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- EMDB-16397: SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody -

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Basic information

Entry
Database: EMDB / ID: EMD-16397
TitleSARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody
Map data
Sample
  • Complex: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
    • Complex: SARS-CoV2 Omicron BA.1 spike
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: CAB-A17 Antibody (FAB)
      • Protein or peptide: CAB-A17 antibody (LC)
      • Protein or peptide: CAB-A17 antibody (HC)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / 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 / Enterobacteria phage T4 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsDas H / Hallberg BM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SARS-CoV-2 omicron Spike (RBD) in complex with CAB-A17 antibody
Authors: Das H / Hallberg BM
History
DepositionDec 22, 2022-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16397.png

Downloads & links

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Map

FileDownload / File: emd_16397.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.)
1.01 Å/pix.
x 400 pix.
= 404. Å		1.01 Å/pix.
x 400 pix.
= 404. Å		1.01 Å/pix.
x 400 pix.
= 404. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0013296953 - 1.7738185
Average (Standard dev.)0.0011501377 (±0.02151378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 404.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: raw map

Fileemd_16397_additional_1.map
Annotationraw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_16397_half_map_1.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap A

Fileemd_16397_half_map_2.map
Annotationhalfmap A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody

EntireName: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
Components
  • Complex: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
    • Complex: SARS-CoV2 Omicron BA.1 spike
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: CAB-A17 Antibody (FAB)
      • Protein or peptide: CAB-A17 antibody (LC)
      • Protein or peptide: CAB-A17 antibody (HC)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody

SupramoleculeName: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 95.7 KDa

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Supramolecule #2: SARS-CoV2 Omicron BA.1 spike

SupramoleculeName: SARS-CoV2 Omicron BA.1 spike / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: CAB-A17 Antibody (FAB)

SupramoleculeName: CAB-A17 Antibody (FAB) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Enterobacteria phage T4 (virus)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 124.773758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVIHVSGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGWI FGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG N FKNLREFV ...String:
PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVIHVSGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGWI FGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG N FKNLREFV FKNIDGYFKI YSKHTPINLV RDLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SSSGWTAGAA AY YVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TESIVRFPNI TNLCPFDEVF NAT RFASVY AWNRKRISNC VADYSVLYNL APFFTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGNIADY NYKL PDDFT GCVIAWNSNK LDSKVSGNYN YLYRLFRKSN LKPFERDIST EIYQAGNKPC NGVAGFNCYF PLRSYSFRPT YGVGH QPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLKGT GVLTESNKKF LPFQQFGRDI ADTTDAVRDP QTLEIL DIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVPVAIHADQ LTPTWRVYST GSNVFQTRAG CLIGAEYVNN SYECDIP IG AGICASYQTQ TNSPRRARSV ASQSIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTEIL PVSMTKTSVD CTMYICGD S TECSNLLLQY GSFCTQLKRA LTGIAVEQDK NTQEVFAQVK QIYKTPPIKY FGGFNFSQIL PDPSKPSKRS PIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF KGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNH NAQALNTLVK QLSSKFGAIS SVLNDIFSRL D PPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QSAPHGVVFL HV TYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGNCDVVIGI VNNTVYDPLQ PEL DS

UniProtKB: Spike glycoprotein

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Macromolecule #2: CAB-A17 antibody (LC)

MacromoleculeName: CAB-A17 antibody (LC) / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.284832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAS LSCRASQSLS TYLAWYQQKP GQAPRLLIFG ASSRASGIPD RFSGGGSGTD FTLTISRLEP EDFAVYYCQ QYGSSPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPGT LSLSPGERAS LSCRASQSLS TYLAWYQQKP GQAPRLLIFG ASSRASGIPD RFSGGGSGTD FTLTISRLEP EDFAVYYCQ QYGSSPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: CAB-A17 antibody (HC)

MacromoleculeName: CAB-A17 antibody (HC) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.900543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVHLVESGGG LIQPGGSLRL SCAASEFIVS ANYMSWVRQA PGEGLQWVSV IYPGGSTFYA ESVKGRFTIS RDNSRNTLYL QMNSLRAED TGVYYCARDY GDFYFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSTAALGCL VKDYFPEPVT VSWNSGALTS G VHTFPAVL ...String:
DVHLVESGGG LIQPGGSLRL SCAASEFIVS ANYMSWVRQA PGEGLQWVSV IYPGGSTFYA ESVKGRFTIS RDNSRNTLYL QMNSLRAED TGVYYCARDY GDFYFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSTAALGCL VKDYFPEPVT VSWNSGALTS G VHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKS

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 22 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration1.5 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
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 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) / Number real images: 25652 / Average exposure time: 1.5 sec. / Average electron dose: 54.6 e/Å2
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:

7a29


Details: 7A29 and 7K8M
Initial angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 398386
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 / Overall B value: 142
Output model

PDB-8c2r:
SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody

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