 2 / Fragment: UNP residues 45-305, Peptidase S1 domain / Mutation: C122S,N127Q,C170S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCAP1, PRSS8 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q16651, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Pancreatic trypsin inhibitor / Basic protease inhibitor / BPTI / BPI / Aprotinin


Mass: 6527.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00974

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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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.6M potassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M sodium chloride in an imidazole buffer at pH 8.0., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 17060 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/σ(I): 9.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1716 / Rsym value: 0.97 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E1X

3e1x


Resolution: 2.8→42.342 Å / SU ML: 2.27 / Isotropic thermal model: group Isotropic per residue / Cross valid method: througout / σ(F): 0.1 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 825 5.18 %random
Rwork0.2253 ---
obs0.2277 15934 84.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.308 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.3 Å20 Å20 Å2
2---4.5 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 0 0 4514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_deg1.02
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1828X-RAY DIFFRACTIONPOSITIONAL0.025
12B1828X-RAY DIFFRACTIONPOSITIONAL0.025
21I429X-RAY DIFFRACTIONPOSITIONAL0.041
22J429X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.97550.38261120.3092248X-RAY DIFFRACTION77
2.9755-3.20520.31641470.26962425X-RAY DIFFRACTION84
3.2052-3.52760.25361480.23632509X-RAY DIFFRACTION85
3.5276-4.03770.27211390.20252575X-RAY DIFFRACTION87
4.0377-5.08570.1921290.18022625X-RAY DIFFRACTION87
5.0857-42.34640.28641500.22142727X-RAY DIFFRACTION87
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)
11.5263-0.3737-0.41660.3814-0.01141.4039-0.0494-0.01480.12710.06030.0654-0.09310.158-0.1726-0.02310.2076-0.02410.00990.16020.03490.22763.083359.18320.2222
21.7541-0.07040.10291.65450.06460.78740.0636-0.09180.0872-0.0671-0.0595-0.04630.16520.13920.01430.24730.0159-0.00830.2329-0.02820.1772-6.232331.960830.2032
3-0.177-0.2447-0.43871.0628-0.68021.4302-0.17350.21950.15810.0818-0.3467-0.3892-0.0192-0.02570.40030.13770.0108-0.01390.24960.11040.41123.98376.7352-17.3167
41.4034-0.31450.01341.48120.52630.8257-0.18080.1013-0.1660.18230.29750.0210.06120.1423-0.05090.18170.0253-0.01040.3132-0.07060.211-5.448848.902948.2725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA16 - 242
2X-RAY DIFFRACTION2chain BB16 - 242
3X-RAY DIFFRACTION3chain II2 - 55
4X-RAY DIFFRACTION4chain JJ2 - 55

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