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6atk

Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N

Method: X-RAY DIFFRACTION Dmax: 205.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Aminopeptidase N

Homo sapiens

UniProt P15144

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 66–967 Fragment：UNP residues 68-967 Spike glycoprotein × 1 （P15423） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A Resolution 3.50 Å R-free 0.267
2 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 66–967 Fragment：UNP residues 68-967 Spike glycoprotein × 1 （P15423） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A Resolution 3.50 Å R-free 0.267
3 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 66–967 Fragment：UNP residues 68-967 Spike glycoprotein × 1 （P15423） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A Resolution 3.50 Å R-free 0.267

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 6ATK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4FYQ Human aminopeptidase N (CD13) Deposited 2012-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 66–967（902 aa） Fragment：UNP residues 66-967
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ZN ZINC ION × 2 SO4 SULFATE ION × 22 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K
Resolution 1.90 Å R-free 0.193
4FYR Human aminopeptidase N (CD13) in complex with bestatin Deposited 2012-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 66–967（902 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 ZN ZINC ION × 2 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 2 SO4 SULFATE ION × 20 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K
Resolution 1.91 Å R-free 0.190
4FYS Human aminopeptidase N (CD13) in complex with angiotensin IV Deposited 2012-07-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 66–967（902 aa） Fragment：UNP residues 66-967
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 SO4 SULFATE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K
Resolution 2.01 Å R-free 0.198
4FYT Human aminopeptidase N (CD13) in complex with amastatin Deposited 2012-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 66–967（902 aa） Fragment：UNP residues 66-967
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ZN ZINC ION × 2 SO4 SULFATE ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K
Resolution 1.85 Å R-free 0.183
5LHD Structure of glycosylated human aminopeptidase N Deposited 2016-07-11 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 36–967（932 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000
Resolution 2.60 Å R-free 0.214
5LHD Structure of glycosylated human aminopeptidase N Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–967（932 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000
Resolution 2.60 Å R-free 0.214
5LHD Structure of glycosylated human aminopeptidase N Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 36–967（932 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000
Resolution 2.60 Å R-free 0.214
5LHD Structure of glycosylated human aminopeptidase N Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain D 36–967（932 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000
Resolution 2.60 Å R-free 0.214
6U7E HCoV-229E RBD Class III in complex with human APN Deposited 2019-09-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5
Resolution 3.00 Å R-free 0.244
6U7E HCoV-229E RBD Class III in complex with human APN Deposited 2019-09-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5
Resolution 3.00 Å R-free 0.244
6U7F HCoV-229E RBD Class IV in complex with human APN Deposited 2019-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5
Resolution 2.75 Å R-free 0.225
6U7F HCoV-229E RBD Class IV in complex with human APN Deposited 2019-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5
Resolution 2.75 Å R-free 0.225
6U7G HCoV-229E RBD Class V in complex with human APN Deposited 2019-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5
Resolution 2.35 Å R-free 0.218
6U7G HCoV-229E RBD Class V in complex with human APN Deposited 2019-09-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5
Resolution 2.35 Å R-free 0.218
7AEW 14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and non-canonical binding motifs Deposited 2020-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain BBB 36–73（38 aa）
Chain CCC 36–73（38 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES pH 7.7 0.19 M CaCl2 5% glycerol 27 % PEG400
Resolution 1.20 Å R-free 0.184
7VPQ Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans Deposited 2021-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 62–963（902 aa）
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride
Resolution 3.10 Å R-free 0.278
7VPQ Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans Deposited 2021-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 62–963（902 aa）
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride
Resolution 3.10 Å R-free 0.278
7VPQ Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans Deposited 2021-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 62–963（902 aa）
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride
Resolution 3.10 Å R-free 0.278
8WDE CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map) Deposited 2023-09-15 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 × 5 PDB declaration: pentameric
Chain D 66–967（902 aa）
Chain E 66–967（902 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9CAM Aminopeptidase N close state Deposited 2024-06-17 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 × 2 PDB declaration: dimeric
Chain A 1–967（967 aa）
Chain B 1–967（967 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9CAO Aminopeptidase N open state Deposited 2024-06-17 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 × 2 PDB declaration: dimeric
Chain A 1–967（967 aa）
Chain B 1–967（967 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMPN_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–905； UniProt 66–967 Author chain B； PDBConstruct 4–905； UniProt 66–967 Author chain C； PDBConstruct 4–905； UniProt 66–967

Spike glycoprotein

Human coronavirus 229E

UniProt P15423

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 293–435 Fragment：UNP residues 294-432 Aminopeptidase N × 1 （P15144） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A Resolution 3.50 Å R-free 0.267
2 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 293–435 Fragment：UNP residues 294-432 Aminopeptidase N × 1 （P15144） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A Resolution 3.50 Å R-free 0.267
3 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 293–435 Fragment：UNP residues 294-432 Aminopeptidase N × 1 （P15144） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A Resolution 3.50 Å R-free 0.267

