7QNW | pdb_00007qnw

The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with Beta-55 and EY6A Fabs

PDB DOI: https://doi.org/10.2210/pdb7QNW/pdb

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2021-12-23 Released: 2022-01-19
Deposition Author(s): Zhou, D., Ren, J., Stuart, D.I.
Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS), Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.247 (Depositor), 0.247 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

Dejnirattisai, W., Huo, J., Zhou, D., Zahradnik, J., Supasa, P., Liu, C., Duyvesteyn, H.M.E., Ginn, H.M., Mentzer, A.J., Tuekprakhon, A., Nutalai, R., Wang, B., Dijokaite, A., Khan, S., Avinoam, O., Bahar, M., Skelly, D., Adele, S., Johnson, S.A., Amini, A., Ritter, T.G., Mason, C., Dold, C., Pan, D., Assadi, S., Bellass, A., Omo-Dare, N., Koeckerling, D., Flaxman, A., Jenkin, D., Aley, P.K., Voysey, M., Costa Clemens, S.A., Naveca, F.G., Nascimento, V., Nascimento, F., Fernandes da Costa, C., Resende, P.C., Pauvolid-Correa, A., Siqueira, M.M., Baillie, V., Serafin, N., Kwatra, G., Da Silva, K., Madhi, S.A., Nunes, M.C., Malik, T., Openshaw, P.J.M., Baillie, J.K., Semple, M.G., Townsend, A.R., Huang, K.A., Tan, T.K., Carroll, M.W., Klenerman, P., Barnes, E., Dunachie, S.J., Constantinides, B., Webster, H., Crook, D., Pollard, A.J., Lambe, T., Paterson, N.G., Williams, M.A., Hall, D.R., Fry, E.E., Mongkolsapaya, J., Ren, J., Schreiber, G., Stuart, D.I., Screaton, G.R.

(2022) Cell 185: 467-484.e15

PubMed: 35081335 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2021.12.046
Primary Citation Related Structures:
7QNW, 7QNX, 7QNY

PubMed Abstract:
On 24 ^th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.

Organizational Affiliation

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.

Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.

Peter Medawar Building for Pathogen Research, Oxford, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK.

NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.

Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK; Department of Respiratory Sciences, University of Leicester, Leicester, UK.

Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK.

Medical Sciences Division, University of Oxford, Oxford, UK.

Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.

Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK.

Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil.

Fundação de Vigilância em Saúde do Amazonas, Manaus, Amazonas, Brazil.

Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil.

Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.

South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK.

National Heart & Lung Institute, Imperial College, London, UK.

Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK.

NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.

Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.

Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital and Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. Electronic address: jmongkol@well.ox.ac.uk.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK. Electronic address: ren@strubi.ox.ac.uk.

Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel. Electronic address: gideon.schreiber@weizmann.ac.il.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK. Electronic address: dave@strubi.ox.ac.uk.

Macromolecule Content

Total Structure Weight: 120.61 kDa
Atom Count: 8,326
Modeled Residue Count: 1,057
Deposited Residue Count: 1,090
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A heavy chain	A [auth H]	226	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A light chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface glycoprotein	C [auth E]	202	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 8
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth E]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-55 heavy chain	D [auth A]	232	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-55 light chain	E [auth B]	215	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth C]	2		N-Glycosylation	Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain J [auth E] SDF format, chain I [auth L] SDF format, chain H [auth L] SDF format, chain G [auth L] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth E] MOL2 format, chain I [auth L] MOL2 format, chain H [auth L] MOL2 format, chain G [auth L] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth E] mmCIF format, chain I [auth L] mmCIF format, chain H [auth L] mmCIF format, chain G [auth L]	G [auth L] H [auth L] I [auth L] J [auth E] L [auth A] G [auth L], H [auth L], I [auth L], J [auth E], L [auth A], M [auth A], N [auth A], O [auth A], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Interactions & Density Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain K [auth E] MOL2 format, chain P [auth A] MOL2 format, chain K [auth E] mmCIF format, chain P [auth A] mmCIF format, chain K [auth E]	K [auth E], P [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth E] Focus chain P [auth A] Interactions & Density Focus chain K [auth E] Focus chain P [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]