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- EMDB-54623: CryoEM structure of WIV1 spike monomer in complex with neutralizi... -

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Basic information

Entry
Database: EMDB / ID: EMD-54623
TitleCryoEM structure of WIV1 spike monomer in complex with neutralizing antibody VA14_26
Map datahalf map 2
Sample
  • Complex: Antibody-antigen complex between VA14_26 antibody FAB and Bat SARS-like coronavirus WIV1 Spike glycoprotein
    • Protein or peptide: VA14_26 Antibody Light Chain
    • Protein or peptide: VA14_26 antibody Heavy Chain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeutralizing Antibody / Sarbecovirus / WIV1 / FAB / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 ...positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesBat SARS-like coronavirus WIV1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.12 Å
AuthorsUpadhyay A / Alguel Y / Cherepanov P
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome TrustCC2058 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2058 United Kingdom
Cancer Research UKCC2058 United Kingdom
CitationJournal: To Be Published
Title: Mechanisms for cross-neutralisation of diverse bat sarbecoviruses
Authors: Upadhyay A / Seow J / Alguel Y / Newman J / Thakur N / Tam JCH / Nans A / Bailey D / Cherepanov P / Doores KJ
History
DepositionJul 31, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54623.png

Downloads & links

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Map

FileReleased
Annotationhalf map 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.924048 - 3.8009195
Average (Standard dev.)0.0007876706 (±0.028740883)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 2

Fileemd_54623_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_54623_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antibody-antigen complex between VA14_26 antibody FAB and Bat SAR...

EntireName: Antibody-antigen complex between VA14_26 antibody FAB and Bat SARS-like coronavirus WIV1 Spike glycoprotein
Components
  • Complex: Antibody-antigen complex between VA14_26 antibody FAB and Bat SARS-like coronavirus WIV1 Spike glycoprotein
    • Protein or peptide: VA14_26 Antibody Light Chain
    • Protein or peptide: VA14_26 antibody Heavy Chain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Antibody-antigen complex between VA14_26 antibody FAB and Bat SAR...

SupramoleculeName: Antibody-antigen complex between VA14_26 antibody FAB and Bat SARS-like coronavirus WIV1 Spike glycoprotein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: The complex formed in vitro using recombinant proteins.
Source (natural)Organism: Bat SARS-like coronavirus WIV1

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Macromolecule #1: VA14_26 Antibody Light Chain

MacromoleculeName: VA14_26 Antibody Light Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.355947 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLTQSPST LSASVGDRVT ITCRASQSIS TWLAWHQQIP GKAPKLLIYR ASTLQSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYYSVRTFGQ GTKVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
DIQLTQSPST LSASVGDRVT ITCRASQSIS TWLAWHQQIP GKAPKLLIYR ASTLQSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYYSVRTFGQ GTKVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #2: VA14_26 antibody Heavy Chain

MacromoleculeName: VA14_26 antibody Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.438379 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SQVQLQQWGA GLLKPSDTLS LTCGISGGPF SGYYWSWIRQ PPGKGLEWLG EINHSGITTY NPSLKSRGTI SVDTSKRQIS LKLASVTAA DTAVYYCARF AYGDYGWDYS SDMDVWGKGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
SQVQLQQWGA GLLKPSDTLS LTCGISGGPF SGYYWSWIRQ PPGKGLEWLG EINHSGITTY NPSLKSRGTI SVDTSKRQIS LKLASVTAA DTAVYYCARF AYGDYGWDYS SDMDVWGKGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DGTKHHHHHH

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Macromolecule #3: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bat SARS-like coronavirus WIV1
Molecular weightTheoretical: 137.395156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKLLVLVFAT LVSSYTIEKC LDFDDRTPPA NTQFLSSHRG VYYPDDIFRS NVLHLVQDHF LPFDSNVTRF ITFGLNFDNP IIPFKDGIY FAATEKSNVI RGWVFGSTMN NKSQSVIIMN NSTNLVIRAC NFELCDNPFF VVLKSNNTQI PSYIFNNAFN C TFEYVSKD ...String:
MKLLVLVFAT LVSSYTIEKC LDFDDRTPPA NTQFLSSHRG VYYPDDIFRS NVLHLVQDHF LPFDSNVTRF ITFGLNFDNP IIPFKDGIY FAATEKSNVI RGWVFGSTMN NKSQSVIIMN NSTNLVIRAC NFELCDNPFF VVLKSNNTQI PSYIFNNAFN C TFEYVSKD FNLDLGEKPG NFKDLREFVF RNKDGFLHVY SGYQPISAAS GLPTGFNALK PIFKLPLGIN ITNFRTLLTA FP PRPDYWG TSAAAYFVGY LKPTTFMLKY DENGTITDAV DCSQNPLAEL KCSVKSFEID KGIYQTSNFR VAPSKEVVRF PNI TNLCPF GEVFNATTFP SVYAWERKRI SNCVADYSVL YNSTSFSTFK CYGVSATKLN DLCFSNVYAD SFVVKGDDVR QIAP GQTGV IADYNYKLPD DFTGCVLAWN TRNIDATQTG NYNYKYRSLR HGKLRPFERD ISNVPFSPDG KPCTPPAFNC YWPLN DYGF YITNGIGYQP YRVVVLSFEL LNAPATVCGP KLSTDLIKNQ CVNFNFNGLT GTGVLTPSSK RFQPFQQFGR DVSDFT DSV RDPKTSEILD ISPCSFGGVS VITPGTNTSS EVAVLYQDVN CTDVPVAIHA DQLTPSWRVH STGNNVFQTQ AGCLIGA EH VDTSYECDIP IGAGICASYH TVSSLSSTSQ KSIVAYTMSL GADSSIAYSN NTIAIPTNFS ISITTEVMPV SMAKTSVD C NMYICGDSTE CANLLLQYGS FCTQLNRALS GIAVEQDRNT REVFAQVKQM YKTPTLKDFG GFNFSQILPD PLKPTKRSF IEDLLFNKVT LADAGFMKQY GECLGDINAR DLICAQKFNG LTVLPPLLTD DMIAAYTAAL VSGTATAGWT FGAGAALQIP FAMQMAYRF NGIGVTQNVL YENQKQIANQ FNKAISQIQE SLTTTSTALG KLQDVVNQNA QALNTLVKQL SSNFGAISSV L NDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQA AP HGVVFLH VTYVPSQERN FTTAPAICHE GKAYFPREGV FVFNGTSWFI TQRNFFSPQI ITTDNTFVSG SCDVVIGIIN NTV YDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESLIDLQEL GKYEQSGREN LYFQ GGGGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMC4H12NO3ClTris-HCl

Details: 150 mM NaCl, 20 mM Tris-HCl, pH 8.0
Sugar embeddingMaterial: vitreous ice
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 32.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab- initio Model from CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 1460644
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8tc0


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9s67:
CryoEM structure of WIV1 spike monomer in complex with neutralizing antibody VA14_26

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