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- EMDB-22128: Structure of the SARS-CoV-2 spike glycoprotein in complex with th... -

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Basic information

Entry
Database: EMDB / ID: EMD-22128
TitleStructure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 2)
Map data
SampleSARS-CoV-2 S 2P trimer complexed with monoclonal Fab fragments from neutralizing antibody C105:
SARS-CoV-2 spike glycoprotein 2P trimer / neutralizing antibody C105 Fab / Spike glycoprotein / C105 Fab Heavy Chain / C105 Fab Light Chain / (ligand) x 3
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell surface receptor binding / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane
Spike glycoprotein S2, coronavirus / Spike receptor binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike receptor binding domain superfamily, coronavirus
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 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: bioRxiv / 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 Hagglof / 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 focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 ...Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their degree of focus on RBD epitopes, recognition of SARS-CoV, MERS-CoV, and mild coronaviruses, and how avidity effects contributed to increased binding/neutralization of IgGs over Fabs. Electron microscopy reconstructions of polyclonal plasma Fab-spike complexes showed recognition of both S1 and RBD epitopes. A 3.4Å cryo-EM structure of a neutralizing monoclonal Fab-S complex revealed an epitope that blocks ACE2 receptor-binding on "up" RBDs. Modeling suggested that IgGs targeting these sites have different potentials for inter-spike crosslinking on viruses and would not be greatly affected by identified SARS-CoV-2 spike mutations. These studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from and similarity to a SARS-CoV antibody, providing criteria for evaluating vaccine-elicited antibodies.
Validation ReportPDB-ID: 6xcn

SummaryFull reportAbout validation report
History
DepositionJun 8, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xcn
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22128.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 352 pix.
= 294.272 Å
0.84 Å/pix.
x 352 pix.
= 294.272 Å
0.84 Å/pix.
x 352 pix.
= 294.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.37918574 - 0.70283484
Average (Standard dev.)0.003918611 (±0.023558956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 294.272 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8360.8360.836
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z294.272294.272294.272
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.3790.7030.004

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Supplemental data

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Segmentation: #1

Fileemd_22128_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Unsharpened, non-uniform refined volume of C105-SARS-CoV-2 S 2P...

Fileemd_22128_additional.map
AnnotationUnsharpened, non-uniform refined volume of C105-SARS-CoV-2 S 2P trimer complex (state 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire SARS-CoV-2 S 2P trimer complexed with monoclonal Fab fragments fr...

EntireName: SARS-CoV-2 S 2P trimer complexed with monoclonal Fab fragments from neutralizing antibody C105
Number of components: 9

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Component #1: protein, SARS-CoV-2 S 2P trimer complexed with monoclonal Fab fra...

ProteinName: SARS-CoV-2 S 2P trimer complexed with monoclonal Fab fragments from neutralizing antibody C105
Recombinant expression: No
MassExperimental: 750 kDa

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Component #2: protein, SARS-CoV-2 spike glycoprotein 2P trimer

ProteinName: SARS-CoV-2 spike glycoprotein 2P trimer / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human) / Vector: pCAGGS / Strain: Expi293F / Cell of expression system: HeLa

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Component #3: protein, neutralizing antibody C105 Fab

ProteinName: neutralizing antibody C105 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: p3BNC / Strain: Expi293F / Cell of expression system: HeLa

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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoprotein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 139.788953 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, C105 Fab Heavy Chain

ProteinName: C105 Fab Heavy Chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 24.662506 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, C105 Fab Light Chain

ProteinName: C105 Fab Light Chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 22.893227 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 54 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #8: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #9: ligand, ALPHA-L-FUCOSE

LigandName: ALPHA-L-FUCOSE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.164156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 8
Support film60 s glow discharge in air at 0.20 mA current
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: 3 microliters added, blotted for 3 s with 0 blot force.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Collected with 3x3 pattern and beam image shift
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 5940

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 14119
Details: Gain-normalized and collected in counting mode with 40 frames per movie
3D reconstructionSoftware: cryoSPARC / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 6VYB
Chain ID: B

Overall bvalue: 90
Output model

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