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- EMDB-30573: A proof of concept for neutralizing antibody-guided vaccine desig... -

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Basic information

Entry
Database: EMDB / ID: EMD-30573
TitleA proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2
Map data
SampleFC05 Fab binds to SARS-CoV-2 Spike:
Spike protein S1 / FC05 Fab / Spike glycoprotein S1 / Light chain of FC05 Fab / Heavy chain of FC05 Fab
Function / homology
Function and homology information


suppression by virus of host tetherin activity / 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 tetherin activity / 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 / go:0009405: / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
Spike receptor binding domain superfamily, coronavirus / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S2, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / in:ipr027400: / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCao L / Wang X
CitationJournal: To Be Published
Title: A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2
Authors: Cao L / Wang X
Validation ReportSummary, Full report, XML, About validation report
History
DepositionSep 23, 2020-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7d4g
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7d4g
  • 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_30573.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å
1.04 Å/pix.
x 320 pix.
= 332.8 Å
1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.095674 - 0.1562097
Average (Standard dev.)-4.646387e-05 (±0.0016868974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0960.156-0.000

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Supplemental data

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Sample components

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Entire FC05 Fab binds to SARS-CoV-2 Spike

EntireName: FC05 Fab binds to SARS-CoV-2 Spike / Number of components: 6

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Component #1: protein, FC05 Fab binds to SARS-CoV-2 Spike

ProteinName: FC05 Fab binds to SARS-CoV-2 Spike / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #2: protein, Spike protein S1

ProteinName: Spike protein S1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #3: protein, FC05 Fab

ProteinName: FC05 Fab / Recombinant expression: No

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Component #4: protein, Spike glycoprotein S1

ProteinName: Spike glycoprotein S1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.663637 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Light chain of FC05 Fab

ProteinName: Light chain of FC05 Fab / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.34548 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Heavy chain of FC05 Fab

ProteinName: Heavy chain of FC05 Fab / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.463899 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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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 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 450378
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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