9jcy

Crystal structure of the HCoV-HKU1 RBD in complex with Fab

Method: X-RAY DIFFRACTION D_max: 123.0 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike protein S1

Human coronavirus HKU1 (isolate N1)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 323–609	Not recorded	Heavy chain of Fab × 1 Light chain of Fab × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；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	Resolution 1.80 Å R-free 0.203

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9JCY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5GNB Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 2.3 angstrom, native-SAD phasing) Deposited 2016-07-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 307–677（371 aa） Fragment：UNP residues 307-677	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1M Tris, 24%PEG4000, 0.2M MgCl2, 4% v/v Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 2.30 Å R-free 0.219
5KWB Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 1.9 angstrom, molecular replacement) Deposited 2016-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 307–677（371 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1M Tris, 24%PEG4000, 0.2M MgCl2	Resolution 1.91 Å R-free 0.201
8DGW Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 isolated from a vaccinated COVID-19 convalescent Deposited 2022-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1226–1250（25 aa） Fragment：stem helix domain, residues 1226-1250	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium formate, 20% (w/v) PEG 3350	Resolution 2.81 Å R-free 0.248
8DGW Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 isolated from a vaccinated COVID-19 convalescent Deposited 2022-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1226–1250（25 aa） Fragment：stem helix domain, residues 1226-1250	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium formate, 20% (w/v) PEG 3350	Resolution 2.81 Å R-free 0.248
8DGW Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 isolated from a vaccinated COVID-19 convalescent Deposited 2022-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1226–1250（25 aa） Fragment：stem helix domain, residues 1226-1250	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium formate, 20% (w/v) PEG 3350	Resolution 2.81 Å R-free 0.248
8DGW Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 isolated from a vaccinated COVID-19 convalescent Deposited 2022-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1226–1250（25 aa） Fragment：stem helix domain, residues 1226-1250	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium formate, 20% (w/v) PEG 3350	Resolution 2.81 Å R-free 0.248
8VGT Structure of the HKU1 RBD bound to the human TMPRSS2 receptor Deposited 2023-12-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 320–614（295 aa） Fragment：RBD	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8Y7X Structure of HCoV-HKU1A spike in the functionally anchored-3up conformation with 3TMPRSS2 Deposited 2024-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 14–1281（1268 aa） Chain B 14–1281（1268 aa） Chain C 14–1281（1268 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
8Y7Y Local structure of HCoV-HKU1A spike in complex with TMPRSS2 and glycan Deposited 2024-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 14–1281（1268 aa） Chain B 14–1281（1268 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MJJ methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8YOY Structure of HKU1A RBD with TMPRSS2 Deposited 2024-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 307–677（371 aa） Fragment：RBD domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
9BSW Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDA state) Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain B 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain C 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.06 Å
9BSX Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (DAA state) Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain B 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain C 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.37 Å
9BSY Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (DAU state) Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain B 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain C 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å
9BSZ Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (AUU state) Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain B 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain C 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 A1AR2 5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->8)-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
9BT0 Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDD state) Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain B 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain C 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.23 Å
9BT1 Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (UUU state) Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain B 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain C 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.22 Å
9BT2 Cryo-EM structure of HCoV-HKU1 glycoprotein D1 (Down State, locally refined) Deposited 2024-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.93 Å
9BT9 Cryo-EM Structure of HKU1 spike D1 Domain (Active state, locally refined) Deposited 2024-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.11 Å
9BTA Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3 sialoglycan (Down_alt state, locally refined) Deposited 2024-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.39 Å
9BTB Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3 sialoglycan (Active state, locally refined) Deposited 2024-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.33 Å
9BTC Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3 sialoglycan (Up state, locally refined) Deposited 2024-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–1223（1210 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.41 Å
9BTD Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (DDA state) Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain B 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain C 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.43 Å
9IZN Crystal structure of HKU1A RBD bound to TMPRSS2 Deposited 2024-08-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 307–677（371 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；2% v/v Tacsimate pH 7.0, 5% v/v 2-Propanol, 0.1 M Imidazole (pH 7.0) and 8% w/v Polyethylene glycol 3350	Resolution 2.40 Å R-free 0.261
9JCX Crystal structure of the HCoV-HKU1 RBD and TMPRSS2 Deposited 2024-08-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 323–609（287 aa）	Not recorded	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2 M Tris pH 7.0, 0.2 M MgCl2, 10% (w/v) Polyethylene glycol 8,000	Resolution 2.75 Å R-free 0.237
9N12 Cryo-EM structure of HCoV-HKU1 glycoprotein (mutant T31VPR34 to GGGG) Deposited 2025-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Chain B 14–1298（1285 aa） Chain C 14–1298（1285 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9N13 Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31VPR34 to GGGG) Deposited 2025-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–1298（1285 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9N14 Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9OAc-GD3(mutant T31VPR34 to GGGG) Deposited 2025-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain B 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298) Chain C 14–1298（1285 aa） Fragment：ectodomain (UNP residues 14-1298)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
9N15 Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain in complex with 9OAc-GD3(mutant T31VPR34 to GGGG) Deposited 2025-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–1298（1285 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9N16 Cryo-EM structure of HCoV-HKU1 glycoprotein (Deletion 33Pro34Arg) Deposited 2025-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Chain B 14–1298（1285 aa） Chain C 14–1298（1285 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9N17 Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (Deletion 33Pro34Arg) Deposited 2025-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–1298（1285 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9N18 Cryo-EM structure of HCoV-HKU1 spike glycoprotein in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg) Deposited 2025-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1298（1285 aa） Chain B 14–1298（1285 aa） Chain C 14–1298（1285 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å
9N19 Cryo-EM structure of HCoV-HKU1spike glycoprotein D1 Domain in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg) Deposited 2025-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–1298（1285 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 A1AR1 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å
9OPQ TMPRSS2 (S441A) bound to the HCoV-NL63 S2'region genetically fused to the HCoV-HKU1 RBD Deposited 2025-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 320–509（190 aa） Chain A 511–614（104 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

