7OR9 | pdb_00007or9

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and COVOX-278 Fabs

PDB DOI: https://doi.org/10.2210/pdb7OR9/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-06-04 Released: 2021-07-07
Deposition Author(s): Zhou, D., Ren, J., Stuart, D.I.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.230 (Depositor), 0.206 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.195 (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

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.

Liu, C., Ginn, H.M., Dejnirattisai, W., Supasa, P., Wang, B., Tuekprakhon, A., Nutalai, R., Zhou, D., Mentzer, A.J., Zhao, Y., Duyvesteyn, H.M.E., Lopez-Camacho, C., Slon-Campos, J., Walter, T.S., Skelly, D., Johnson, S.A., Ritter, T.G., Mason, C., Costa Clemens, S.A., Gomes Naveca, F., Nascimento, V., Nascimento, F., Fernandes da Costa, C., Resende, P.C., Pauvolid-Correa, A., Siqueira, M.M., Dold, C., Temperton, N., Dong, T., Pollard, A.J., Knight, J.C., Crook, D., Lambe, T., Clutterbuck, E., Bibi, S., Flaxman, A., Bittaye, M., Belij-Rammerstorfer, S., Gilbert, S.C., Malik, T., Carroll, M.W., Klenerman, P., Barnes, E., Dunachie, S.J., Baillie, V., Serafin, N., Ditse, Z., Da Silva, K., Paterson, N.G., Williams, M.A., Hall, D.R., Madhi, S., Nunes, M.C., Goulder, P., Fry, E.E., Mongkolsapaya, J., Ren, J., Stuart, D.I., Screaton, G.R.

(2021) Cell 184: 4220-4236.e13

PubMed: 34242578 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2021.06.020
Primary Citation Related Structures:
7OR9, 7ORA, 7ORB

PubMed Abstract:
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone progressive change, with variants conferring advantage rapidly becoming dominant lineages, e.g., B.1.617. With apparent increased transmissibility, variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the United Kingdom. Here we study the ability of monoclonal antibodies and convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2, complement this with structural analyses of Fab/receptor binding domain (RBD) complexes, and map the antigenic space of current variants. Neutralization of both viruses is reduced compared with ancestral Wuhan-related strains, but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2, suggesting that individuals infected previously by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insights for immunization policy with future variant vaccines in non-immune populations.

Organizational Affiliation

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.

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

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

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

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.

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

Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich, Chatham Maritime, Kent ME4 4TB, UK.

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

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

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

National Infection Service, Public Health England (PHE), Porton Down, Salisbury, 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; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, 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; Department of Medicine, University of Oxford, Oxford, UK.

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.

Peter Medawar Building for Pathogen Research, Oxford, UK; 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, Thailand. Electronic address: jmongkol@well.ox.ac.uk.

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

Macromolecule Content

Total Structure Weight: 118.69 kDa
Atom Count: 8,282
Modeled Residue Count: 1,057
Deposited Residue Count: 1,086
Unique protein chains: 5

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth E]	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
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 A [auth E]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-222 Fab heavy chain	B [auth A]	224	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-222 Fab light chain	C [auth B]	214	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-278 Fab heavy chain	D [auth H]	228	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-278 Fab light chain	E [auth L]	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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth C]	3		N-Glycosylation	Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain M [auth H] MOL2 format, chain M [auth H] mmCIF format, chain M [auth H]	M [auth H]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain M [auth H] Interactions & Density Focus chain M [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth E] SDF format, chain K [auth B] MOL2 format, chain G [auth E] MOL2 format, chain K [auth B] mmCIF format, chain G [auth E] mmCIF format, chain K [auth B]	G [auth E], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth E] Focus chain K [auth B] Interactions & Density Focus chain G [auth E] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth E] SDF format, chain H [auth E] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth E] MOL2 format, chain H [auth E] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth E] mmCIF format, chain H [auth E]	H [auth E], I [auth E], J [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth E] Focus chain I [auth E] Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth E] Focus chain I [auth E] Focus chain J [auth A] Focus chain L [auth B]