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- EMDB-23695: Structure of the SARS-CoV-2 S 6P trimer in complex with the human... -

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Basic information

Entry
Database: EMDB / ID: EMD-23695
TitleStructure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG7-15
Map data
SampleTernary complex of BG7-15 Fab bound to SARS-CoV-2 spike trimer:
SARS-CoV-2 spike trimer / BG7-15 Fab / Spike glycoproteinSpike protein / BG7-15 Fab Heavy Chain / BG7-15 Fab Light Chain / ligand
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral entry into host cell / viral envelope / : / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
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 C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / : ...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 C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / : / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBarnes CO / Bjorkman PJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138398-S1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150464-13 United States
CitationJournal: Cell / Year: 2021
Title: B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.
Authors: Johannes F Scheid / Christopher O Barnes / Basak Eraslan / Andrew Hudak / Jennifer R Keeffe / Lisa A Cosimi / Eric M Brown / Frauke Muecksch / Yiska Weisblum / Shuting Zhang / Toni Delorey / ...Authors: Johannes F Scheid / Christopher O Barnes / Basak Eraslan / Andrew Hudak / Jennifer R Keeffe / Lisa A Cosimi / Eric M Brown / Frauke Muecksch / Yiska Weisblum / Shuting Zhang / Toni Delorey / Ann E Woolley / Fadi Ghantous / Sung-Moo Park / Devan Phillips / Betsabeh Tusi / Kathryn E Huey-Tubman / Alexander A Cohen / Priyanthi N P Gnanapragasam / Kara Rzasa / Theodora Hatziioanno / Michael A Durney / Xiebin Gu / Takuya Tada / Nathaniel R Landau / Anthony P West / Orit Rozenblatt-Rosen / Michael S Seaman / Lindsey R Baden / Daniel B Graham / Jacques Deguine / Paul D Bieniasz / Aviv Regev / Deborah Hung / Pamela J Bjorkman / Ramnik J Xavier /
Abstract: Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell ...Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell sorting with single-cell VDJ and RNA sequencing (RNA-seq) and mAb structures to characterize B cell responses against SARS-CoV-2. We show that the SARS-CoV-2-specific B cell repertoire consists of transcriptionally distinct B cell populations with cells producing potently neutralizing antibodies (nAbs) localized in two clusters that resemble memory and activated B cells. Cryo-electron microscopy structures of selected nAbs from these two clusters complexed with SARS-CoV-2 spike trimers show recognition of various receptor-binding domain (RBD) epitopes. One of these mAbs, BG10-19, locks the spike trimer in a closed conformation to potently neutralize SARS-CoV-2, the recently arising mutants B.1.1.7 and B.1.351, and SARS-CoV and cross-reacts with heterologous RBDs. Together, our results characterize transcriptional differences among SARS-CoV-2-specific B cells and uncover cross-neutralizing Ab targets that will inform immunogen and therapeutic design against coronaviruses.
History
DepositionMar 25, 2021-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateJun 23, 2021-
Current statusJun 23, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7m6g
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7m6g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_23695.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 432 pix.
= 375.408 Å
0.87 Å/pix.
x 432 pix.
= 375.408 Å
0.87 Å/pix.
x 432 pix.
= 375.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.869 Å
Density
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.34594503 - 0.6840844
Average (Standard dev.)-9.10547e-05 (±0.017850343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 375.40802 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8690.8690.869
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z375.408375.408375.408
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.3460.684-0.000

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Supplemental data

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Additional map: unsharpened map

Fileemd_23695_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Ternary complex of BG7-15 Fab bound to SARS-CoV-2 spike trimer

EntireName: Ternary complex of BG7-15 Fab bound to SARS-CoV-2 spike trimer
Number of Components: 7

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Component #1: protein, Ternary complex of BG7-15 Fab bound to SARS-CoV-2 spike ...

ProteinName: Ternary complex of BG7-15 Fab bound to SARS-CoV-2 spike trimer
Recombinant expression: No
MassExperimental: 720 kDa

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

ProteinName: SARS-CoV-2 spike trimer / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293

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Component #3: protein, BG7-15 Fab

ProteinName: BG7-15 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293

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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoproteinSpike protein
Details: Pre-fusion stabilized HexaPro construct, including six proline substitutions and furin cleavage site RRAR 682-685 mutated to GSAS
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 142.427438 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, BG7-15 Fab Heavy Chain

ProteinName: BG7-15 Fab Heavy Chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.825682 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, BG7-15 Fab Light Chain

ProteinName: BG7-15 Fab Light Chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.323867 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 295 K / Humidity: 100 % / Details: 3s blot, 0 blot force.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 60 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 45000.0 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 700.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of Digital Images: 3065

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 130297
3D reconstructionSoftware: cryoSPARC / Resolution: 3.7 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: 6XKL
Output model

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