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- EMDB-25072: Fab22 bound to MERS-CoV Spike -

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Basic information

Entry
Database: EMDB / ID: EMD-25072
TitleFab22 bound to MERS-CoV Spike
Map dataFab22 bound to MERS-CoV Spike
Sample
  • Complex: Fab22 bound to MERS-CoV spike protein
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to 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, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsHsieh C-L / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI127521 United States
CitationJournal: Cell Rep / Year: 2021
Title: Stabilized coronavirus spike stem elicits a broadly protective antibody.
Authors: Ching-Lin Hsieh / Anne P Werner / Sarah R Leist / Laura J Stevens / Ester Falconer / Jory A Goldsmith / Chia-Wei Chou / Olubukola M Abiona / Ande West / Kathryn Westendorf / Krithika ...Authors: Ching-Lin Hsieh / Anne P Werner / Sarah R Leist / Laura J Stevens / Ester Falconer / Jory A Goldsmith / Chia-Wei Chou / Olubukola M Abiona / Ande West / Kathryn Westendorf / Krithika Muthuraman / Ethan J Fritch / Kenneth H Dinnon / Alexandra Schäfer / Mark R Denison / James D Chappell / Ralph S Baric / Barney S Graham / Kizzmekia S Corbett / Jason S McLellan /
Abstract: Current coronavirus (CoV) vaccines primarily target immunodominant epitopes in the S1 subunit, which are poorly conserved and susceptible to escape mutations, thus threatening vaccine efficacy. Here, ...Current coronavirus (CoV) vaccines primarily target immunodominant epitopes in the S1 subunit, which are poorly conserved and susceptible to escape mutations, thus threatening vaccine efficacy. Here, we use structure-guided protein engineering to remove the S1 subunit from the Middle East respiratory syndrome (MERS)-CoV spike (S) glycoprotein and develop stabilized stem (SS) antigens. Vaccination with MERS SS elicits cross-reactive β-CoV antibody responses and protects mice against lethal MERS-CoV challenge. High-throughput screening of antibody-secreting cells from MERS SS-immunized mice led to the discovery of a panel of cross-reactive monoclonal antibodies. Among them, antibody IgG22 binds with high affinity to both MERS-CoV and severe acute respiratory syndrome (SARS)-CoV-2 S proteins, and a combination of electron microscopy and crystal structures localizes the epitope to a conserved coiled-coil region in the S2 subunit. Passive transfer of IgG22 protects mice against both MERS-CoV and SARS-CoV-2 challenge. Collectively, these results provide a proof of principle for cross-reactive CoV antibodies and inform the development of pan-CoV vaccines and therapeutic antibodies.
History
DepositionSep 30, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25072.png

Downloads & links

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Map

FileDownload / File: emd_25072.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFab22 bound to MERS-CoV Spike
Voxel sizeX=Y=Z: 1.043 Å
Density
Contour LevelBy AUTHOR: 0.22 / Movie #1: 0.22
Minimum - Maximum-1.2040237 - 2.0764816
Average (Standard dev.)-0.00015296141 (±0.04478567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 450.576 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0431.0431.043
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z450.576450.576450.576
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-1.2042.076-0.000

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Supplemental data

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Half map: Half Map 1

Fileemd_25072_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_25072_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fab22 bound to MERS-CoV spike protein

EntireName: Fab22 bound to MERS-CoV spike protein
Components
  • Complex: Fab22 bound to MERS-CoV spike protein

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Supramolecule #1: Fab22 bound to MERS-CoV spike protein

SupramoleculeName: Fab22 bound to MERS-CoV spike protein / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 174.23 kDa/nm

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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

Concentration1.0 mg/mL
BufferpH: 8 / Details: 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: Sample was then deposited on a plasma-cleaned CF-400 1.2/1.3 grid before being blotted for 5 seconds with +1 force in a Vitrobot Mark IV (ThermoFisher) and plunge-frozen into liquid ethane..
DetailsPurified MERS-CoV S-2P at 1 mg/mL was incubated with 2-fold molar excess of Fab22 in 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3 at room temperature for 30 min prior to the freezing

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 22500
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC
Initial angle assignmentType: RANDOM ASSIGNMENT / Details: Ab initio reconstruction in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 89372
FSC plot (resolution estimation)

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