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- EMDB-23578: SARS-CoV-2 S/S2M11/S2L28 Local Refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-23578
TitleSARS-CoV-2 S/S2M11/S2L28 Local Refinement
Map data
SampleSARS-CoV-2 S hexapro bound to S2L28 Fab:
S2L28 Fab Heavy Chain variable region / S2L28 Fab Light Chain variable region / Spike glycoproteinPeplomer / ligand
Function / homology
Function and homology information


Translation of structural proteins / Virion Assembly and Release / Maturation of spike protein / 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 ...Translation of structural proteins / Virion Assembly and Release / Maturation of spike protein / 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 envelope / viral entry into host cell / : / 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 speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMcCallum M / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
CitationJournal: Cell / Year: 2021
Title: N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.
Authors: Matthew McCallum / Anna De Marco / Florian A Lempp / M Alejandra Tortorici / Dora Pinto / Alexandra C Walls / Martina Beltramello / Alex Chen / Zhuoming Liu / Fabrizia Zatta / Samantha ...Authors: Matthew McCallum / Anna De Marco / Florian A Lempp / M Alejandra Tortorici / Dora Pinto / Alexandra C Walls / Martina Beltramello / Alex Chen / Zhuoming Liu / Fabrizia Zatta / Samantha Zepeda / Julia di Iulio / John E Bowen / Martin Montiel-Ruiz / Jiayi Zhou / Laura E Rosen / Siro Bianchi / Barbara Guarino / Chiara Silacci Fregni / Rana Abdelnabi / Shi-Yan Caroline Foo / Paul W Rothlauf / Louis-Marie Bloyet / Fabio Benigni / Elisabetta Cameroni / Johan Neyts / Agostino Riva / Gyorgy Snell / Amalio Telenti / Sean P J Whelan / Herbert W Virgin / Davide Corti / Matteo Samuele Pizzuto / David Veesler /
Abstract: The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about ...The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.
History
DepositionMar 5, 2021-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateMay 12, 2021-
Current statusMay 12, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lxx
  • Surface level: 1.2
  • 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_23578.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å
1.05 Å/pix.
x 400 pix.
= 420. Å
1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-3.9180136 - 10.827056
Average (Standard dev.)0.00028744337 (±0.028739275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ645365
NX/NY/NZ139143124
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-3.91810.8270.000

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Supplemental data

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Additional map: Unsharpened map

Fileemd_23578_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half Map B

Fileemd_23578_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half Map A

Fileemd_23578_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire SARS-CoV-2 S hexapro bound to S2L28 Fab

EntireName: SARS-CoV-2 S hexapro bound to S2L28 Fab / Number of components: 5

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Component #1: protein, SARS-CoV-2 S hexapro bound to S2L28 Fab

ProteinName: SARS-CoV-2 S hexapro bound to S2L28 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, S2L28 Fab Heavy Chain variable region

ProteinName: S2L28 Fab Heavy Chain variable region / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.849299 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, S2L28 Fab Light Chain variable region

ProteinName: S2L28 Fab Light Chain variable region / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.183054 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer / Number of Copies: 1 / 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: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 1 / 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 solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 81887
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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