8WDE | pdb_00008wde

CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map)

PDB DOI: https://doi.org/10.2210/pdb8WDE/pdb
EM Map EMD-37462: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human coronavirus 229E, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-09-15 Released: 2025-03-05
Deposition Author(s): Hsu, S.T.D., Tsai, Y.X.
Funding Organization(s): Academia Sinica (Taiwan), National Science Council (NSC, Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Molecular basis of host recognition of human coronavirus 229E.

Tsai, Y.X., Chien, Y.C., Hsu, M.F., Khoo, K.H., Hsu, S.D.

(2025) Nat Commun 16: 2045-2045

PubMed: 40016196 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-57359-8
Primary Citation of Related Structures:
8WDE

PubMed 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 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.

Organizational Affiliation

Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.

Macromolecule Content

Total Structure Weight: 607.44 kDa
Atom Count: 33,348
Modeled Residue Count: 4,161
Deposited Residue Count: 5,381
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,165	Human coronavirus 229E	Mutation(s): 0
UniProt
Find proteins for P15423 (Human coronavirus 229E) Explore P15423 Go to UniProtKB: P15423
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15423
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	D, E	943	Homo sapiens	Mutation(s): 0 Gene Names: ANPEP EC: 3.4.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for P15144 (Homo sapiens) Explore P15144 Go to UniProtKB: P15144
PHAROS: P15144 GTEx: ENSG00000166825
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15144
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D Focus chain E	Go to GlyGen: P15144-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, J	3		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain J Interactions & Density Focus chain F Focus chain H Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K, L	2		N-Glycosylation	Interactions Focus chain G Focus chain I Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain I Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth D] DA [auth D] EA [auth D] AA [auth C], BA [auth C], CA [auth D], DA [auth D], EA [auth D], FA [auth E], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-05

Deposition Author(s):

Hsu, S.T.D.

Tsai, Y.X.

Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-CDA-109-L08
Academia Sinica (Taiwan)	Taiwan	AS-IDR-112-04
Academia Sinica (Taiwan)	Taiwan	AS-IDR-111-03
National Science Council (NSC, Taiwan)	Taiwan	110-2113-M-001-050-MY3
National Science Council (NSC, Taiwan)	Taiwan	110-2311-B-001-013-MY3
Academia Sinica (Taiwan)	Taiwan	AS-CFII-111-201
Academia Sinica (Taiwan)	Taiwan	AS-CFII-111-209
Academia Sinica (Taiwan)	Taiwan	AS-CFII-111-210
Academia Sinica (Taiwan)	Taiwan	AS-KPQ-109-TPP2