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- PDB-9jcx: Crystal structure of the HCoV-HKU1 RBD and TMPRSS2 -

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Basic information

Entry
Database: PDB / ID: 9jcx
TitleCrystal structure of the HCoV-HKU1 RBD and TMPRSS2
Components
  • (Transmembrane protease serine 2 ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / Complex / Receptor / HCoV-HKU1
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Spike glycoprotein S2, coronavirus, C-terminal ...Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Transmembrane protease serine 2 / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus HKU1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWang, H. / Li, M. / 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

Downloads & links

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Assembly

Deposited unit
A: Transmembrane protease serine 2 non-catalytic chain
C: Transmembrane protease serine 2 catalytic chain
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8747
Polymers78,1703
Non-polymers7044
Water43224
1
A: Transmembrane protease serine 2 non-catalytic chain
C: Transmembrane protease serine 2 catalytic chain
hetero molecules

B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8747
Polymers78,1703
Non-polymers7044
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area4060 Å2
ΔGint-6 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.350, 120.720, 126.130
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 AC

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


Mass: 27840.742 Da / Num. of mol.: 1 / Mutation: S441A
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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Protein / Sugars , 2 types, 4 molecules B

#3: Protein Spike protein S1


Mass: 34275.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: We choose the segment of spike (residues 323-609) for expression. The recombinant protein encompasses a C-terminal linker ("SGLEVLFQGPGGS") followed by an 8 x His tag.
Source: (gene. exp.) Human coronavirus HKU1 (isolate N1) / Gene: S, 3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5MQD0
#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.: 3 / 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 , 2 types, 25 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2 M Tris pH 7.0, 0.2 M MgCl2, 10% (w/v) Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→19.95 Å / Num. obs: 25815 / % possible obs: 99.6 % / Redundancy: 13.27 % / CC1/2: 0.998 / Net I/σ(I): 15.24
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.75-2.9140180.9211
2.91-3.1138100.9491
3.11-3.3535880.9871
3.35-3.6632840.9921
3.66-4.0730190.9951
4.07-4.6726850.9971
4.67-5.6423290.9981
5.64-7.6818550.9981
7.68-19.9512270.9991

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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: 2.75→19.95 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 1288 5 %
Rwork0.2054 --
obs0.207 25737 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5072 0 43 24 5139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025265
X-RAY DIFFRACTIONf_angle_d0.5267179
X-RAY DIFFRACTIONf_dihedral_angle_d13.6681893
X-RAY DIFFRACTIONf_chiral_restr0.045783
X-RAY DIFFRACTIONf_plane_restr0.004935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.35491400.29392653X-RAY DIFFRACTION100
2.86-2.990.31751400.28792671X-RAY DIFFRACTION100
2.99-3.150.28981420.25892688X-RAY DIFFRACTION100
3.15-3.340.2991410.24252683X-RAY DIFFRACTION100
3.34-3.60.23251410.2162679X-RAY DIFFRACTION100
3.6-3.960.22381440.22722X-RAY DIFFRACTION100
3.96-4.530.21071430.16452728X-RAY DIFFRACTION100
4.53-5.680.19351450.17582753X-RAY DIFFRACTION100
5.68-19.950.21811520.19192872X-RAY DIFFRACTION100

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