7MZI | pdb_00007mzi

SARS-CoV-2 receptor binding domain bound to Fab WCSL 129

PDB DOI: https://doi.org/10.2210/pdb7MZI/pdb

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

Deposited: 2021-05-24 Released: 2021-10-06
Deposition Author(s): Pymm, P., Tan, L.L., Dietrich, M.H., Chan, L.J., Tham, W.H.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.207 (Depositor), 0.207 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.176 (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

Landscape of human antibody recognition of the SARS-CoV-2 receptor binding domain.

Wheatley, A.K., Pymm, P., Esterbauer, R., Dietrich, M.H., Lee, W.S., Drew, D., Kelly, H.G., Chan, L.J., Mordant, F.L., Black, K.A., Adair, A., Tan, H.X., Juno, J.A., Wragg, K.M., Amarasena, T., Lopez, E., Selva, K.J., Haycroft, E.R., Cooney, J.P., Venugopal, H., Tan, L.L., O Neill, M.T., Allison, C.C., Cromer, D., Davenport, M.P., Bowen, R.A., Chung, A.W., Pellegrini, M., Liddament, M.T., Glukhova, A., Subbarao, K., Kent, S.J., Tham, W.H.

(2021) Cell Rep 37: 109822-109822

PubMed: 34610292 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.celrep.2021.109822
Primary Citation Related Structures:
7MZF, 7MZG, 7MZH, 7MZI, 7MZJ, 7MZK, 7MZL, 7MZM, 7MZN, 7RR0

PubMed Abstract:
Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike protein can exhibit neutralization resistance, potentially affecting the effectiveness of some antibody-based therapeutics. Here, the generation of a diverse panel of 91 human, neutralizing monoclonal antibodies provides an in-depth structural and phenotypic definition of receptor binding domain (RBD) antigenic sites on the viral spike. These RBD antibodies ameliorate SARS-CoV-2 infection in mice and hamster models in a dose-dependent manner and in proportion to in vitro, neutralizing potency. Assessing the effect of mutations in the spike protein on antibody recognition and neutralization highlights both potent single antibodies and stereotypic classes of antibodies that are unaffected by currently circulating VOCs, such as B.1.351 and P.1. These neutralizing monoclonal antibodies and others that bind analogous epitopes represent potentially useful future anti-SARS-CoV-2 therapeutics.

Organizational Affiliation

Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia.

The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.

Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.

The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.

Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.

Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia.

Laboratory of Animal Reproduction and Biotechnology, Colorado State University, Fort Collins, CO 80523, USA.

CSL Limited, Parkville, VIC 3052, Australia.

The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia; Drug Discovery Biology, Monash Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville VIC 3052, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia.

Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia.

Department of Microbiology and Immunology, University of Melbourne, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC 3004, Australia. Electronic address: skent@unimelb.edu.au.

Macromolecule Content

Total Structure Weight: 71.46 kDa
Atom Count: 5,301
Modeled Residue Count: 628
Deposited Residue Count: 645
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WCSL 129 light chain	A [auth L]	216	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WCSL 129 heavy chain	B [auth H]	224	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth A]	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 C [auth A]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	3		N-Glycosylation	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

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