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- EMDB-30486: SARS-CoV-2 Spike Proteins Trimer in Complex with FC05 and H014 Fa... -

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Basic information

Entry
Database: EMDB / ID: EMD-30486
TitleSARS-CoV-2 Spike Proteins Trimer in Complex with FC05 and H014 Fabs Cocktail
Map data
SampleSARS-CoV-2 spike proteins trimer in complex with FC05 and H014 fabs Cocktail:
FC05 Fab / H014 Fab / SARS-CoV-2 spike protein / (Heavy Chain of ...) x 2 / (Light Chain of ...) x 2 / Spike glycoproteinPeplomer / ligand
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 / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope ...suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike glycoprotein S2, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal
Spike glycoprotein
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang L / Wang X
CitationJournal: Cell Res / Year: 2021
Title: Structure-based development of human antibody cocktails against SARS-CoV-2.
Authors: Nan Wang / Yao Sun / Rui Feng / Yuxi Wang / Yan Guo / Li Zhang / Yong-Qiang Deng / Lei Wang / Zhen Cui / Lei Cao / Yan-Jun Zhang / Weimin Li / Feng-Cai Zhu / Cheng-Feng Qin / Xiangxi Wang /
Validation ReportSummary, Full report, XML, About validation report
History
DepositionAug 31, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7cws
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30486.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 312. Å
1.04 Å/pix.
x 300 pix.
= 312. Å
1.04 Å/pix.
x 300 pix.
= 312. 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: 0.003 / Movie #1: 0.006
Minimum - Maximum-0.011618243 - 0.046734292
Average (Standard dev.)0.00025859085 (±0.0014816652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0120.0470.000

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Supplemental data

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Sample components

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Entire SARS-CoV-2 spike proteins trimer in complex with FC05 and H014 fa...

EntireName: SARS-CoV-2 spike proteins trimer in complex with FC05 and H014 fabs Cocktail
Number of components: 10

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Component #1: protein, SARS-CoV-2 spike proteins trimer in complex with FC05 an...

ProteinName: SARS-CoV-2 spike proteins trimer in complex with FC05 and H014 fabs Cocktail
Recombinant expression: No

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Component #2: protein, FC05 Fab

ProteinName: FC05 Fab / 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, H014 Fab

ProteinName: H014 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #4: protein, SARS-CoV-2 spike protein

ProteinName: SARS-CoV-2 spike protein / 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 #5: protein, Heavy Chain of FC05 Fab

ProteinName: Heavy Chain of FC05 Fab / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 13.289744 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Light Chain of FC05 Fab

ProteinName: Light Chain of FC05 Fab / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 11.231378 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Light Chain of H014 Fab

ProteinName: Light Chain of H014 Fab / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 12.010525 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, Heavy Chain of H014 Fab

ProteinName: Heavy Chain of H014 Fab / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 13.385787 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 125.612219 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 16 / 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: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 99382
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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