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- PDB-9dpf: Crystal structure of TMPRSS11D S368A complexed with its own zymog... -

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Basic information

Entry
Database: PDB / ID: 9dpf
TitleCrystal structure of TMPRSS11D S368A complexed with its own zymogen activation motif
Components
  • Transmembrane protease serine 11D
  • Transmembrane protease serine 11D non-catalytic chain
KeywordsHYDROLASE / human protease / zymogen motif
Function / homology
Function and homology information


respiratory gaseous exchange by respiratory system / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, HAT/DESC1 / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...Peptidase S1A, HAT/DESC1 / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / 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
Transmembrane protease serine 11D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFraser, B.J. / Dong, A. / Ilyassov, O. / Seitova, A. / Li, Y. / Edwards, A. / Benard, F. / Arrowsmith, C. / Structural Genomics Consortium (SGC)
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN154328 Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of TMPRSS11D specificity and autocleavage activation.
Authors: Fraser, B.J. / Wilson, R.P. / Ferkova, S. / Ilyassov, O. / Lac, J. / Dong, A. / Li, Y.Y. / Seitova, A. / Li, Y. / Hejazi, Z. / Kenney, T.M.G. / Penn, L.Z. / Edwards, A. / Leduc, R. / ...Authors: Fraser, B.J. / Wilson, R.P. / Ferkova, S. / Ilyassov, O. / Lac, J. / Dong, A. / Li, Y.Y. / Seitova, A. / Li, Y. / Hejazi, Z. / Kenney, T.M.G. / Penn, L.Z. / Edwards, A. / Leduc, R. / Boudreault, P.L. / Morin, G.B. / Benard, F. / Arrowsmith, C.H.
History
DepositionSep 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protease serine 11D
B: Transmembrane protease serine 11D non-catalytic chain
C: Transmembrane protease serine 11D
D: Transmembrane protease serine 11D non-catalytic chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6216
Polymers54,4974
Non-polymers1242
Water4,774265
1
A: Transmembrane protease serine 11D
B: Transmembrane protease serine 11D non-catalytic chain


Theoretical massNumber of molelcules
Total (without water)27,2492
Polymers27,2492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-8 kcal/mol
Surface area11430 Å2
MethodPISA
2
C: Transmembrane protease serine 11D
D: Transmembrane protease serine 11D non-catalytic chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3734
Polymers27,2492
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-3 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.034, 76.640, 88.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transmembrane protease serine 11D / Airway trypsin-like protease


Mass: 25318.490 Da / Num. of mol.: 2 / Mutation: S368A
Source method: isolated from a genetically manipulated source
Details: Catalytic chain is covalently linked to the non-catalytic chain through a C173-C292 disulfide bond
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS11D, HAT / Plasmid: pFHMSP-LIC-N
Details (production host): pFAST-BAC HTA derivative that enables secreted protein production from Sf9 insect cells
Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O60235, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Transmembrane protease serine 11D non-catalytic chain


Mass: 1930.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Non-catatlyic chain is covalently linked to the catalytic chain through a C173-C292 disulfide bond. Most of the non-catalytic domain is not observed in the crystal structure, and has likely ...Details: Non-catatlyic chain is covalently linked to the catalytic chain through a C173-C292 disulfide bond. Most of the non-catalytic domain is not observed in the crystal structure, and has likely been cleaved based on SDS-PAGE gel migration patterns.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS11D, HAT / Plasmid: pFHMSP-LIC-N
Details (production host): pFAST-BAC HTA derivative vector that enables secreted protein production from Sf9 insect cells
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60235
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.5M Mg form, 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo cooled / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 14, 2024
RadiationMonochromator: Cryo-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 37404 / % possible obs: 99.2 % / Redundancy: 11.4 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.056 / Rrim(I) all: 0.192 / Χ2: 1.76 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.98-2.019.41.30817290.8170.9480.4261.380.37399.7
2.01-2.059.91.07517140.8680.9640.3431.1310.38899.9
2.05-2.0910.50.917240.9260.980.280.9440.4100
2.09-2.13110.83217360.9420.9850.2530.870.414100
2.13-2.1811.60.81617300.9430.9850.2440.8530.411100
2.18-2.2310.40.83517100.9340.9830.2610.8760.45599.8
2.23-2.295.70.67916130.7690.9320.270.7342.79691.9
2.29-2.3511.70.62117350.9650.9910.1890.650.48899.8
2.35-2.42130.51417310.9740.9930.1470.5350.522100
2.42-2.4912.30.45617400.9760.9940.1350.4760.518100
2.49-2.5812.80.37617370.9820.9960.1090.3920.533100
2.58-2.6913.80.34417530.9740.9930.0950.3570.703100
2.69-2.8113.70.28917500.9860.9970.080.30.789100
2.81-2.9613.60.24317510.9860.9960.0680.2520.975100
2.96-3.1413.40.20417580.960.990.0580.2131.573100
3.14-3.3913.20.1617610.9870.9970.0460.1672.139100
3.39-3.7310.10.16816950.9770.9940.0530.1765.51995.7
3.73-4.269.30.12817850.9260.980.0440.1365.68298.7
4.26-5.3710.50.11217880.9860.9960.0360.1188.44399.5
5.37-4012.30.07919280.9970.9990.0240.0824.15599.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.391 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25411 1976 5 %RANDOM
Rwork0.19868 ---
obs0.20141 37404 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.976 Å2
Baniso -1Baniso -2Baniso -3
1-3.31 Å2-0 Å20 Å2
2--0.95 Å2-0 Å2
3----4.26 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 8 265 4053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0113977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163445
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.6425452
X-RAY DIFFRACTIONr_angle_other_deg0.5181.5588043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0245519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.068526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26710586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6463.2022023
X-RAY DIFFRACTIONr_mcbond_other2.6463.2022023
X-RAY DIFFRACTIONr_mcangle_it3.6454.7892531
X-RAY DIFFRACTIONr_mcangle_other3.6464.7892532
X-RAY DIFFRACTIONr_scbond_it3.8893.6331954
X-RAY DIFFRACTIONr_scbond_other3.8883.6351955
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8065.282912
X-RAY DIFFRACTIONr_long_range_B_refined7.46149.1414476
X-RAY DIFFRACTIONr_long_range_B_other7.46149.1354476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 141 -
Rwork0.394 2490 -
obs--90.2 %

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