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- EMDB-25792: Cryo-EM structure of the spike of SARS-CoV-2 Omicron variant of c... -

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Basic information

Entry
Database: EMDB / ID: EMD-25792
TitleCryo-EM structure of the spike of SARS-CoV-2 Omicron variant of concern
Map datacryo-EM map for the SARS-CoV-2 Omicron spike protein
Sample
  • Complex: SARS-CoV-2 spike of the Omicron Variant of Concern
    • Protein or peptide: Surface glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homologySurface glycoprotein
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsZhou T / Tsybovsky T / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Intramural United States
CitationJournal: bioRxiv / Year: 2021
Title: Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants.
Authors: Lingshu Wang / Tongqing Zhou / Yi Zhang / Eun Sung Yang / Chaim A Schramm / Wei Shi / Amarendra Pegu / Olamide K Oloninyi / Amy Ransier / Samuel Darko / Sandeep R Narpala / Christian Hatcher ...Authors: Lingshu Wang / Tongqing Zhou / Yi Zhang / Eun Sung Yang / Chaim A Schramm / Wei Shi / Amarendra Pegu / Olamide K Oloninyi / Amy Ransier / Samuel Darko / Sandeep R Narpala / Christian Hatcher / David R Martinez / Yaroslav Tsybovsky / Emily Phung / Olubukola M Abiona / Evan M Cale / Lauren A Chang / Kizzmekia S Corbett / Anthony T DiPiazza / Ingelise J Gordon / Kwanyee Leung / Tracy Liu / Rosemarie D Mason / Alexandra Nazzari / Laura Novik / Adam S Olia / Nicole A Doria-Rose / Tyler Stephens / Christopher D Stringham / Chloe Adrienna Talana / I-Ting Teng / Danielle Wagner / Alicia T Widge / Baoshan Zhang / Mario Roederer / Julie E Ledgerwood / Tracy J Ruckwardt / Martin R Gaudinski / Ralph S Baric / Barney S Graham / Adrian B McDermott / Daniel C Douek / Peter D Kwong / John R Mascola / Nancy J Sullivan / John Misasi /
Abstract: The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We ...The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identify four receptor-binding domain targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 12 variants including the B.1.1.7 and B.1.351 VOCs. Two of them are ultrapotent, with sub-nanomolar neutralization titers (IC50 <0.0006 to 0.0102 μ g/mL; IC80 < 0.0006 to 0.0251 μ g/mL). We define the structural and functional determinants of binding for all four VOC-targeting antibodies, and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting potential means to mitigate resistance development. These results define the basis of therapeutic cocktails against VOCs and suggest that targeted boosting of existing immunity may increase vaccine breadth against VOCs.
History
DepositionDec 21, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.191
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.191
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7tb4
  • Surface level: 0.191
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25792.png

Downloads & links

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Map

FileDownload / File: emd_25792.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map for the SARS-CoV-2 Omicron spike protein
Voxel sizeX=Y=Z: 0.855 Å
Density
Contour LevelBy AUTHOR: 0.191 / Movie #1: 0.191
Minimum - Maximum-0.24842821 - 0.9367863
Average (Standard dev.)0.00047631533 (±0.029577166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8550.8550.855
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z342.000342.000342.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2480.9370.000

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Supplemental data

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Mask #1

Fileemd_25792_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened cryo-EM map for the SARS-CoV-2 Omicron spike protein

Fileemd_25792_additional_1.map
AnnotationSharpened cryo-EM map for the SARS-CoV-2 Omicron spike protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half map for the SARS-CoV-2 Omicron spike protein

Fileemd_25792_half_map_1.map
Annotationcryo-EM half map for the SARS-CoV-2 Omicron spike protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half map for the SARS-CoV-2 Omicron spike protein

Fileemd_25792_half_map_2.map
Annotationcryo-EM half map for the SARS-CoV-2 Omicron spike protein
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 of the Omicron Variant of Concern

EntireName: SARS-CoV-2 spike of the Omicron Variant of Concern
Components
  • Complex: SARS-CoV-2 spike of the Omicron Variant of Concern
    • Protein or peptide: Surface glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 spike of the Omicron Variant of Concern

SupramoleculeName: SARS-CoV-2 spike of the Omicron Variant of Concern / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 414 KDa

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Macromolecule #1: Surface glycoprotein

MacromoleculeName: Surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 132.465094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF ...String:
QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF KNLREFVFKN IDGYFKIYSK HTPIIVREPE DLPQGFSALE PLVDLPIGIN ITRFQTLLAL HRSYLTPGDS SS GWTAGAA AYYVGYLQPR TFLLKYNENG TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESIVRFPNIT NLC PFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNLA PFFTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTG NIADY NYKLPDDFTG CVIAWNSNKL DSKVSGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP LRSYS FRPT YGVGHQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLKGTG VLTESNKKFL PFQQFGRDIA DTTDAV RDP QTLEILDITP CSFGGVSVIT PGTNTSNQVA VLYQGVNCTE VPVAIHADQL TPTWRVYSTG SNVFQTRAGC LIGAEYV NN SYECDIPIGA GICASYQTQT KSHGSASSVA SQSIIAYTMS LGAENSVAYS NNSIAIPTNF TISVTTEILP VSMTKTSV D CTMYICGDST ECSNLLLQYG SFCTQLKRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPIKYF GGFNFSQILP DPSKPSKRS FIEDLLFNKV TLADAGFIKQ YGDCLGDIAA RDLICAQKFK GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGAALQI PFAMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTASAL GKLQDVVNHN AQALNTLVKQ LSSKFGAISS V LNDIFSRL DPPEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KGYHLMSFPQ SA PHGVVFL HVTYVPAQEK NFTTAPAICH DGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GNCDVVIGIV NNT VYDPLQ PELDSFKEEL DKYFKNHTSP DVDLGDISGI NASVVNIQKE IDRLNEVAKN LNESLIDLQE LGKYEQ

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 29 / 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

Concentration0.5 mg/mL
BufferpH: 7.4 / Details: 100 mM HEPES, 150 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2-3.5 seconds before plugging..
DetailsComplex at 0.5 mg/mL concentration in the buffer

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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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: OTHER / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2.15)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lrs


Details: SARS-CoV-2 receptor-binding domain in complex with antibody A23-58.1
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 266434

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Atomic model buiding 1

Initial modelPDB ID:

7kls

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7tb4:
Cryo-EM structure of the spike of SARS-CoV-2 Omicron variant of concern

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