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- PDB-8vis: Human TMPRSS11D complexed with a disulfide-linked autoinhibitory ... -

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Basic information

Entry
Database: PDB / ID: 8vis
TitleHuman TMPRSS11D complexed with a disulfide-linked autoinhibitory DDDDK peptide
Components(Transmembrane protease serine 11D ...) x 2
KeywordsHYDROLASE / Human protease / viral entry / Structural Genomics / Structural Genomics Consortium / SGC
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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: 1.59 Å
AuthorsFraser, B.J. / Dong, A. / Ilyassov, O. / Kenney, T. / Li, Y.Y. / Seitova, A. / Li, Y. / Hejazi, Z. / Edwards, A. / Benard, F. / Arrowsmith, C.
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: Biorxiv / Year: 2024
Title: Structural basis of TMPRSS11D specificity and autocleavage activation
Authors: Fraser, B.J. / Wilson, R.P. / Ilyassov, O. / Lac, J. / Dong, A. / Li, Y.Y. / Seitova, A. / Li, Y. / Hejazi, Z. / Kenney, T.M. / Penn, L.Z. / Edwards, A. / Morin, G.B. / Benard, F. / Arrowsmith, C.H.
History
DepositionJan 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)173,47820
Polymers173,0978
Non-polymers38112
Water20,6991149
1
A: Transmembrane protease serine 11D non-catalytic chain
B: Transmembrane protease serine 11D catalytic chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4535
Polymers43,2742
Non-polymers1783
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-12 kcal/mol
Surface area10920 Å2
MethodPISA
2
C: Transmembrane protease serine 11D non-catalytic chain
D: Transmembrane protease serine 11D catalytic chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3665
Polymers43,2742
Non-polymers923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-10 kcal/mol
Surface area11830 Å2
MethodPISA
3
E: Transmembrane protease serine 11D non-catalytic chain
F: Transmembrane protease serine 11D catalytic chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2994
Polymers43,2742
Non-polymers242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-18 kcal/mol
Surface area11350 Å2
MethodPISA
4
G: Transmembrane protease serine 11D non-catalytic chain
H: Transmembrane protease serine 11D catalytic chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3616
Polymers43,2742
Non-polymers864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-11 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.676, 119.676, 134.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11F-827-

HOH

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Components

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Transmembrane protease serine 11D ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Transmembrane protease serine 11D non-catalytic chain


Mass: 16330.101 Da / Num. of mol.: 4 / Mutation: L182D,S183D,E184D,Q185D,R186K
Source method: isolated from a genetically manipulated source
Details: Remainder of protein appears to have undergone autocleavage and has been shed. Molecular weight of the target protein structure matches the molecular weight found on SDS-PAGE.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS11D, HAT / Plasmid: pFHMSP-LIC C
Details (production host): baculovirus donor vector for secreted protein production
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60235
#2: Protein
Transmembrane protease serine 11D catalytic chain


Mass: 26944.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Linked to the non-catalytic domain through a disulfide bond (Cys173-Cys292) after proteolytic cleavage at Lys186/Ile187 peptide bond.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS11D, HAT / Plasmid: pFHMSP-LIC C
Details (production host): baculovirus donor vector for secreted protein production
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60235

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Non-polymers , 5 types, 1161 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1149 / 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: 1.94 Å3/Da / Density % sol: 36.6 % / Description: tetrahedral
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.5 uL protein (30 mg/mL; in 50 mM Tris pH 8.0, 200 mM NaCl) mixed 1:1 with precipitant (20%PEG1500, 0.2M MgCl2, 0.1M HEPES pH 7.5) through automated addition with Art Robbin Phoenix robot.
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 129049 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.954 / CC star: 0.988 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.115 / Rrim(I) all: 0.261 / Χ2: 1.173 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.39-2.434.32.00432790.2690.6511.0252.2560.48599.7
2.43-2.484.41.90333080.1250.4710.9752.1440.50899.7
2.48-2.524.51.61832800.3240.70.8211.8180.50399.9
2.52-2.574.61.17233500.4140.7650.5921.3160.54399.8
2.57-2.634.51.01133230.7780.9360.5081.1330.55699.7
2.63-2.694.60.99933390.5290.8320.5021.1210.568100
2.69-2.764.60.80732630.5330.8340.4040.9040.60799.9
2.76-2.834.70.73633090.8630.9630.3650.8230.66999.9
2.83-2.924.80.60333540.7830.9370.3010.6760.673100
2.92-3.014.90.533040.8560.9610.2470.5590.77799.9
3.01-3.124.90.41733280.8080.9450.2090.4670.88999.8
3.12-3.244.80.35732850.8670.9640.1810.4011.10699.6
3.24-3.394.50.31732960.8430.9560.1660.361.29399.3
3.39-3.574.90.25732640.880.9680.1280.2881.50499
3.57-3.795.40.19933250.960.990.0950.2211.819100
3.79-4.095.40.1633340.9850.9960.0760.1782.01499.9
4.09-4.55.30.12733160.9790.9950.0610.1412.34599.9
4.5-5.155.40.09833180.9930.9980.0470.1092.142100
5.15-6.485.10.09333160.9920.9980.0450.1041.70499.9
6.48-505.40.05933120.9970.9990.0280.0661.71199.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→49.77 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.656 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 1331 1 %RANDOM
Rwork0.15502 ---
obs0.15535 129049 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0 Å2
2---0.11 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.59→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7732 0 28 1149 8909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0118410
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167291
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.64211578
X-RAY DIFFRACTIONr_angle_other_deg0.5661.55917112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59551137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.265558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.489101283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.21266
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021677
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_it1.5711.4414219
X-RAY DIFFRACTIONr_mcbond_other1.5681.4414219
X-RAY DIFFRACTIONr_mcangle_it2.3932.1535299
X-RAY DIFFRACTIONr_mcangle_other2.3942.1545300
X-RAY DIFFRACTIONr_scbond_it2.6331.7574191
X-RAY DIFFRACTIONr_scbond_other2.6311.7564190
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9832.5286220
X-RAY DIFFRACTIONr_long_range_B_refined5.81328.70610171
X-RAY DIFFRACTIONr_long_range_B_other5.58825.4939859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.591→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 106 -
Rwork0.24 9407 -
obs--99.93 %

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