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- EMDB-72934: HCoV-HKU1 C S 2P in complex with H501-008 Fab (global cryoEM) -

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Basic information

Entry
Database: EMDB / ID: EMD-72934
TitleHCoV-HKU1 C S 2P in complex with H501-008 Fab (global cryoEM)
Map dataHCov-HKU1 C S 2P in complex with H501-008 Fab
Sample
  • Complex: HCoV-HKU1 C S 2P in complex with H501-008 Fab
    • Complex: HCoV-HKU1 C S 2P
    • Complex: H501-008 Fab
Keywordscoronavirus / HKU1 / mAb / cryoEM / VIRAL PROTEIN
Biological speciesHuman coronavirus HKU1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsVasquez S / Barnes CO
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2025
Title: Human Coronavirus HKU1 Neutralizing Monoclonal Antibodies Target Diverse Epitopes Within and Around the TMPRSS2 Receptor Binding Site.
Authors: Lingshu Wang / Jeswin Joseph / Sheena Vasquez / Daniel Wrapp / Timothy P Sheahan / Christian K O Dzuvor / Osnat Rosen / Robert N Kirchdoerfer / Olubukola M Abiona / Catherine Hammond / Wei ...Authors: Lingshu Wang / Jeswin Joseph / Sheena Vasquez / Daniel Wrapp / Timothy P Sheahan / Christian K O Dzuvor / Osnat Rosen / Robert N Kirchdoerfer / Olubukola M Abiona / Catherine Hammond / Wei Shi / Sydney P Moak / Wing-Pui Kong / Yi Zhang / Michael R Eso / Ariane J Brown / Andrew B Ward / Ralph Baric / Jason S McLellan / Theodore C Pierson / John Mascola / Barney S Graham / Hadi M Yassine / Christopher O Barnes / Kizzmekia S Corbett-Helaire /
Abstract: Endemic human coronaviruses (HCoVs), like HCoV-HKU1, account for ~30% of common cold/year and can cause serious upper and lower respiratory infections, yet no licensed vaccines target HCoVs. In fact, ...Endemic human coronaviruses (HCoVs), like HCoV-HKU1, account for ~30% of common cold/year and can cause serious upper and lower respiratory infections, yet no licensed vaccines target HCoVs. In fact, little is known about HCoV-HKU1's antigenic landscape. Thus, we characterized key interactions between HCoV-HKU1 spike (S) with monoclonal antibodies (mAbs) isolated from pre-pandemic HCoV-HKU1 convalescent PBMCs. We isolated 14 mAbs, which bound distinct S regions: receptor binding domain (RBD), N-terminal domain (NTD), and S2 subunit. Structural and functional studies revealed three groups of RBD-specific mAbs targeting diverse footprints within and around the TMPRSS2 receptor binding site, exemplified by: (1) The most potently neutralizing mAb, H501-022 (IC = 0.01 μg/mL), which recognizes the TMPRSS2 binding motif, thereby blocking receptor engagement; (2) mAb H501-008 (IC = 0.05 μg/mL) that binds a conserved, cross-reactive epitope outside of the TMPRSS2 binding site that is shared with HCoV-OC43; and (3) H501-018 (IC = 0.28 μg/mL) that recognizes both "up" and "down" RBD conformations at a distinct, non-overlapping site outside of the TMPRSS2 binding motif, distinguishing itself from H501-022 and H501-008, which bind exclusively to the "up" RBD conformation. These mAbs represent the first type-specific HCoV-HKU1 mAbs isolated from a convalescent donor. Our findings provide molecular insight into HCoV-HKU1 antibody recognition and neutralization mechanisms, importantly highlighting antigenic differences comparing HCoVs and pandemic CoVs - a critical step towards advancing universal CoV vaccine design.
History
DepositionSep 29, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72934.png

Downloads & links

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Map

FileDownload / File: emd_72934.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHCov-HKU1 C S 2P in complex with H501-008 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 500 pix.
= 460. Å		0.92 Å/pix.
x 500 pix.
= 460. Å		0.92 Å/pix.
x 500 pix.
= 460. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.19526835 - 0.3898753
Average (Standard dev.)-0.00008650155 (±0.009573313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 460.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: HCov-HKU1 C S 2P in complex with H501-008 Fab

Fileemd_72934_additional_1.map
AnnotationHCov-HKU1 C S 2P in complex with H501-008 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HCov-HKU1 C S 2P in complex with H501-008 Fab half map B

Fileemd_72934_half_map_1.map
AnnotationHCov-HKU1 C S 2P in complex with H501-008 Fab half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HCov-HKU1 C S 2P in complex with H501-008 Fab half map A

Fileemd_72934_half_map_2.map
AnnotationHCov-HKU1 C S 2P in complex with H501-008 Fab half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HCoV-HKU1 C S 2P in complex with H501-008 Fab

EntireName: HCoV-HKU1 C S 2P in complex with H501-008 Fab
Components
  • Complex: HCoV-HKU1 C S 2P in complex with H501-008 Fab
    • Complex: HCoV-HKU1 C S 2P
    • Complex: H501-008 Fab

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Supramolecule #1: HCoV-HKU1 C S 2P in complex with H501-008 Fab

SupramoleculeName: HCoV-HKU1 C S 2P in complex with H501-008 Fab / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: HCoV-HKU1 C S 2P

SupramoleculeName: HCoV-HKU1 C S 2P / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human coronavirus HKU1 / Strain: isolate N5

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Supramolecule #3: H501-008 Fab

SupramoleculeName: H501-008 Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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

Concentration7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMTris Hydrochloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2938 / Average exposure time: 3.4 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54647
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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