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- EMDB-38816: Local refinement of receptor binding domain and hinge region of s... -

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Basic information

Entry
Database: EMDB / ID: EMD-38816
TitleLocal refinement of receptor binding domain and hinge region of single S protein
Map data
Sample
  • Complex: CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map)
Keywordshuman coronavirus 229E / spike protein / human aminopeptidase N / VIRAL PROTEIN
Biological speciesHuman coronavirus 229E
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsHsu STD / Tsai YX
Funding support Taiwan, 9 items
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
DepositionJan 23, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38816.png

Downloads & links

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Map

FileDownload / File: emd_38816.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 600 pix.
= 885.6 Å		1.48 Å/pix.
x 600 pix.
= 885.6 Å		1.48 Å/pix.
x 600 pix.
= 885.6 Å

Surface

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.476 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-11.075710000000001 - 23.032693999999999
Average (Standard dev.)-0.0013061429 (±0.0647191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 885.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38816_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38816_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of the spike protein of human CoV 229E in comple...

EntireName: CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map)
Components
  • Complex: CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map)

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Supramolecule #1: CryoEM structure of the spike protein of human CoV 229E in comple...

SupramoleculeName: CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Human coronavirus 229E

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6u7h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 253164
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)

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