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- PDB-9bos: Human mesotrypsin (PRSS3) unliganded and in an active (E) conformation -

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Basic information

Entry
Database: PDB / ID: 9bos
TitleHuman mesotrypsin (PRSS3) unliganded and in an active (E) conformation
ComponentsTrypsin-3
KeywordsHYDROLASE / Serine protease / autoinhibited / conformational variability
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / antimicrobial humoral response / Alpha-defensins / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / zymogen activation / Antimicrobial peptides / trypsin / endothelial cell migration / digestion / serine-type peptidase activity ...Uptake of dietary cobalamins into enterocytes / antimicrobial humoral response / Alpha-defensins / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / zymogen activation / Antimicrobial peptides / trypsin / endothelial cell migration / digestion / serine-type peptidase activity / tertiary granule lumen / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
dimethyl ether / Trypsin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCoban, M. / Vargas, L.M.F. / Sankaran, B. / Radisky, E.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM144393-01 United States
CitationJournal: Sci Adv / Year: 2025
Title: Discovery of an autoinhibited conformation in mesotrypsin reveals a new strategy for selective serine protease inhibition.
Authors: Coban, M. / Gokara, M. / Vargas, L.M.F. / Tanzer, S. / Zhou, S. / Hockla, A. / Sankaran, B. / Caulfield, T.R. / Radisky, E.S.
History
DepositionMay 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4555
Polymers24,2871
Non-polymers1684
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.849, 55.849, 142.358
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Protein Trypsin-3 / Brain trypsinogen / Mesotrypsin / Mesotrypsinogen / Serine protease 3 / Serine protease 4 / Trypsin ...Brain trypsinogen / Mesotrypsin / Mesotrypsinogen / Serine protease 3 / Serine protease 4 / Trypsin III / Trypsin IV


Mass: 24287.482 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS3, PRSS4, TRY3, TRY4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35030, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-2F2 / dimethyl ether


Mass: 46.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.29 Å3/Da / Density % sol: 46.18 % / Description: large rectangular crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 15% PEG 20000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 1, 2023
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.7→43.94 Å / Num. obs: 25656 / % possible obs: 99.8 % / Redundancy: 21.2 % / Biso Wilson estimate: 29.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.026 / Rrim(I) all: 0.12 / Net I/σ(I): 19.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 19.15 % / Rmerge(I) obs: 1.951 / Mean I/σ(I) obs: 2 / Num. unique obs: 2494 / CC1/2: 0.952 / Rpim(I) all: 0.45 / Rrim(I) all: 2.004 / % possible all: 99.52

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.94 Å / SU ML: 0.2037 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.2481
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2622 1232 5.01 %
Rwork0.2398 23370 -
obs0.241 24602 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.78 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 8 151 1854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01791752
X-RAY DIFFRACTIONf_angle_d1.51842385
X-RAY DIFFRACTIONf_chiral_restr0.0894263
X-RAY DIFFRACTIONf_plane_restr0.0113312
X-RAY DIFFRACTIONf_dihedral_angle_d16.0955639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.40641360.3682572X-RAY DIFFRACTION97.73
1.77-1.850.42221340.36312553X-RAY DIFFRACTION96.14
1.85-1.950.42861280.38462406X-RAY DIFFRACTION90.6
1.95-2.070.3811330.33492532X-RAY DIFFRACTION94.24
2.07-2.230.35751310.32612482X-RAY DIFFRACTION92.86
2.23-2.450.38841340.30032543X-RAY DIFFRACTION94.93
2.45-2.810.30111380.26662625X-RAY DIFFRACTION96.81
2.81-3.540.22951440.22132742X-RAY DIFFRACTION99.11
3.54-43.940.19271540.17992915X-RAY DIFFRACTION99.48
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)
11.600526887910.5211246132950.7965864216391.649068177910.5028724234741.18460210322-0.21269956544-0.0387846870366-0.00153921202763-0.6554379037550.45959851341-0.596893825405-0.3471164406971.35410896113-0.1729813326520.167588976866-0.02762851461090.164021204991.14006328155-0.1751517306440.4572908183144.7980959067425.993607817814.2965692168
24.459966691293.147345431482.009028986664.528562241521.458621062972.09395799813-0.150632991510.0982790273811-0.483296496637-0.3109511451510.488414781412-0.7928097386420.04617607630180.945431953395-0.3168700972310.2496616737910.1045037923360.06929650172120.765446314189-0.04903379646490.4304642015272.3125182949516.771170441617.1406500859
33.020526967821.55522461049-0.05542355396785.33477882139-0.07813802824953.85690002978-0.151285609747-0.2401974700850.00648909223452-0.6552586724290.2594709371310.2583323008540.03407212615570.292173079999-0.08887123541260.275727380878-0.000963355692638-0.0412403262520.2893765627410.0134907749060.238616876308-11.320983666122.49015931619.75318258118
44.92639893204-0.8416286545610.5209728839556.99829067268-1.961588842554.21616837784-0.0164817860274-0.532486937147-0.291503819189-0.4832575549360.377798731427-0.06635877777360.6271713146110.122844872653-0.4053872517270.1917327657120.0148947936210.05424971692650.305715532844-0.06097810620020.270708066278-6.8671348468114.348479186514.259591711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 246 )

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