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- PDB-9bot: Human mesotrypsin (PRSS3) unliganded and in autoinhibited (E*) co... -

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Basic information

Entry
Database: PDB / ID: 9bot
TitleHuman mesotrypsin (PRSS3) unliganded and in autoinhibited (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
ACETATE ION / Trypsin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCoban, M. / 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

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Assembly

Deposited unit
A: Trypsin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6716
Polymers24,2871
Non-polymers3835
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.024, 77.700, 93.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Trypsin-3 / Brain trypsinogen / 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

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Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.77 % / Description: large irregular rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.8M ammonium sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.6→40.1 Å / Num. obs: 31270 / % possible obs: 98.72 % / Redundancy: 5.59 % / CC1/2: 0.949 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.053 / Rrim(I) all: 0.125 / Net I/σ(I): 14.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.68 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2996 / CC1/2: 0.872 / Rpim(I) all: 0.272 / Rrim(I) all: 0.665 / % possible all: 97.46

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Processing

Software
NameVersionClassification
PHENIX(dev_2902: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→40.097 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 1550 5 %
Rwork0.1473 --
obs0.1497 31019 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→40.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 21 201 1881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181780
X-RAY DIFFRACTIONf_angle_d1.7732443
X-RAY DIFFRACTIONf_dihedral_angle_d11.113625
X-RAY DIFFRACTIONf_chiral_restr0.104269
X-RAY DIFFRACTIONf_plane_restr0.015317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65160.27641360.18332580X-RAY DIFFRACTION97
1.6516-1.71070.20251390.16962634X-RAY DIFFRACTION98
1.7107-1.77920.26781390.15332655X-RAY DIFFRACTION98
1.7792-1.86010.23721390.14992629X-RAY DIFFRACTION98
1.8601-1.95820.23821380.15472638X-RAY DIFFRACTION98
1.9582-2.08090.19541390.14032652X-RAY DIFFRACTION98
2.0809-2.24150.19921410.1352691X-RAY DIFFRACTION98
2.2415-2.46710.19111430.13782712X-RAY DIFFRACTION98
2.4671-2.8240.18531410.15472681X-RAY DIFFRACTION98
2.824-3.55760.18581440.14632733X-RAY DIFFRACTION97
3.5576-40.0970.16071510.14232864X-RAY DIFFRACTION98

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