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- PDB-9p1c: Crystal structure of human TMPRSS11A S368A interacting with its o... -

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Basic information

Entry
Database: PDB / ID: 9p1c
TitleCrystal structure of human TMPRSS11A S368A interacting with its own zymogen activation motif
Components(Transmembrane protease serine 11A) x 2
KeywordsHYDROLASE / serine protease / zymogen activation
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, HAT/DESC1 / 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. ...Peptidase S1A, HAT/DESC1 / 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
PHOSPHATE ION / Transmembrane protease serine 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsFraser, B.J. / Dong, A. / Hastings, K. / Wilson, R.P. / Seitova, A. / Li, Y. / Arrowsmith, C.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human TMPRSS11A S368A interacting with its own zymogen activation motif
Authors: Fraser, B.J. / Dong, A. / Hastings, K. / Wilson, R.P. / Seitova, A. / Li, Y. / Arrowsmith, C.H.
History
DepositionJun 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 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: Transmembrane protease serine 11A
B: Transmembrane protease serine 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8957
Polymers47,2942
Non-polymers6015
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-18 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.785, 81.785, 44.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Transmembrane protease serine 11A / Airway trypsin-like protease 1 / Epidermal type-II transmembrane serine protease / Esophageal ...Airway trypsin-like protease 1 / Epidermal type-II transmembrane serine protease / Esophageal cancer-susceptibility gene 1 protein


Mass: 21239.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TMPRSS11A non-catalytic chain remains attached to the catalytic chain via a C175-C292 disulfide bond after zymogen cleavage activation. Most of the non-catalytic chain was removed from the ...Details: TMPRSS11A non-catalytic chain remains attached to the catalytic chain via a C175-C292 disulfide bond after zymogen cleavage activation. Most of the non-catalytic chain was removed from the crystallization experiment through proteolytic cleavage at an unknown site.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS11A, ECRG1, HATL1, HESP / Plasmid: pFHMSP-LIC-N
Details (production host): baculovirus donor vector for secreted protein production from Sf9 insect cells
Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6ZMR5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Transmembrane protease serine 11A / Airway trypsin-like protease 1 / Epidermal type-II transmembrane serine protease / Esophageal ...Airway trypsin-like protease 1 / Epidermal type-II transmembrane serine protease / Esophageal cancer-susceptibility gene 1 protein


Mass: 26054.576 Da / Num. of mol.: 1 / Mutation: S368A
Source method: isolated from a genetically manipulated source
Details: TMPRSS11A catalytic chain remains attached to the non-catalytic chain via a C175-C292 disulfide bond.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS11A, ECRG1, HATL1, HESP / Plasmid: pFHMSP-LIC-N
Details (production host): baculovirus donor vector for secreted protein production from Sf9 insect cells
Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6ZMR5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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

CrystalDescription: rhombus shaped crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.4 M sodium/potassium phosphate pH 7.4. TMPRSS11A protein (20 mg/mL) was mixed 1:1 with precipitant (0.5 uL: 0.5 uL) using an Art Robbins Phoenix crystallization robot. Crystals were ...Details: 1.4 M sodium/potassium phosphate pH 7.4. TMPRSS11A protein (20 mg/mL) was mixed 1:1 with precipitant (0.5 uL: 0.5 uL) using an Art Robbins Phoenix crystallization robot. Crystals were mounted with reservoir solution containing 10% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo cooled stream of LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.53→40 Å / Num. obs: 9798 / % possible obs: 98.9 % / Redundancy: 5.4 % / CC1/2: 0.974 / CC star: 0.993 / Rmerge(I) obs: 0.334 / Rpim(I) all: 0.153 / Rrim(I) all: 0.368 / Χ2: 1.285 / Net I/σ(I): 3.2 / Num. measured all: 103418
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.53-2.572.71.3139440.2370.6190.8441.5710.34495.6
2.57-2.623.21.2989360.3360.7090.7911.5280.36299.4
2.62-2.673.61.2939640.3890.7480.7241.4890.33397.7
2.67-2.734.21.2069710.3870.7470.6321.3660.344100
2.73-2.784.71.1599530.4830.8070.5771.2970.426100
2.78-2.854.81.149700.5190.8270.5611.2740.3798.5
2.85-2.925.40.9789560.6430.8850.4581.0820.477100
2.92-35.40.9119920.6750.8980.4291.0090.53199.6
3-3.095.80.8229520.7540.9270.3720.9030.52599.7
3.09-3.195.80.6959740.8270.9520.3150.7640.65899.9
3.19-3.360.6029500.8530.9590.2660.6590.78799.3
3.3-3.435.90.4989840.8910.9710.2240.5480.939100
3.43-3.595.60.49490.8970.9730.1830.4421.20997.8
3.59-3.786.10.3589310.9270.9810.1570.3921.44495.8
3.78-4.026.60.3269720.9610.990.1390.3551.592100
4.02-4.326.60.2819430.9720.9930.120.3061.93599.1
4.32-4.766.30.2169700.9760.9940.0950.2372.35398.7
4.76-5.456.50.199710.980.9950.0830.2082.45499.3
5.45-6.866.10.1589650.9830.9960.070.1732.28299.7
6.86-406.40.1059500.9920.9980.0460.1153.25897.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→39.38 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.891 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.565 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24644 482 4.9 %RANDOM
Rwork0.19163 ---
obs0.19431 9316 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.118 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å2-0 Å2-0 Å2
2--1.93 Å20 Å2
3----3.86 Å2
Refinement stepCycle: 1 / Resolution: 2.54→39.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 34 17 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121979
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161808
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.7872699
X-RAY DIFFRACTIONr_angle_other_deg0.5691.7594136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9575243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.709514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99610297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
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_it4.3965.166978
X-RAY DIFFRACTIONr_mcbond_other4.3935.166978
X-RAY DIFFRACTIONr_mcangle_it6.6799.2841219
X-RAY DIFFRACTIONr_mcangle_other6.6779.2821220
X-RAY DIFFRACTIONr_scbond_it5.755.6441001
X-RAY DIFFRACTIONr_scbond_other5.7475.651002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.03810.2051481
X-RAY DIFFRACTIONr_long_range_B_refined10.48252.352164
X-RAY DIFFRACTIONr_long_range_B_other10.4852.372165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.544→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 38 -
Rwork0.347 593 -
obs--86.91 %

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