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 6ATK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5YL9 1.86 Angstrom crystal structure of human Coronavirus 229E fusion core Deposited 2017-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 785–872（88 aa） Fragment：UNP residues 785-872
Chain B 1052–1104（53 aa） Fragment：UNP residues 1052-1104
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；citric acid, BIS-TRIS propane, PEG3350
Resolution 1.86 Å R-free 0.206
5ZHY Structural characterization of the HCoV-229E fusion core Deposited 2018-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain A 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain B 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain B 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain C 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain C 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.5 M Ammonium sulfate, 12% (v/v) Glycerol, 100 mM Tris/HCl, PH 8.5
Resolution 2.44 Å R-free 0.263
5ZHY Structural characterization of the HCoV-229E fusion core Deposited 2018-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain D 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain E 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain E 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain F 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Chain F 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.5 M Ammonium sulfate, 12% (v/v) Glycerol, 100 mM Tris/HCl, PH 8.5
Resolution 2.44 Å R-free 0.263
5ZUV Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs inhibitor EK1 Deposited 2018-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 785–873（89 aa） Fragment：UNP residues 785-873
Chain B 785–873（89 aa） Fragment：UNP residues 785-873
Chain C 785–873（89 aa） Fragment：UNP residues 785-873
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；0.05M MgCl2, 0.1M HEPES, pH 7.5, 30% PEG550MME
Resolution 2.21 Å R-free 0.248
7CYC Cryo-EM structures of Alphacoronavirus spike glycoprotein Deposited 2020-09-03 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 1–1116（1116 aa）
Chain B 1–1116（1116 aa）
Chain C 1–1116（1116 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
7CYD Cryo-EM structures of Alphacoronavirus spike glycoprotein Deposited 2020-09-03 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 1–1116（1116 aa）
Chain B 1–1116（1116 aa）
Chain C 1–1116（1116 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
7VN9 Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab Deposited 2021-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 294–435（142 aa） Fragment：receptor-binding domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；1.6M AmSO4, 0.1M Critic Acid pH 5.0
Resolution 4.49 Å R-free 0.288
7VN9 Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab Deposited 2021-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 294–435（142 aa） Fragment：receptor-binding domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；1.6M AmSO4, 0.1M Critic Acid pH 5.0
Resolution 4.49 Å R-free 0.288
7VNG Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with S11 Fab Deposited 2021-10-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 294–435（142 aa） Fragment：receptor binding domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；3.6M Sodium Formate, 10% Glycerol
Resolution 3.80 Å R-free 0.318
7YI6 bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein Deposited 2022-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 835–841（7 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS buffer at pH 5.5 and 25% (w/v) polyethylene glycol 3350
Resolution 2.28 Å R-free 0.220
7YI6 bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein Deposited 2022-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 835–841（7 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS buffer at pH 5.5 and 25% (w/v) polyethylene glycol 3350
Resolution 2.28 Å R-free 0.220

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPIKE_CVH22
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 4–146； UniProt 293–435 Author chain E； PDBConstruct 4–146； UniProt 293–435 Author chain F； PDBConstruct 4–146； UniProt 293–435

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

SAXS profile for 6atk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6atk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6atk
Deposition date deposition_date2017-08-29
Structure title titleCrystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N
Keywords keywordscoronavirus, spike, receptor, Hydrolase-Viral protein complex; Hydrolase/Viral protein
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier58.38 Å
Radius of gyration Rg (electron density) rg_electron58.54 Å
Forward intensity I(0) i01569950000.00
Molecular weight molecular_weight335260.0 kDa
Excluded volume excluded_volume419660 ų
Envelope volume envelope_volume597400 ų
Hydration-shell volume shell_volume85204 ų
Envelope diameter envelope_diameter218.1 Å
Shell Rg shell_rg61.04 Å
Envelope Rg envelope_rg57.70 Å
Shape Rg shape_rg58.52 Å
Total Rg total_rg58.67 Å
Total atoms total_atoms23660
Residues n_residues2898
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax205.2 Å
Rg (real space) rg_real58.61 Å
Rg uncertainty (real space) rg_real_error1.93 Å
I(0) (real space) i0_real1.5700e+09
I(0) uncertainty (real space) i0_real_error3.1580e+07
Rg (reciprocal space) rg_reciprocal58.16 Å
I(0) (reciprocal space) i0_reciprocal1569000000.0000
Solution quality estimate total_estimate0.8511
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary45.6 Å
Skewness Skewness skewness0.351
Kurtosis Kurtosis kurtosis-0.391
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha227600000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.849; Smooth: 0.903
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id6atkA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1730 — tricorn interacting facor f3 domain
Domain ID domain_id6atkA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily10 — Neutral Protease Domain 2
Domain ID domain_id6atkA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1910 —
Domain ID domain_id6atkA04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology50 — Zincin-like fold
Homologous superfamily homologous superfamily20 —
Domain ID domain_id6atkB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1730 — tricorn interacting facor f3 domain
Domain ID domain_id6atkB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily10 — Neutral Protease Domain 2
Domain ID domain_id6atkB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1910 —
Domain ID domain_id6atkB04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology50 — Zincin-like fold
Homologous superfamily homologous superfamily20 —
Domain ID domain_id6atkC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1730 — tricorn interacting facor f3 domain
Domain ID domain_id6atkC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily10 — Neutral Protease Domain 2
Domain ID domain_id6atkC03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1910 —
Domain ID domain_id6atkC04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology50 — Zincin-like fold
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)