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- EMDB-26256: Local refinement of cryo-EM structure of the interface of the Omi... -

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Entry
Database: EMDB / ID: EMD-26256
TitleLocal refinement of cryo-EM structure of the interface of the Omicron RBD in complex with antibodies B-182.1 and A19-46.1
Map dataLocal refinement map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1
Sample
  • Complex: Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibodies B1-182.1 and A19-46.1
    • Protein or peptide: Surface glycoprotein
    • Protein or peptide: Heavy chain of SARS-CoV-2 antibody A19-46.1
    • Protein or peptide: Light chain of SARS-CoV-2 antibody A19-46.1
    • Protein or peptide: Heavy chain of SARS-CoV-2 antibody B1-182.1
    • Protein or peptide: Light chain of SARS-CoV-2 antibody B1-182.1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homologyBetacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Surface glycoprotein
Function and homology information
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsZhou T / kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Science / Year: 2022
Title: Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529.
Authors: Tongqing Zhou / Lingshu Wang / John Misasi / Amarendra Pegu / Yi Zhang / Darcy R Harris / Adam S Olia / Chloe Adrienna Talana / Eun Sung Yang / Man Chen / Misook Choe / Wei Shi / I-Ting Teng ...Authors: Tongqing Zhou / Lingshu Wang / John Misasi / Amarendra Pegu / Yi Zhang / Darcy R Harris / Adam S Olia / Chloe Adrienna Talana / Eun Sung Yang / Man Chen / Misook Choe / Wei Shi / I-Ting Teng / Adrian Creanga / Claudia Jenkins / Kwanyee Leung / Tracy Liu / Erik-Stephane D Stancofski / Tyler Stephens / Baoshan Zhang / Yaroslav Tsybovsky / Barney S Graham / John R Mascola / Nancy J Sullivan / Peter D Kwong /
Abstract: The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a ...The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants.
History
DepositionFeb 17, 2022-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateOct 19, 2022-
Current statusOct 19, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26256.png

Downloads & links

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Map

FileDownload / File: emd_26256.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1
Voxel sizeX=Y=Z: 0.855 Å
Density
Contour LevelBy AUTHOR: 0.235
Minimum - Maximum-0.40156403 - 0.87982863
Average (Standard dev.)-0.0009964088 (±0.011409314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 513.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26256_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened local refinement half map for the interface...

Fileemd_26256_additional_1.map
AnnotationSharpened local refinement half map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement half map for the interface of...

Fileemd_26256_half_map_1.map
AnnotationLocal refinement half map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement half map for the interface of...

Fileemd_26256_half_map_2.map
AnnotationLocal refinement half map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibod...

EntireName: Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibodies B1-182.1 and A19-46.1
Components
  • Complex: Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibodies B1-182.1 and A19-46.1
    • Protein or peptide: Surface glycoprotein
    • Protein or peptide: Heavy chain of SARS-CoV-2 antibody A19-46.1
    • Protein or peptide: Light chain of SARS-CoV-2 antibody A19-46.1
    • Protein or peptide: Heavy chain of SARS-CoV-2 antibody B1-182.1
    • Protein or peptide: Light chain of SARS-CoV-2 antibody B1-182.1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibod...

SupramoleculeName: Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibodies B1-182.1 and A19-46.1
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Surface glycoprotein

MacromoleculeName: Surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.297182 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NITNLCPFDE VFNATRFASV YAWNRKRISN CVADYSVLYN LAPFFTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKVSGNY NYLYRLFRKS NLKPFERDIS TEIYQAGNKP CNGVAGFNCY F PLRSYSFR ...String:
NITNLCPFDE VFNATRFASV YAWNRKRISN CVADYSVLYN LAPFFTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKVSGNY NYLYRLFRKS NLKPFERDIS TEIYQAGNKP CNGVAGFNCY F PLRSYSFR PTYGVGHQPY RVVVLSFELL HAPATVCG

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Macromolecule #2: Heavy chain of SARS-CoV-2 antibody A19-46.1

MacromoleculeName: Heavy chain of SARS-CoV-2 antibody A19-46.1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.8699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGRSLRL SCAASGFTLS SYGMHWVRQA PGKGLEWVAV ISYDGSNKYY VDSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARG WAYWELLPDY YYGMDVWGQG TTVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLVESGGG VVQPGRSLRL SCAASGFTLS SYGMHWVRQA PGKGLEWVAV ISYDGSNKYY VDSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARG WAYWELLPDY YYGMDVWGQG TTVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDK

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Macromolecule #3: Light chain of SARS-CoV-2 antibody A19-46.1

MacromoleculeName: Light chain of SARS-CoV-2 antibody A19-46.1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.760273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTVVTQEPSF SVSPGGTVTL TCGLSSGSVS TAYFPSWYQQ TPGQAPRTLI YGTNTRSSGV PDRFSGSILG NKAALTITGA QADDESDYY CVLYMGRGIV VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QTVVTQEPSF SVSPGGTVTL TCGLSSGSVS TAYFPSWYQQ TPGQAPRTLI YGTNTRSSGV PDRFSGSILG NKAALTITGA QADDESDYY CVLYMGRGIV VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #4: Heavy chain of SARS-CoV-2 antibody B1-182.1

MacromoleculeName: Heavy chain of SARS-CoV-2 antibody B1-182.1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.285312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QMQLVQSGPE VKKPGTSVKV SCKASGFTFT SSAVQWVRQA RGQRLEWIGW IVVGSGNTNY AQKFQERVTI TRDMSTSTAY MELSSLRSE DTAVYYCAAP YCSGGSCFDG FDIWGQGTMV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QMQLVQSGPE VKKPGTSVKV SCKASGFTFT SSAVQWVRQA RGQRLEWIGW IVVGSGNTNY AQKFQERVTI TRDMSTSTAY MELSSLRSE DTAVYYCAAP YCSGGSCFDG FDIWGQGTMV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK

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Macromolecule #5: Light chain of SARS-CoV-2 antibody B1-182.1

MacromoleculeName: Light chain of SARS-CoV-2 antibody B1-182.1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.536008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGFP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGNSPWTF GQGTKVEIRR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGFP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGNSPWTF GQGTKVEIRR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
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 / Calibrated magnification: 105000 / 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 46244
Details: SARS-CoV-2 receptor-binding domain in complex with antibodies B1-182.1 and A19-46.1
CTF correctionSoftware - Name: cryoSPARC (ver. 3)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7tcc

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 46244

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