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- EMDB-17451: SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab) -

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Basic information

Entry
Database: EMDB / ID: EMD-17451
TitleSARS-CoV-2 Spike RBD in complex with Mab-23 (Fab)
Map data
Sample
  • Complex: Spike RBD (two molecules) in complex with two FU2 nanobodies
    • Complex: SARS-CoV-2 spike (RBD)
      • Protein or peptide: Spike protein S1
    • Complex: Monoclonal Antibody Mab-23
      • Protein or peptide: Mab-23 (Heavy chain variable domain)
      • Protein or peptide: Mab-23 (Light chain variable domain)
KeywordsAntibody / Spike / Complex / VIRAL PROTEIN
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / identical protein binding / membrane / 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 / Enterobacteria phage T4 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDas H / Hallberg BM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab domains)
Authors: Das H / Hallberg BM
History
DepositionMay 24, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17451.png

Downloads & links

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Map

FileDownload / File: emd_17451.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.01 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.8419012 - 2.759686
Average (Standard dev.)0.036652256 (±0.23679206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin219253252
Dimensions799446
Spacing467994
CellA: 46.46 Å / B: 79.79 Å / C: 94.94 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17451_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17451_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Spike RBD (two molecules) in complex with two FU2 nanobodies

EntireName: Spike RBD (two molecules) in complex with two FU2 nanobodies
Components
  • Complex: Spike RBD (two molecules) in complex with two FU2 nanobodies
    • Complex: SARS-CoV-2 spike (RBD)
      • Protein or peptide: Spike protein S1
    • Complex: Monoclonal Antibody Mab-23
      • Protein or peptide: Mab-23 (Heavy chain variable domain)
      • Protein or peptide: Mab-23 (Light chain variable domain)

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Supramolecule #1: Spike RBD (two molecules) in complex with two FU2 nanobodies

SupramoleculeName: Spike RBD (two molecules) in complex with two FU2 nanobodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 95.7 KDa

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Supramolecule #2: SARS-CoV-2 spike (RBD)

SupramoleculeName: SARS-CoV-2 spike (RBD) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Monoclonal Antibody Mab-23

SupramoleculeName: Monoclonal Antibody Mab-23 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Enterobacteria phage T4 (virus)

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.002676 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String:
TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPK

UniProtKB: Spike glycoprotein

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Macromolecule #2: Mab-23 (Heavy chain variable domain)

MacromoleculeName: Mab-23 (Heavy chain variable domain) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.500398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCTASGFTFS NYGFHWVRQA PGKGLEWVTI ISYDGITKHY ADSVKDRFTV SRDNSKTMVY LQMNNLKLD DTAVYYCARD LGTYDDSWGQ GVLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGLVKDYF PEVTSWNSGA L TSGVHTFP ...String:
EVQLVESGGG LVQPGGSLRL SCTASGFTFS NYGFHWVRQA PGKGLEWVTI ISYDGITKHY ADSVKDRFTV SRDNSKTMVY LQMNNLKLD DTAVYYCARD LGTYDDSWGQ GVLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGLVKDYF PEVTSWNSGA L TSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKVEPKSCDK THTCPPCPAP ELLGGPSVFL FP PKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP REEQYNSTYR VVSVLTVLHQ DWLNGKEYKC KVS NKALPA PIEKTISKAK GQPREPQVYT LPPSRDETKN QVSLTCLVKG FYPSDIAVEW ESNGQPENNY KTTPPVLDSD GSFF LYSKL TVDKSRWQQG NVFSCSVMHE ALHNHYTQKS LSLSPGK

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Macromolecule #3: Mab-23 (Light chain variable domain)

MacromoleculeName: Mab-23 (Light chain variable domain) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.234852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSA LSASVGDRVT ISCRASQNID GFLAWYQQKP GKAPKLLIYA ASRLQSGIPS RFSGSGSGTD FTLTISSLQP EDFAAYYCQ QVYSAPLTFG GGTKVEFKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSA LSASVGDRVT ISCRASQNID GFLAWYQQKP GKAPKLLIYA ASRLQSGIPS RFSGSGSGTD FTLTISSLQP EDFAAYYCQ QVYSAPLTFG GGTKVEFKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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

Concentration2.1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4774 / Average exposure time: 1.5 sec. / Average electron dose: 48.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7a25

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF
Software: (Name: cryoSPARC (ver. 3.2.0), cryoSPARC (ver. 4.1.1))
Number images used: 135612
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ksg


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8p5m:
SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab)

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