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- EMDB-49708: cryo-EM structure of broad betacoronavirus binding antibody 1871 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-49708
Titlecryo-EM structure of broad betacoronavirus binding antibody 1871 in complex with OC43 S2 subunit
Map data
Sample
  • Complex: OC43 S2 subunit complex with Fab 1871
    • Complex: OC43 S2 subunit
      • Protein or peptide: Spike glycoprotein
    • Complex: Fab 1871
      • Protein or peptide: 1871 Fab light chain
      • Protein or peptide: 1871 Fab heavy chain
KeywordsOC43 / Betacoronavirus / antibody / viral glycoprotein / IMMUNE SYSTEM-VIRAL PROTEIN complex / 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
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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. / 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 S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 OC43 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMuthuraman K / Jackman MJ / Julien JP
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-023398 United States
CitationJournal: To Be Published
Title: Human antibody targeting of coronavirus spike S2 subunit is associated with protection mediated by Fc effector functions
Authors: Muthuraman K / Jackman MJ / Julien JP
History
DepositionMar 13, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49708.png

Downloads & links

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Map

FileDownload / File: emd_49708.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 300 pix.
= 309. Å		1.03 Å/pix.
x 300 pix.
= 309. Å		1.03 Å/pix.
x 300 pix.
= 309. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.252
Minimum - Maximum-2.044818 - 3.0093458
Average (Standard dev.)-0.00047517693 (±0.060947817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 309.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49708_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49708_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 : OC43 S2 subunit complex with Fab 1871

EntireName: OC43 S2 subunit complex with Fab 1871
Components
  • Complex: OC43 S2 subunit complex with Fab 1871
    • Complex: OC43 S2 subunit
      • Protein or peptide: Spike glycoprotein
    • Complex: Fab 1871
      • Protein or peptide: 1871 Fab light chain
      • Protein or peptide: 1871 Fab heavy chain

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Supramolecule #1: OC43 S2 subunit complex with Fab 1871

SupramoleculeName: OC43 S2 subunit complex with Fab 1871 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: OC43 spike protein S2 subunit trimer, Fab fragment generated by recombinant expression
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: OC43 S2 subunit

SupramoleculeName: OC43 S2 subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human coronavirus OC43

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Supramolecule #3: Fab 1871

SupramoleculeName: Fab 1871 / 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: 3 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus OC43
Molecular weightTheoretical: 64.176945 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AITTGYRFTN FEPFTVNSVN DSLEPVGGLY EIQIPSEFTI GNMEEFIQTS SPKVTIDCAA FVCGDYAACK LQLVEYGSFC DNINAILTE VNELLDTTQL QVANSLMNGV TLSTKLKDGV NFNVDDINFS PVLGCLGSEC SKASSRSAIE DLLFDKVKLS D VGFVEAYN ...String:
AITTGYRFTN FEPFTVNSVN DSLEPVGGLY EIQIPSEFTI GNMEEFIQTS SPKVTIDCAA FVCGDYAACK LQLVEYGSFC DNINAILTE VNELLDTTQL QVANSLMNGV TLSTKLKDGV NFNVDDINFS PVLGCLGSEC SKASSRSAIE DLLFDKVKLS D VGFVEAYN NCTGGAEIRD LICVQSYKGI KVLPPLLSEN QISGYTLAAT SASLFPPWTA AAGVPFYLNV QYRINGLGVT MD VLSQNQK LIANAFNNAL HAIQQGFDAT NSALVKIQAV VNANAEALNN LLQQLSNRFG AISASLQEIL SRLDALEAEA QID RLINGR LTALNAYVSQ QLSDSTLVKF SAAQAMEKVN ECVKSQSSRI NFCGNGNHII SLVQNAPYGL YFIHFNYVPT KYVT AKVSP GLCIAGNRGI APKSGYFVNV NNTWMYTGSG YYYPEPITEN NVVVMSTCAV NYTKAPYVML NTSIPNLPDF KEELD QWFK NQTSVAPDLS LDYINVTFLD LQVEMNRLQE AIKVLNHSYI NKDIGTYEYG SENLYFQSGS GGGGSGYIPE APRDGQ AYV RKDGEWVLLS TFLGHHHHHH HH

UniProtKB: Spike glycoprotein

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Macromolecule #2: 1871 Fab light chain

MacromoleculeName: 1871 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.022502 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVMTQSPAT LSVSPGERVT LSCRASQSVR SRLAWFQQKP GQAPRLLIYD ASIRATGIPA RFSGSGSGTE FTLIISSLQS EDFAVYYCQ QYDNWPPAYT FGQGTKLEIK

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Macromolecule #3: 1871 Fab heavy chain

MacromoleculeName: 1871 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.589204 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKPGGSLRL SCVASGFSFS IYSMNWVRQA PGKGLEWVSY ISSSSSYKYY ADSVKGRFSV SRDNAKNSLY LQLNGLRAE DTAVYYCARD GYCPKGVCTY YGMDVWGQGT TVTVSA

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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

Concentration0.25 mg/mL
BufferpH: 7.4
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
DetailsThe sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 4795 / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
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: INSILICO MODEL
In silico model: Generated using Ab-initio reconstruction job.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Non-uniform refinement job in CryoSPARC. / Number images used: 109156
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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