9DHY | pdb_00009dhy

Structure of SARS-CoV-2 spike in complex with antibody Fab COVIC-154

PDB DOI: https://doi.org/10.2210/pdb9DHY/pdb
EM Map EMD-46892: EMDB EMDataResource

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

Deposited: 2024-09-04 Released: 2025-04-16
Deposition Author(s): Yu, X., Saphire, E.O.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation, GHR Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A global collaboration for systematic analysis of broad-ranging antibodies against the SARS-CoV-2 spike protein.

Schendel, S.L., Yu, X., Halfmann, P.J., Mahita, J., Ha, B., Hastie, K.M., Li, H., Bedinger, D., Troup, C., Li, K., Kuzmina, N., Torrelles, J.B., Munt, J.E., Maddocks, M., Osei-Twum, M., Callaway, H.M., Reece, S., Palser, A., Kellam, P., Dennison, S.M., Huntwork, R.H.C., Horn, G.Q., Abraha, M., Feeney, E., Martinez-Sobrido, L., Pino, P.A., Hicks, A., Ye, C., Park, J.G., Maingot, B., Periasamy, S., Mallory, M., Scobey, T., Lepage, M.N., St-Amant, N., Khan, S., Gambiez, A., Baric, R.S., Bukreyev, A., Gagnon, L., Germann, T., Kawaoka, Y., Tomaras, G.D., Peters, B., Saphire, E.O.

(2025) Cell Rep 44: 115499-115499

PubMed: 40184253 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.celrep.2025.115499
Primary Citation Related Structures:
9DHY

PubMed Abstract:
The Coronavirus Immunotherapeutic Consortium (CoVIC) conducted side-by-side comparisons of over 400 anti-SARS-CoV-2 spike therapeutic antibody candidates contributed by large and small companies as well as academic groups on multiple continents. Nine reference labs analyzed antibody features, including in vivo protection in a mouse model of infection, spike protein affinity, high-resolution epitope binning, ACE-2 binding blockage, structures, and neutralization of pseudovirus and authentic virus infection, to build a publicly accessible dataset in the database CoVIC-DB. High-throughput, high-resolution binning of CoVIC antibodies defines a broad and predictive landscape of antibody epitopes on the SARS-CoV-2 spike protein and identifies features associated with durable potency against multiple SARS-CoV-2 variants of concern and high in vivo efficacy. Results of the CoVIC studies provide a guide for selecting effective and durable antibody therapeutics and for immunogen design as well as providing a framework for rapid response to future viral disease outbreaks.

Organizational Affiliation

Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.

Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA.

Carterra, Inc., Salt Lake City, UT 84103, USA.

Center for Human Systems Immunology, Departments of Surgery and Integrative Immunobiology, Duke University, Durham, NC 27701, USA.

Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; Population Health Program, International Center for the Advancement of Research & Education (I-CARE), Texas Biomedical Research Institute, San Antonio, TX 78227, USA.

Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.

Nexelis, a Q2 Solutions Company, 525 Boulevard Cartier Ouest, Laval, QC H7V 3S8, Canada.

Kymab, a Sanofi Company, Babraham Research Campus, Cambridge CB22 3AT, UK.

RQ Biotechnology Ltd., London W12 7RZ, UK.

RQ Biotechnology Ltd., London W12 7RZ, UK; Department of Infectious Diseases, Faculty of Medicine, Imperial College, London SW7 2AZ, UK.

Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.

Galveston National Laboratory, 301 University Boulevard, Galveston, TX 77550, USA.

Population Health Program, International Center for the Advancement of Research & Education (I-CARE), Texas Biomedical Research Institute, San Antonio, TX 78227, USA; Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Department of Pathology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA; Galveston National Laboratory, 301 University Boulevard, Galveston, TX 77550, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.

Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan; Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan.

Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address: bpeters@lji.org.

Macromolecule Content

Total Structure Weight: 486.04 kDa
Atom Count: 27,227
Modeled Residue Count: 3,427
Deposited Residue Count: 4,326
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab COVIC-154 Heavy Chain	A, D, G [auth I]	123	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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab COVIC-154 Light Chain	B, E, H [auth J]	107	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

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C, F, I [auth K]	1,212	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: 10	Glycosylation Focus chain C Focus chain F Focus chain I [auth K]	Go to GlyGen: P0DTC2-1
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 M], K [auth G], L [auth H], M [auth N], N [auth L], J [auth M], K [auth G], L [auth H], M [auth N], N [auth L], O, P, Q, R	2		N-Glycosylation	Interactions Focus chain J [auth M] Focus chain K [auth G] Focus chain L [auth H] Focus chain M [auth N] Focus chain N [auth L] Focus chain O Focus chain P Focus chain Q Focus chain R Interactions & Density Focus chain J [auth M] Focus chain K [auth G] Focus chain L [auth H] Focus chain M [auth N] Focus chain N [auth L] Focus chain O Focus chain P Focus chain Q Focus chain R
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 Z [auth F] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain MA [auth K] SDF format, chain LA [auth K] SDF format, chain KA [auth K] SDF format, chain JA [auth K] SDF format, chain IA [auth K] SDF format, chain HA [auth K] SDF format, chain GA [auth K] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain MA [auth K] MOL2 format, chain LA [auth K] MOL2 format, chain KA [auth K] MOL2 format, chain JA [auth K] MOL2 format, chain IA [auth K] MOL2 format, chain HA [auth K] MOL2 format, chain GA [auth K] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain MA [auth K] mmCIF format, chain LA [auth K] mmCIF format, chain KA [auth K] mmCIF format, chain JA [auth K] mmCIF format, chain IA [auth K] mmCIF format, chain HA [auth K] mmCIF format, chain GA [auth K] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] CA [auth F] DA [auth F] EA [auth F] AA [auth F], BA [auth F], CA [auth F], DA [auth F], EA [auth F], FA [auth F], GA [auth K], HA [auth K], IA [auth K], JA [auth K], KA [auth K], LA [auth K], MA [auth K], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth K] Focus chain HA [auth K] Focus chain IA [auth K] Focus chain JA [auth K] Focus chain KA [auth K] Focus chain LA [auth K] Focus chain MA [auth K] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth K] Focus chain HA [auth K] Focus chain IA [auth K] Focus chain JA [auth K] Focus chain KA [auth K] Focus chain LA [auth K] Focus chain MA [auth K] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	v3.3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

Yu, X.

Saphire, E.O.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI142790-03S1
Bill & Melinda Gates Foundation	United States	INV-0006133
GHR Foundation	United States	--