7PO5

Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes.

Wang, C.Hesketh, E.L.Shamorkina, T.M.Li, W.Franken, P.J.Drabek, D.van Haperen, R.Townend, S.van Kuppeveld, F.J.M.Grosveld, F.Ranson, N.A.Snijder, J.de Groot, R.J.Hurdiss, D.L.Bosch, B.J.

(2022) Nat Commun 13: 2921-2921

  • DOI: https://doi.org/10.1038/s41467-022-30658-0
  • Primary Citation of Related Structures:  
    7PNM, 7PNQ, 7PO5

  • PubMed Abstract: 

    Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus on viral glycoprotein S, the target for neutralizing antibodies, and provide an in-depth analysis of its antigenic structure. Neutralizing antibodies are directed to the sialoglycan-receptor binding site in S1 A domain, but, remarkably, also to S1 B . The latter block infection yet do not prevent sialoglycan binding. While two distinct neutralizing S1 B epitopes are readily accessible in the prefusion S trimer, other sites are occluded such that their accessibility must be subject to conformational changes in S during cell-entry. While non-neutralizing antibodies were broadly reactive against a collection of natural OC43 variants, neutralizing antibodies generally displayed restricted binding breadth. Our data provide a structure-based understanding of protective immunity and adaptive evolution for this endemic coronavirus which emerged in humans long before SARS-CoV-2.


  • Organizational Affiliation

    Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
47C9 antibody heavy chainA [auth Z],
D [auth X],
G [auth H]
124Homo sapiensMutation(s): 0 
Gene Names: VH
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
47C9 antibody light chainB [auth D],
E [auth F],
H [auth L]
107Homo sapiensMutation(s): 0 
Gene Names: VL
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 [auth B],
F [auth C],
I [auth A]
1,322Human coronavirus OC43Mutation(s): 0 
UniProt
Find proteins for P36334 (Human coronavirus OC43)
Explore P36334 
Go to UniProtKB:  P36334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36334
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth B]
K [auth B]
L [auth B]
M [auth B]
N [auth B]
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Health-HollandNetherlandsLSHM19136
Chinese Scholarship CouncilChinaCSC201708620178

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Refinement description, Structure summary