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- PDB-8wde: CryoEM structure of the spike protein of human CoV 229E in comple... -

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Basic information

Entry
Database: PDB / ID: 8wde
TitleCryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map)
Components
  • Aminopeptidase N
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / human aminopeptidase N
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane ...alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane / metallopeptidase activity / signaling receptor activity / virus receptor activity / angiogenesis / cell differentiation / external side of plasma membrane / lysosomal membrane / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy ...Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Biological speciesHuman coronavirus 229E
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHsu, S.T.D. / Tsai, Y.X.
Funding support Taiwan, 9items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-109-L08 Taiwan
Academia Sinica (Taiwan)AS-IDR-112-04 Taiwan
Academia Sinica (Taiwan)AS-IDR-111-03 Taiwan
National Science Council (NSC, Taiwan)110-2113-M-001-050-MY3 Taiwan
National Science Council (NSC, Taiwan)110-2311-B-001-013-MY3 Taiwan
Academia Sinica (Taiwan)AS-CFII-111-201 Taiwan
Academia Sinica (Taiwan)AS-CFII-111-209 Taiwan
Academia Sinica (Taiwan)AS-CFII-111-210 Taiwan
Academia Sinica (Taiwan)AS-KPQ-109-TPP2 Taiwan
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis of host recognition of human coronavirus 229E.
Authors: Yu-Xi Tsai / Yu-Chun Chien / Min-Feng Hsu / Kay-Hooi Khoo / Shang-Te Danny Hsu /
Abstract: Human coronavirus 229E (HCoV-229E) is the earliest CoV found to infect humans. It binds to the human aminopeptidase N (hAPN) through the receptor binding domain (RBD) of its spike (S) protein to ...Human coronavirus 229E (HCoV-229E) is the earliest CoV found to infect humans. It binds to the human aminopeptidase N (hAPN) through the receptor binding domain (RBD) of its spike (S) protein to achieve host recognition. We present the cryo-electron microscopy structure of two HCoV-229E S protein in complex with a dimeric hAPN to provide structural insights on how the HCoV-229E S protein opens up its RBD to engage with its host receptor, information that is currently missing among alphacoronaviruses to which HCoV-229E belong. We quantitatively profile the glycosylation of HCoV-229E S protein and hAPN to deduce the glyco-shielding effects pertinent to antigenicity and host recognition. Finally, we present an atomic model of fully glycosylated HCoV-229E S in complex with hAPN anchored on their respective membrane bilayers to recapitulate the structural basis of the first step of host infection by HCoV-229E.
History
DepositionSep 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
D: Aminopeptidase N
E: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)607,44132
Polymers599,5605
Non-polymers7,88127
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Spike glycoprotein


Mass: 127915.492 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein Aminopeptidase N


Mass: 107906.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANPEP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P15144
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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.: 20 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map)
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Human coronavirus 229E
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.1.1particle selection
4cryoSPARC4.1.1CTF correctionContrast transfer function (CTF) estimation was conducted by patch-CTF estimation function in CryoSPARC v4.1.1
10cryoSPARC4.1.1initial Euler assignment
11cryoSPARC4.1.1final Euler assignment
12cryoSPARC4.1.1classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 253164 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 85.83 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010634137
ELECTRON MICROSCOPYf_angle_d0.922546447
ELECTRON MICROSCOPYf_chiral_restr0.0595419
ELECTRON MICROSCOPYf_plane_restr0.00915868
ELECTRON MICROSCOPYf_dihedral_angle_d13.403512123

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