7BEO | pdb_00007beo

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253H55L and COVOX-75 Fabs

PDB DOI: https://doi.org/10.2210/pdb7BEO/pdb

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

Deposited: 2020-12-24 Released: 2021-03-03
Deposition Author(s): Zhou, D., Zhao, Y., Ren, J., Stuart, D.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free:
0.274 (Depositor), 0.272 (DCC)
R-Value Work:
0.234 (Depositor), 0.235 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The antigenic anatomy of SARS-CoV-2 receptor binding domain.

Dejnirattisai, W., Zhou, D., Ginn, H.M., Duyvesteyn, H.M.E., Supasa, P., Case, J.B., Zhao, Y., Walter, T.S., Mentzer, A.J., Liu, C., Wang, B., Paesen, G.C., Slon-Campos, J., Lopez-Camacho, C., Kafai, N.M., Bailey, A.L., Chen, R.E., Ying, B., Thompson, C., Bolton, J., Fyfe, A., Gupta, S., Tan, T.K., Gilbert-Jaramillo, J., James, W., Knight, M., Carroll, M.W., Skelly, D., Dold, C., Peng, Y., Levin, R., Dong, T., Pollard, A.J., Knight, J.C., Klenerman, P., Temperton, N., Hall, D.R., Williams, M.A., Paterson, N.G., Bertram, F.K.R., Siebert, C.A., Clare, D.K., Howe, A., Radecke, J., Song, Y., Townsend, A.R., Huang, K.A., Fry, E.E., Mongkolsapaya, J., Diamond, M.S., Ren, J., Stuart, D.I., Screaton, G.R.

(2021) Cell 184: 2183

PubMed: 33756110 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2021.02.032
Primary Citation Related Structures:
7BEH, 7BEI, 7BEJ, 7BEK, 7BEL, 7BEM, 7BEN, 7BEO, 7BEP, 7ND3, 7ND4, 7ND5, 7ND6, 7ND7, 7ND8, 7ND9, 7NDA, 7NDB, 7NDC, 7NDD

PubMed Abstract:
Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC ₅₀ < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.

Organizational Affiliation

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK.

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK.

Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA.

Peter Medawar Building for Pathogen Research, Oxford OX1 3SY, UK; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.

Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.

MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.

Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury SP4 0JG, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.

Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford OX3 7LE, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK.

Worthing Hospital, Worthing BN11 2DH, UK.

Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford OX3 7LE, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford OX1 3SY, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.

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

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

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, 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.

Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, St. Louis, MO 63110 USA. Electronic address: mdiamond@wustl.edu.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK. Electronic address: ren@strubi.ox.ac.uk.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK. Electronic address: dave@strubi.ox.ac.uk.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK. Electronic address: gavin.screaton@medsci.ox.ac.uk.

Macromolecule Content

Total Structure Weight: 246.04 kDa
Atom Count: 16,313
Modeled Residue Count: 2,105
Deposited Residue Count: 2,240
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth R], F [auth X]	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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 R] Focus chain F [auth X]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-253H55L heavy chain	B [auth H], G [auth C]	228	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-253H55L light chain	C [auth L], H [auth D]	215	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-75 heavy chain	D [auth A], I [auth E]	245	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-75 light chain	E [auth B], J [auth F]	227	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	K [auth G], L [auth I], M [auth J]	3		N-Glycosylation	Interactions Focus chain K [auth G] Focus chain L [auth I] Focus chain M [auth J] Interactions & Density Focus chain K [auth G] Focus chain L [auth I] Focus chain M [auth J]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain N [auth R] MOL2 format, chain N [auth R] mmCIF format, chain N [auth R]	N [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth R] Interactions & Density Focus chain N [auth R]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth H] SDF format, chain T [auth X] MOL2 format, chain O [auth H] MOL2 format, chain T [auth X] mmCIF format, chain O [auth H] mmCIF format, chain T [auth X]	O [auth H], T [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth H] Focus chain T [auth X] Interactions & Density Focus chain O [auth H] Focus chain T [auth X]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain P [auth L] SDF format, chain R [auth A] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain S [auth A] SDF format, chain Q [auth A] MOL2 format, chain P [auth L] MOL2 format, chain R [auth A] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain P [auth L] mmCIF format, chain R [auth A] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A]	P [auth L] Q [auth A] R [auth A] S [auth A] U [auth C] P [auth L], Q [auth A], R [auth A], S [auth A], U [auth C], W [auth D], X [auth D], Y [auth E], Z [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth L] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain P [auth L] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]