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- PDB-9u8g: Crystal structure of TMPRSS2 in complex with nanobody77_10 -

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Basic information

Entry
Database: PDB / ID: 9u8g
TitleCrystal structure of TMPRSS2 in complex with nanobody77_10
Components
  • (Transmembrane protease serine 2 ...) x 2
  • Nanobody
KeywordsIMMUNE SYSTEM / Complex / Antibody / Host protease / ANTIVIRAL PROTEIN
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)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDuan, Y. / Zhao, Z. / Liu, X. / Wang, H. / 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
DepositionMar 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 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 2 non-catalytic chain
B: Transmembrane protease serine 2 catalytic chain
C: Transmembrane protease serine 2 non-catalytic chain
D: Transmembrane protease serine 2 catalytic chain
E: Nanobody
F: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,30014
Polymers117,4106
Non-polymers8918
Water10,791599
1
A: Transmembrane protease serine 2 non-catalytic chain
B: Transmembrane protease serine 2 catalytic chain
E: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1507
Polymers58,7053
Non-polymers4454
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-16 kcal/mol
Surface area20470 Å2
MethodPISA
2
C: Transmembrane protease serine 2 non-catalytic chain
D: Transmembrane protease serine 2 catalytic chain
F: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1507
Polymers58,7053
Non-polymers4454
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-17 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.616, 69.827, 82.192
Angle α, β, γ (deg.)104.97, 112.85, 102.10
Int Tables number1
Space group name H-MP1

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Components

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Transmembrane protease serine 2 ... , 2 types, 4 molecules ACBD

#1: Protein Transmembrane protease serine 2 non-catalytic chain


Mass: 16054.661 Da / Num. of mol.: 2 / 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 with a 6xHis tag at C-termini. Residues 250-255 responsible for autocleavage are substituted ...Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression with a 6xHis tag at C-termini. Residues 250-255 responsible for autocleavage are substituted with enterokinase cleavage site DDDDK. The recombinant protein was cleaved into two chains in the purification.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393
#2: Protein Transmembrane protease serine 2 catalytic chain


Mass: 27856.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression with a 6xHis tag at C-termini. Residues 250-255 responsible for autocleavage are substituted ...Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression with a 6xHis tag at C-termini. Residues 250-255 responsible for autocleavage are substituted with enterokinase cleavage site DDDDK. The recombinant protein was cleaved into two chains 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 / Sugars , 2 types, 4 molecules EF

#3: Antibody Nanobody


Mass: 14793.356 Da / Num. of mol.: 2
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.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
#5: 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.: 2 / 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

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Non-polymers , 3 types, 605 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 100 mM HEPES/ Sodium hydroxide pH 7.0, 10% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2→18.29 Å / Num. obs: 81800 / % possible obs: 96.2 % / Redundancy: 3.18 % / CC1/2: 0.998 / Net I/σ(I): 13.18
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
2-2.121.67129270.5551
2.12-2.262.67122520.7791
2.26-2.444.58114680.9171
2.44-2.677.26106550.9751
2.67-2.9812.0796730.9891
2.98-3.4221.2485250.9961
3.42-4.1632.9273080.9981
4.16-5.7340.2556840.9991
5.73-18.2938.333080.9991

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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: 2→18.29 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 4088 5 %Random selection
Rwork0.193 ---
obs0.1949 81780 96.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→18.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7511 0 54 599 8164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047831
X-RAY DIFFRACTIONf_angle_d0.71910660
X-RAY DIFFRACTIONf_dihedral_angle_d13.2342789
X-RAY DIFFRACTIONf_chiral_restr0.0511143
X-RAY DIFFRACTIONf_plane_restr0.0061382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.34721340.32382543X-RAY DIFFRACTION92
2.02-2.050.32211420.31462696X-RAY DIFFRACTION96
2.05-2.070.31511350.29082589X-RAY DIFFRACTION95
2.07-2.10.33021400.2812677X-RAY DIFFRACTION96
2.1-2.130.31461380.27722633X-RAY DIFFRACTION96
2.13-2.160.29121420.26382679X-RAY DIFFRACTION96
2.16-2.190.3251410.26432683X-RAY DIFFRACTION96
2.19-2.230.32111380.26352631X-RAY DIFFRACTION96
2.23-2.260.33021440.26772732X-RAY DIFFRACTION97
2.26-2.30.32611380.24632619X-RAY DIFFRACTION97
2.3-2.340.26051420.23192698X-RAY DIFFRACTION96
2.34-2.390.29141410.22022687X-RAY DIFFRACTION97
2.39-2.440.22421410.21922679X-RAY DIFFRACTION97
2.44-2.490.29961430.21882713X-RAY DIFFRACTION97
2.49-2.550.25271420.21582690X-RAY DIFFRACTION97
2.55-2.610.23481430.20182733X-RAY DIFFRACTION97
2.61-2.680.24441420.19742686X-RAY DIFFRACTION98
2.68-2.760.25661410.20552681X-RAY DIFFRACTION97
2.76-2.850.28131420.2042687X-RAY DIFFRACTION97
2.85-2.950.26321420.20522707X-RAY DIFFRACTION97
2.95-3.070.22681440.20582731X-RAY DIFFRACTION98
3.07-3.210.21591430.19632717X-RAY DIFFRACTION98
3.21-3.380.27461410.19592679X-RAY DIFFRACTION97
3.38-3.590.21151420.17982696X-RAY DIFFRACTION97
3.59-3.860.191420.1692697X-RAY DIFFRACTION98
3.86-4.240.20311430.1582718X-RAY DIFFRACTION98
4.24-4.850.14551420.1372713X-RAY DIFFRACTION98
4.85-6.070.19671420.15812693X-RAY DIFFRACTION97
6.07-18.290.18321380.162605X-RAY DIFFRACTION94

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