9DHY | pdb_00009dhy

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


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

  • DOI: https://doi.org/10.1016/j.celrep.2025.115499
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab COVIC-154 Heavy ChainA,
D,
G [auth I]
123Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab COVIC-154 Light ChainB,
E,
H [auth J]
107Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinC,
F,
I [auth K]
1,212Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 10Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARCv3.3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19 AI142790-03S1
Bill & Melinda Gates FoundationUnited StatesINV-0006133
GHR FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release