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- PDB-7u0d: Local refinement of cryo-EM structure of the interface of the Omi... -

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Basic information

Entry
Database: PDB / ID: 7u0d
TitleLocal refinement of cryo-EM structure of the interface of the Omicron RBD in complex with antibodies B-182.1 and A19-46.1
Components
  • (Heavy chain of SARS-CoV-2 antibody ...) x 2
  • (Light chain of SARS-CoV-2 antibody ...) x 2
  • Surface glycoprotein
KeywordsVral Protein/IMMUNE SYSTEM / antibody / SARS-CoV-2 / Omicron / B.1.1.529 / Receptor binding domain / IMMUNE SYSTEM / Vral Protein-IMMUNE SYSTEM complex
Function / homologyCoronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Surface glycoprotein
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsZhou, T. / kwong, P.D.
Funding support United States, 1items
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, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Jun 4, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Surface glycoprotein
M: Heavy chain of SARS-CoV-2 antibody A19-46.1
N: Light chain of SARS-CoV-2 antibody A19-46.1
O: Heavy chain of SARS-CoV-2 antibody B1-182.1
P: Light chain of SARS-CoV-2 antibody B1-182.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9706
Polymers117,7495
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antibody , 4 types, 4 molecules MNOP

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


Mass: 24869.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Light chain of SARS-CoV-2 antibody A19-46.1


Mass: 22760.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293F / Production host: Homo sapiens (human)
#4: Antibody Heavy chain of SARS-CoV-2 antibody B1-182.1


Mass: 24285.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293F / Production host: Homo sapiens (human)
#5: Antibody Light chain of SARS-CoV-2 antibody B1-182.1


Mass: 23536.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules B

#1: Protein Surface glycoprotein


Mass: 22297.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A7U3CI26
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibodies B1-182.1 and A19-46.1
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: 100 mM HEPES, 150 mM NaCl
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Complex at 0.5 mg/mL concentration in the buffer
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: Blot for 2-3.5 seconds before plugging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC3particle selection
4cryoSPARC3CTF correction
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 46244
Details: SARS-CoV-2 receptor-binding domain in complex with antibodies B1-182.1 and A19-46.1
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 46244 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0198390
ELECTRON MICROSCOPYf_angle_d0.82411425
ELECTRON MICROSCOPYf_dihedral_angle_d5.5051164
ELECTRON MICROSCOPYf_chiral_restr0.0491278
ELECTRON MICROSCOPYf_plane_restr0.0081461

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