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- EMDB-72939: HCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM) -

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Basic information

Entry
Database: EMDB / ID: EMD-72939
TitleHCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM)
Map data
Sample
  • Complex: HCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM)
    • Complex: HCoV-HKU1 C S 2P
      • Protein or peptide: Spike glycoprotein
    • Complex: H501-022 Fab
      • Protein or peptide: H501-022 Fab heavy chain
      • Protein or peptide: H501-022 Fab light chain
Keywordscoronavirus / HKU1 / mAb / cryoEM / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHuman coronavirus HKU1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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_72939.png

Downloads & links

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Map

FileDownload / File: emd_72939.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 480 pix.
= 441.6 Å		0.92 Å/pix.
x 480 pix.
= 441.6 Å		0.92 Å/pix.
x 480 pix.
= 441.6 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: 0.14
Minimum - Maximum-1.7642334 - 1.5176361
Average (Standard dev.)0.000064236025 (±0.012161285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 441.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_72939_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HuCoV-HKU1 C S 2P in complex with H501-022 (half map A local map)

Fileemd_72939_half_map_1.map
AnnotationHuCoV-HKU1 C S 2P in complex with H501-022 (half map A local map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HuCoV-HKU1 C S 2P in complex with H501-022 (half map B local map)

Fileemd_72939_half_map_2.map
AnnotationHuCoV-HKU1 C S 2P in complex with H501-022 (half map B local 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 : HCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM)

EntireName: HCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM)
Components
  • Complex: HCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM)
    • Complex: HCoV-HKU1 C S 2P
      • Protein or peptide: Spike glycoprotein
    • Complex: H501-022 Fab
      • Protein or peptide: H501-022 Fab heavy chain
      • Protein or peptide: H501-022 Fab light chain

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Supramolecule #1: HCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM)

SupramoleculeName: HCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 700 KDa

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Supramolecule #2: HCoV-HKU1 C S 2P

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

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Supramolecule #3: H501-022 Fab

SupramoleculeName: H501-022 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus HKU1 / Strain: isolate N5
Molecular weightTheoretical: 148.411547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFLIIFILPT TLAVIGDFNC TNSFINDYNK TIPRISEDVV DVSLGLGTYY VLNRVYLNTT LLFTGYFPKS GANFRDLALK GSIYLSTLW YKPPFLSDFN NGIFSKVKNT KLYVNNTLYS EFSTIVIGSV FVNTSYTIVV QPHNGILEIT ACQYTMCEYP H TVCKSKGS ...String:
MFLIIFILPT TLAVIGDFNC TNSFINDYNK TIPRISEDVV DVSLGLGTYY VLNRVYLNTT LLFTGYFPKS GANFRDLALK GSIYLSTLW YKPPFLSDFN NGIFSKVKNT KLYVNNTLYS EFSTIVIGSV FVNTSYTIVV QPHNGILEIT ACQYTMCEYP H TVCKSKGS IRNESWHIDS SEPLCLFKKN FTYNVSADWL YFHFYQERGV FYAYYADVGM PTTFLFSLYL GTILSHYYVM PL TCNAISS NTDNETLEYW VTPLSRRQYL LNFDEHGVIT NAVDCSSSFL SEIQCKTQSF APNTGVYDLS GFTVKPVATV YRR IPNLPD CDIDNWLNNV SVPSPLNWER RIFSNCNFNL STLLRLVHVD SFSCNNLDKS KIFGSCFNSI TVDKFAIPNR RRDD LQLGS SGFLQSSNYK IDISSSSCQL YYSLPLVNVT INNFNPSSWN RRYGFGSFNL SSYDVVYSDH CFSVNSDFCP CADPS VVNS CAKSKPPSAI CPAGTKYRHC DLDTTLYVKN WCRCSCLPDP ISTYSPNTCP QKKVVVGIGE HCPGLGINEE KCGTQL NHS SCFCSPDAFL GWSFDSCISN NRCNIFSNFI FNGINSGTTC SNDLLYSNTE ISTGVCVNYD LYGITGQGIF KEVSAAY YN NWQNLLYDSN GNIIGFKDFL TNKTYTILPC YSGRVSAAFY QNSSSPALLY RNLKCSYVLN NISFISQPFY FDSYLGCV L NAVNLTSYSV SSCDLRMGSG FCIDYALPSS GGSGSGISSP YRFVTFEPFN VSFVNDSVET VGGLFEIQIP TNFTIAGHE EFIQTSSPKV TIDCSAFVCS NYAACHDLLS EYGTFCDNIN SILNEVNDLL DITQLQVANA LMQGVTLSSN LNTNLHSDVD NIDFKSLLG CLGSQCGSSS RSLLEDLLFN KVKLSDVGFV EAYNNCTGGS EIRDLLCVQS FNGIKVLPPI LSETQISGYT T AATVAAMF PPWSAAAGVP FSLNVQYRIN GLGVTMDVLN KNQKLIANAF NKALLSIQNG FTATNSALAK IQSVVNANAQ AL NSLLQQL FNKFGAISSS LQEILSRLDP PEAQVQIDRL INGRLTALNA YVSQQLSDIT LIKAGASRAI EKVNECVKSQ SPR INFCGN GNHILSLVQN APYGLLFIHF SYKPTSFKTV LVSPGLCLSG DRGIAPKQGY FIKQNDSWMF TGSSYYYPEP ISDK NVVFM NSCSVNFTKA PFIYLNNSIP NLSDFEAELS LWFKNHTSIA PNLTFNSHIN ATFLDLYYEM NVIQESIKSL NSGRL EVLF QGPGGYIPEA PRDGQAYVRK DGEWVLLSTF LGHHHHHHHH SAWSHPQFEK

UniProtKB: Spike glycoprotein

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Macromolecule #2: H501-022 Fab heavy chain

MacromoleculeName: H501-022 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.204467 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QGTLKESGPM LVKPTQTLTL TCNFSGFSLS TSGVGVGWIR QPPGKALECL ALIYWNDDQR YSPSLKTRLT ITKDTSKNQV VLTMTNMDP VDTATYYCVY SMSRPVAGGV IDHWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QGTLKESGPM LVKPTQTLTL TCNFSGFSLS TSGVGVGWIR QPPGKALECL ALIYWNDDQR YSPSLKTRLT ITKDTSKNQV VLTMTNMDP VDTATYYCVY SMSRPVAGGV IDHWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK

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Macromolecule #3: H501-022 Fab light chain

MacromoleculeName: H501-022 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.319734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLTQSPSS LSASEGDRVT ITCWASQNIR GYLNWYQQKP GKAPKLLIYA TSTLESGVPS RFSGSGSVTD YTLTISSLQP EDFATYSCQ QSYSSPPTFG GGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQLTQSPSS LSASEGDRVT ITCWASQNIR GYLNWYQQKP GKAPKLLIYA TSTLESGVPS RFSGSGSVTD YTLTISSLQP EDFATYSCQ QSYSSPPTFG GGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5853 / Average exposure time: 2.31 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 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: 0.4 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 139880
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 50000 / Software - Name: RELION (ver. 5)

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Atomic model buiding 1

Initial model
PDB IDChain

8y8a

chain_id: A, source_name: PDB, initial_model_type: experimental model

5o7p

chain_id: L, source_name: PDB, initial_model_type: experimental model

7t3m

chain_id: H, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9ygr:
HCoV-HKU1 C S 2P in complex with H501-022 Fab (local cryoEM)

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