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- PDB-9jcy: Crystal structure of the HCoV-HKU1 RBD in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 9jcy
TitleCrystal structure of the HCoV-HKU1 RBD in complex with Fab
Components
  • Heavy chain of Fab
  • Light chain of Fab
  • Spike protein S1
KeywordsANTIVIRAL PROTEIN / Complex / Antibody / HCoV-HKU1
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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
Similarity search - Domain/homology
Biological speciesHuman coronavirus HKU1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, H. / Zhao, Z. / Liu, X. / 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: Spike protein S1
C: Heavy chain of Fab
B: Light chain of Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3289
Polymers82,5173
Non-polymers8116
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-27 kcal/mol
Surface area30720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.235, 161.286, 57.060
Angle α, β, γ (deg.)90.00, 108.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules CB

#2: Antibody Heavy chain of Fab


Mass: 24898.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The heavy chain of Fab was expressed with a C-termianl linker ("GS") followed by a 6 x His tag.
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Light chain of Fab


Mass: 23343.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 3 molecules A

#1: 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
#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.: 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 , 2 types, 644 molecules

#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2% (w/v) Ala-Ala, 0.2% (w/v) Ala-Gln, 0.2% (w/v) Gly-Glu, 0.2% (w/v) Gly-L-Ala, 0.2% (w/v) Gly-L-Asp, 0.2% (w/v) Gly-Sar, 0.2% (w/v) L-Carnosine, 0.2% (w/v) Leu-Ala hydrate, 0.1 M Buffer ...Details: 0.2% (w/v) Ala-Ala, 0.2% (w/v) Ala-Gln, 0.2% (w/v) Gly-Glu, 0.2% (w/v) Gly-L-Ala, 0.2% (w/v) Gly-L-Asp, 0.2% (w/v) Gly-Sar, 0.2% (w/v) L-Carnosine, 0.2% (w/v) Leu-Ala hydrate, 0.1 M Buffer System 3 [Tris (base); BICINE] pH 8.5, 20% (v/v) PEG 500* MME, 10 % w/v PEG 20,000; for TMPRSS2:VHH77, 0.2 M sodium malonate pH 6.0, 10% (w/v) Polyethylene glycol 3,350

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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: Apr 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→30.74 Å / Num. obs: 79102 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.101 / Net I/σ(I): 11.65
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.910.601127110.8770.6511
1.91-2.040.349119940.9490.381
2.04-2.20.243111560.9740.2631
2.2-2.410.178103060.9820.1941
2.41-2.70.13393050.9910.1441
2.7-3.110.09382550.9940.1021
3.11-3.810.06769630.9960.0741
3.81-5.370.05753810.9960.0631
5.37-30.740.05430310.9970.0591

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207-000)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.74 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 3955 5 %
Rwork0.1729 --
obs0.1744 79025 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5512 0 52 640 6204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065727
X-RAY DIFFRACTIONf_angle_d0.867795
X-RAY DIFFRACTIONf_dihedral_angle_d13.0442063
X-RAY DIFFRACTIONf_chiral_restr0.056867
X-RAY DIFFRACTIONf_plane_restr0.0071003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.31951380.27642615X-RAY DIFFRACTION99
1.82-1.840.28181430.2622720X-RAY DIFFRACTION100
1.84-1.870.28121390.23252627X-RAY DIFFRACTION99
1.87-1.890.28241410.22512694X-RAY DIFFRACTION100
1.89-1.920.24141420.20682695X-RAY DIFFRACTION100
1.92-1.950.24041400.19782651X-RAY DIFFRACTION100
1.95-1.980.22851390.18612653X-RAY DIFFRACTION100
1.98-2.010.2351440.18542719X-RAY DIFFRACTION100
2.01-2.050.19081390.18052649X-RAY DIFFRACTION100
2.05-2.080.21891420.18012701X-RAY DIFFRACTION100
2.08-2.120.24721390.19232644X-RAY DIFFRACTION100
2.12-2.170.25511420.19022688X-RAY DIFFRACTION100
2.17-2.220.24421410.18692674X-RAY DIFFRACTION100
2.22-2.270.23111430.18792712X-RAY DIFFRACTION100
2.27-2.320.23371390.18512650X-RAY DIFFRACTION100
2.32-2.390.21381430.18232723X-RAY DIFFRACTION100
2.39-2.460.21571390.18052637X-RAY DIFFRACTION100
2.46-2.540.22171420.17612703X-RAY DIFFRACTION100
2.54-2.630.20261430.18142706X-RAY DIFFRACTION100
2.63-2.730.21671430.17532710X-RAY DIFFRACTION100
2.73-2.860.20851400.17622669X-RAY DIFFRACTION100
2.86-3.010.22141420.17212697X-RAY DIFFRACTION100
3.01-3.190.20291400.16762666X-RAY DIFFRACTION100
3.19-3.440.19391410.15612679X-RAY DIFFRACTION100
3.44-3.790.16621430.1562716X-RAY DIFFRACTION100
3.79-4.330.17841420.14352697X-RAY DIFFRACTION100
4.33-5.450.14511430.14422705X-RAY DIFFRACTION100
5.45-30.740.19451430.18332723X-RAY DIFFRACTION100

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