8VCR | pdb_00008vcr

SARS-CoV-2 Spike S2 bound to Fab 54043-5

PDB DOI: https://doi.org/10.2210/pdb8VCR/pdb
EM Map EMD-43139: EMDB EMDataResource

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

Deposited: 2023-12-14 Released: 2024-07-31
Deposition Author(s): Johnson, N.V., McLellan, J.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Discovery and characterization of a pan-betacoronavirus S2-binding antibody.

Johnson, N.V., Wall, S.C., Kramer, K.J., Holt, C.M., Periasamy, S., Richardson, S.I., Manamela, N.P., Suryadevara, N., Andreano, E., Paciello, I., Pierleoni, G., Piccini, G., Huang, Y., Ge, P., Allen, J.D., Uno, N., Shiakolas, A.R., Pilewski, K.A., Nargi, R.S., Sutton, R.E., Abu-Shmais, A.A., Parks, R., Haynes, B.F., Carnahan, R.H., Crowe Jr., J.E., Montomoli, E., Rappuoli, R., Bukreyev, A., Ross, T.M., Sautto, G.A., McLellan, J.S., Georgiev, I.S.

(2024) Structure 32: 1893

PubMed: 39326419 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2024.08.022
Primary Citation Related Structures:
8VCR

PubMed Abstract:
The continued emergence of deadly human coronaviruses from animal reservoirs highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using linking B cell receptor to antigen specificity through sequencing (LIBRA-seq), we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryoelectron microscopy (cryo-EM) structure of 54043-5 bound to the prefusion S2 subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses in vitro, including antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.

Organizational Affiliation

Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.

Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.

National Institute for Communicable Diseases of the National Health Laboratory Service, 2131 Johannesburg, South Africa; South African MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.

Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy.

VisMederi Research S.r.l., 53100 Siena, Italy.

Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.

Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA.

Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA.

Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA.

Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Departments of Medicine and Immunology, Duke University, Durham, NC 27710, USA.

Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

VisMederi Research S.r.l., 53100 Siena, Italy; VisMederi S.r.l, 53100 Siena, Italy; Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy.

Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy; Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.

Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.

Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA. Electronic address: sauttog@ccf.org.

Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA. Electronic address: jmclellan@austin.utexas.edu.

Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 73232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Computer Science, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: ivelin.georgiev@vanderbilt.edu.

Macromolecule Content

Total Structure Weight: 347.71 kDa
Atom Count: 15,987
Modeled Residue Count: 2,040
Deposited Residue Count: 3,132
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2	A, H [auth B], I [auth C]	597	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9 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: 5	Glycosylation Focus chain A Focus chain H [auth B] Focus chain I [auth C]	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
54043-5 Fab Heavy Chain	B [auth D], C [auth E], F [auth H]	233	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth D] Focus chain C [auth E] Focus chain F [auth H]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
54043-5 Fab Light Chain	D [auth F], E [auth G], G [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain S [auth H] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth H] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth H] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] M [auth A] N [auth A] O [auth A] P [auth A] AA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth D], R [auth E], S [auth H], T [auth B], U [auth B], V [auth B], W [auth B], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth H] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth H] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2_3874:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Johnson, N.V.

McLellan, J.S.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-07-31
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Structure summary
Version 1.2: 2024-10-23
Changes: Data collection
Version 1.3: 2024-11-27
Changes: Data collection, Database references