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- EMDB-22126: SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from recove... -

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Basic information

Entry
Database: EMDB / ID: EMD-22126
TitleSARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from recovered COVID-19 individual COV21
Map dataNegative-stain EM of SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from recovered COVID-19 individual COV21
Sample
  • Complex: SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from COV21 individual
    • Complex: SARS-CoV-2 spike glycoprotein 2P trimer
    • Complex: COV21 polyclonal Fab fragment
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsBarnes CO / Bjorkman PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138398-S1 United States
CitationJournal: Cell / Year: 2020
Title: Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies.
Authors: Christopher O Barnes / Anthony P West / Kathryn E Huey-Tubman / Magnus A G Hoffmann / Naima G Sharaf / Pauline R Hoffman / Nicholas Koranda / Harry B Gristick / Christian Gaebler / Frauke ...Authors: Christopher O Barnes / Anthony P West / Kathryn E Huey-Tubman / Magnus A G Hoffmann / Naima G Sharaf / Pauline R Hoffman / Nicholas Koranda / Harry B Gristick / Christian Gaebler / Frauke Muecksch / Julio C Cetrulo Lorenzi / Shlomo Finkin / Thomas Hägglöf / Arlene Hurley / Katrina G Millard / Yiska Weisblum / Fabian Schmidt / Theodora Hatziioannou / Paul D Bieniasz / Marina Caskey / Davide F Robbiani / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID- ...Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1 and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryo-electron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.
History
DepositionJun 8, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22126.png

Downloads & links

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Map

FileDownload / File: emd_22126.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative-stain EM of SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from recovered COVID-19 individual COV21
Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.25375202 - 1.2320291
Average (Standard dev.)-0.0020731925 (±0.05814107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2541.232-0.002

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from COV21 ...

EntireName: SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from COV21 individual
Components
  • Complex: SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from COV21 individual
    • Complex: SARS-CoV-2 spike glycoprotein 2P trimer
    • Complex: COV21 polyclonal Fab fragment

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Supramolecule #1: SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from COV21 ...

SupramoleculeName: SARS-CoV-2 S 2P trimer complexed with polyclonal Fabs from COV21 individual
type: complex / ID: 1 / Parent: 0
Molecular weightExperimental: 600 KDa

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Supramolecule #2: SARS-CoV-2 spike glycoprotein 2P trimer

SupramoleculeName: SARS-CoV-2 spike glycoprotein 2P trimer / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293F / Recombinant plasmid: pCAGGS
Molecular weightExperimental: 585 KDa

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Supramolecule #3: COV21 polyclonal Fab fragment

SupramoleculeName: COV21 polyclonal Fab fragment / type: complex / ID: 3 / Parent: 1
Details: COV21 polyclonal Fab fragments were generated by proteolytic cleavage of plasma-purified IgG antibodies.
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 50 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 1% uranyl formate staining
GridDetails: unspecified
DetailsMonodisperse sample taken after size-exclusion chromatography

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 12.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio volume generated in cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.14.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14.2) / Number images used: 9524
DetailsGain-normalized and collected in counting mode with 10 frames per movie

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Atomic model buiding 1

Detailsunspecified

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