30 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPIKE_CVHN1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–287； UniProt 323–609

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9jcy
Deposition date deposition_date	2024-08-30
最后修订 last_revision	2025-07-30
Structure title title	Crystal structure of the HCoV-HKU1 RBD in complex with Fab
Keywords keywords	Complex, Antibody, HCoV-HKU1, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.06 Å
Radius of gyration Rg (electron density) rg_electron	35.28 Å
Forward intensity I(0) i0	105186000.00
Molecular weight molecular_weight	79239.0 kDa
Excluded volume excluded_volume	97854 Å³
Envelope volume envelope_volume	127070 Å³
Hydration-shell volume shell_volume	32980 Å³
Envelope diameter envelope_diameter	132.7 Å
Shell Rg shell_rg	37.82 Å
Envelope Rg envelope_rg	35.48 Å
Shape Rg shape_rg	35.23 Å
Total Rg total_rg	35.61 Å
Total atoms total_atoms	5564
Residues n_residues	724
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	123.0 Å
Rg (real space) rg_real	35.42 Å
Rg uncertainty (real space) rg_real_error	1.35 Å
I(0) (real space) i0_real	1.0520e+08
I(0) uncertainty (real space) i0_real_error	1.8350e+06
Rg (reciprocal space) rg_reciprocal	35.19 Å
I(0) (reciprocal space) i0_reciprocal	105200000.0000
Solution quality estimate total_estimate	0.8198
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.8 Å
Skewness Skewness skewness	0.555
Kurtosis Kurtosis kurtosis	-0.304
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9021000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.684; Smooth: 0.771

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Spike protein S1
Molecular weight formula_weight	34275.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6231

DLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTDSFSCNNFDESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLYYSLPAINVTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCKSHKPPSASCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDEEKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLSGLEVLFQGPGGSHHHHHHHH

来源 Source

来源生物 organism	Human coronavirus HKU1 (isolate N1)
NCBI Class编号 ncbi_taxonomy_id	443239
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Heavy chain of Fab
Molecular weight formula_weight	24898.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QVQLQESGPGLVKPSGTLSLTCAVSGGSISSSNWWSWVRQPPGKGLEWIGSMHYSGSSHYKPSLKSRIAMSVDTSKNQFSLNLNSVTAADTAVYYCAREGGSSGYDYVYYFDDWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Light chain of Fab
Molecular weight formula_weight	23343.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	640

▶

8. Citations (1)

▶

Unit-cell length a length_a	50.235 Å
Unit-cell length b length_b	161.286 Å
Unit-cell length c length_c	57.060 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	30.740 Å
R factor r_factor	0.1744
R_work r_work	0.1729
R_free r_free	0.2029

fit	/app/data/saxs_computation/jc/9jcy/9jcy.fit
pddf	/app/data/pr_computation/jc/9jcy/9jcy.pr.out
profile	/app/data/saxs_computation/jc/9jcy/9jcy.dat

Crystal structure of the HCoV-HKU1 RBD in complex with Fab

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike protein S1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)