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- EMDB-22994: SARS-CoV-2 Spike protein in complex with Fab 2H4 -

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Basic information

Entry
Database: EMDB / ID: EMD-22994
TitleSARS-CoV-2 Spike protein in complex with Fab 2H4Coronavirus spike protein
Map dataSpike:2H4 Complex III raw map from non-uniform refinement in cryoSPARC v2.15
Sample
  • Complex: SARS-CoV-2 Spike protein trimer in complex with Fab 2H4
    • Complex: SARS-CoV-2 Spike protein trimer
    • Complex: Fab 2H4
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
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 N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...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 N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAsarnow D / Charles C / Cheng Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50AI150476 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021741 United States
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionNov 14, 2020-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 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: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22994.png

Downloads & links

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Map

FileDownload / File: emd_22994.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSpike:2H4 Complex III raw map from non-uniform refinement in cryoSPARC v2.15
Voxel sizeX=Y=Z: 1.18756 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.6
Minimum - Maximum-0.39711884 - 2.670205
Average (Standard dev.)0.0050516017 (±0.09187013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 356.26797 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.187561.187561.18756
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z356.268356.268356.268
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3972.6700.005

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Supplemental data

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Additional map: Spike:2H4 Complex II raw map from non-uniform refinement...

Fileemd_22994_additional_1.map
AnnotationSpike:2H4 Complex II raw map from non-uniform refinement in cryoSPARC v2.15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Spike:2H4 Complex II half-map A map from non-uniform...

Fileemd_22994_additional_2.map
AnnotationSpike:2H4 Complex II half-map A map from non-uniform refinement in cryoSPARC v2.15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Spike:2H4 Complex II half-map B from non-uniform refinement...

Fileemd_22994_additional_3.map
AnnotationSpike:2H4 Complex II half-map B from non-uniform refinement in cryoSPARC v2.15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Spike:2H4 Complex I raw map from non-uniform refinement...

Fileemd_22994_additional_4.map
AnnotationSpike:2H4 Complex I raw map from non-uniform refinement in cryoSPARC v2.15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Spike:2H4 Complex I half-map A from non-uniform refinement...

Fileemd_22994_additional_5.map
AnnotationSpike:2H4 Complex I half-map A from non-uniform refinement in cryoSPARC v2.15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Spike:2H4 Complex I half-map B from non-uniform refinement...

Fileemd_22994_additional_6.map
AnnotationSpike:2H4 Complex I half-map B from non-uniform refinement in cryoSPARC v2.15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Spike:2H4 Complex III half-map A from non-uniform refinement...

Fileemd_22994_half_map_1.map
AnnotationSpike:2H4 Complex III half-map A from non-uniform refinement in cryoSPARC v2.15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Spike:2H4 Complex III half-map B from non-uniform refinement...

Fileemd_22994_half_map_2.map
AnnotationSpike:2H4 Complex III half-map B from non-uniform refinement in cryoSPARC v2.15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 Spike protein trimer in complex with Fab 2H4

EntireName: SARS-CoV-2 Spike protein trimer in complex with Fab 2H4
Components
  • Complex: SARS-CoV-2 Spike protein trimer in complex with Fab 2H4
    • Complex: SARS-CoV-2 Spike protein trimer
    • Complex: Fab 2H4

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Supramolecule #1: SARS-CoV-2 Spike protein trimer in complex with Fab 2H4

SupramoleculeName: SARS-CoV-2 Spike protein trimer in complex with Fab 2H4
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 457.1 KDa

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Supramolecule #2: SARS-CoV-2 Spike protein trimer

SupramoleculeName: SARS-CoV-2 Spike protein trimer / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant strain: expiCHO / Recombinant cell: Ovary

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Supramolecule #3: Fab 2H4

SupramoleculeName: Fab 2H4 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
10.0 mMHEPES
200.0 mMsodium chlorideNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV / Details: 8-10 seconds, blot force 0.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 7536 / Average exposure time: 5.9 sec. / Average electron dose: 67.7 e/Å2
Details: Movies were collected at super-resolution using correlated double sampling, with a frame time of 0.05 seconds and dose rate 8 e-/px/s
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1689358
CTF correctionSoftware - Name: cryoSPARC (ver. 2.15.0)
Startup modelType of model: OTHER / Details: Ab initio model from cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 71687

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Atomic model buiding 1

Initial modelPDB ID:

7a95

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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