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- PDB-9jd1: Crystal structure of TMPRSS2 in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 9jd1
TitleCrystal structure of TMPRSS2 in complex with Fab
Components
  • (Transmembrane protease serine 2 ...) x 2
  • Heavy chain of Fab
  • Light chain of Fab
KeywordsANTIVIRAL PROTEIN / Complex / Antibody / Host protease
Function / homology
Function and homology information


transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat ...Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, H. / Liu, X. / Zhao, Z. / Duan, Y. / Yang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169109 China
CitationJournal: Nat Commun / Year: 2025
Title: The crystal structure of coronavirus RBD-TMPRSS2 complex provides basis for the discovery of therapeutic antibodies.
Authors: Zhao, Z. / Yang, Q. / Liu, X. / Li, M. / Duan, Y. / Du, M. / Zhou, A. / Liu, H. / He, Y. / Wang, W. / Lu, Y. / Zhang, X. / Wang, H. / Yang, X. / Zhang, H. / Chen, X. / Rao, Z. / Yang, H.
History
DepositionAug 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Transmembrane protease serine 2 catalytic chain
A: Light chain of Fab
B: Heavy chain of Fab
C: Transmembrane protease serine 2 non-catalytic chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7419
Polymers93,4114
Non-polymers1,3305
Water12,016667
1
D: Transmembrane protease serine 2 catalytic chain
C: Transmembrane protease serine 2 non-catalytic chain
hetero molecules

A: Light chain of Fab
B: Heavy chain of Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7419
Polymers93,4114
Non-polymers1,3305
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area8040 Å2
ΔGint-21 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.164, 89.176, 201.533
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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Transmembrane protease serine 2 ... , 2 types, 2 molecules DC

#1: Protein Transmembrane protease serine 2 catalytic chain


Mass: 27856.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression. Residues 250-255 responsible for autocleavage are substituted with DDDDK. The recombinant ...Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression. Residues 250-255 responsible for autocleavage are substituted with DDDDK. The recombinant protein was cleaved into two chains (A and C) in the purification.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393
#4: Protein Transmembrane protease serine 2 non-catalytic chain


Mass: 16054.661 Da / Num. of mol.: 1 / Mutation: S250D,S251D,R252D,Q253D, S254K
Source method: isolated from a genetically manipulated source
Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression. Residues 250-255 responsible for autocleavage are substituted with DDDDK. The recombinant ...Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression. Residues 250-255 responsible for autocleavage are substituted with DDDDK. The recombinant protein was cleaved into two chains (A and C) in the purification.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393

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Antibody , 2 types, 2 molecules AB

#2: Antibody Light chain of Fab


Mass: 23615.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Heavy chain of Fab


Mass: 25883.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The recombinant protein encompasses a C-terminal linker ("GS") followed by a 6 x His tag.
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 1 types, 1 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 671 molecules

#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 50 mM MES pH 5.6, 8.6% (w/v) Polyethylene glycol 4,000, 17.1% (v/v) Polyethylene glycol 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.9→31.43 Å / Num. obs: 66877 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.124 / Net I/σ(I): 12.55
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.9-2.010.836106220.9240.8711
2.01-2.150.54499860.9630.5661
2.15-2.320.37393920.9820.3891
2.32-2.540.26586410.9890.2761
2.54-2.840.17478650.9940.1821
2.84-3.280.11669760.9970.1211
3.28-4.010.08659460.9970.091
4.01-5.650.07346840.9970.0761
5.65-31.430.06427650.9980.0671

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.43 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 3798 2.99 %
Rwork0.1901 --
obs0.1911 126953 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→31.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6180 0 62 667 6909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056442
X-RAY DIFFRACTIONf_angle_d0.8028772
X-RAY DIFFRACTIONf_dihedral_angle_d16.1032322
X-RAY DIFFRACTIONf_chiral_restr0.056970
X-RAY DIFFRACTIONf_plane_restr0.0071128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.39651370.36044491X-RAY DIFFRACTION98
1.92-1.950.3311400.30074497X-RAY DIFFRACTION100
1.95-1.970.29061400.2844594X-RAY DIFFRACTION100
1.97-20.30031450.26874619X-RAY DIFFRACTION100
2-2.030.30871410.25974523X-RAY DIFFRACTION100
2.03-2.060.25291370.2434546X-RAY DIFFRACTION100
2.06-2.10.27611430.24054628X-RAY DIFFRACTION100
2.1-2.130.30791400.22644548X-RAY DIFFRACTION100
2.13-2.170.2731450.2334561X-RAY DIFFRACTION100
2.17-2.210.2991350.22614553X-RAY DIFFRACTION100
2.21-2.260.25661430.21084536X-RAY DIFFRACTION100
2.26-2.310.28931390.21764589X-RAY DIFFRACTION100
2.31-2.360.27231410.21124532X-RAY DIFFRACTION100
2.36-2.420.29141480.20834616X-RAY DIFFRACTION100
2.42-2.490.22651390.20964511X-RAY DIFFRACTION100
2.49-2.560.24561410.21124632X-RAY DIFFRACTION100
2.56-2.640.26671390.20084520X-RAY DIFFRACTION100
2.64-2.740.26781400.20794590X-RAY DIFFRACTION100
2.74-2.850.23941410.20174565X-RAY DIFFRACTION100
2.85-2.980.23631430.19994538X-RAY DIFFRACTION100
2.98-3.130.22241400.19484612X-RAY DIFFRACTION100
3.13-3.330.19011410.18484548X-RAY DIFFRACTION100
3.33-3.580.18151400.16774583X-RAY DIFFRACTION100
3.58-3.940.19511380.15964530X-RAY DIFFRACTION100
3.95-4.510.18021420.13844568X-RAY DIFFRACTION100
4.51-5.680.18781350.14574585X-RAY DIFFRACTION100
5.68-31.430.17931450.18754540X-RAY DIFFRACTION100

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