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- EMDB-24533: SARS-CoV-2 spike protein bound to the S2P6 and S2M11 Fab fragments -

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Basic information

Entry
Database: EMDB / ID: EMD-24533
TitleSARS-CoV-2 spike protein bound to the S2P6 and S2M11 Fab fragments
Map datasharpened map
Sample
  • Complex: S2P6 and S2M11 Fab fragments bound to the SARS-CoV-2 Spike protein
    • Complex: S2P6 Fab fragment
    • Complex: S2M11 Fab fragment
    • Complex: SARS-CoV-2 spike protein
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSauer MM / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM120553 United States
CitationJournal: Science / Year: 2021
Title: Broad betacoronavirus neutralization by a stem helix-specific human antibody.
Authors: Dora Pinto / Maximilian M Sauer / Nadine Czudnochowski / Jun Siong Low / M Alejandra Tortorici / Michael P Housley / Julia Noack / Alexandra C Walls / John E Bowen / Barbara Guarino / Laura ...Authors: Dora Pinto / Maximilian M Sauer / Nadine Czudnochowski / Jun Siong Low / M Alejandra Tortorici / Michael P Housley / Julia Noack / Alexandra C Walls / John E Bowen / Barbara Guarino / Laura E Rosen / Julia di Iulio / Josipa Jerak / Hannah Kaiser / Saiful Islam / Stefano Jaconi / Nicole Sprugasci / Katja Culap / Rana Abdelnabi / Caroline Foo / Lotte Coelmont / Istvan Bartha / Siro Bianchi / Chiara Silacci-Fregni / Jessica Bassi / Roberta Marzi / Eneida Vetti / Antonino Cassotta / Alessandro Ceschi / Paolo Ferrari / Pietro E Cippà / Olivier Giannini / Samuele Ceruti / Christian Garzoni / Agostino Riva / Fabio Benigni / Elisabetta Cameroni / Luca Piccoli / Matteo S Pizzuto / Megan Smithey / David Hong / Amalio Telenti / Florian A Lempp / Johan Neyts / Colin Havenar-Daughton / Antonio Lanzavecchia / Federica Sallusto / Gyorgy Snell / Herbert W Virgin / Martina Beltramello / Davide Corti / David Veesler /
Abstract: The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We ...The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We describe five monoclonal antibodies (mAbs) cross-reacting with the stem helix of multiple betacoronavirus spike glycoproteins isolated from COVID-19 convalescent individuals. Using structural and functional studies, we show that the mAb with the greatest breadth (S2P6) neutralizes pseudotyped viruses from three different subgenera through the inhibition of membrane fusion, and we delineate the molecular basis for its cross-reactivity. S2P6 reduces viral burden in hamsters challenged with SARS-CoV-2 through viral neutralization and Fc-mediated effector functions. Stem helix antibodies are rare, oftentimes of narrow specificity, and can acquire neutralization breadth through somatic mutations. These data provide a framework for structure-guided design of pan-betacoronavirus vaccines eliciting broad protection.
History
DepositionJul 23, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24533.png

Downloads & links

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Map

FileDownload / File: emd_24533.map.gz / Format: CCP4 / Size: 294.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 426 pix.
= 511.626 Å		1.2 Å/pix.
x 426 pix.
= 511.626 Å		1.2 Å/pix.
x 426 pix.
= 511.626 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.201 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115 / Movie #1: 0.15
Minimum - Maximum-0.4584674 - 1.4741306
Average (Standard dev.)0.00282812 (±0.03538361)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions426426426
Spacing426426426
CellA=B=C: 511.62598 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2011.2011.201
M x/y/z426426426
origin x/y/z0.0000.0000.000
length x/y/z511.626511.626511.626
α/β/γ90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS426426426
D min/max/mean-0.4581.4740.003

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Supplemental data

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Mask #1

Fileemd_24533_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_24533_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_24533_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_24533_half_map_2.map
AnnotationHalf 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 : S2P6 and S2M11 Fab fragments bound to the SARS-CoV-2 Spike protein

EntireName: S2P6 and S2M11 Fab fragments bound to the SARS-CoV-2 Spike protein
Components
  • Complex: S2P6 and S2M11 Fab fragments bound to the SARS-CoV-2 Spike protein
    • Complex: S2P6 Fab fragment
    • Complex: S2M11 Fab fragment
    • Complex: SARS-CoV-2 spike protein

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Supramolecule #1: S2P6 and S2M11 Fab fragments bound to the SARS-CoV-2 Spike protein

SupramoleculeName: S2P6 and S2M11 Fab fragments bound to the SARS-CoV-2 Spike protein
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: S2P6 Fab fragment

SupramoleculeName: S2P6 Fab fragment / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: S2M11 Fab fragment

SupramoleculeName: S2M11 Fab fragment / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: SARS-CoV-2 spike protein

SupramoleculeName: SARS-CoV-2 spike protein / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: 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

BufferpH: 7.4
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryosparc ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81519
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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