7SB4

Structure of OC43 spike in complex with polyclonal Fab2 (Donor 1412)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural mapping of antibody landscapes to human betacoronavirus spike proteins.

Bangaru, S.Antanasijevic, A.Kose, N.Sewall, L.M.Jackson, A.M.Suryadevara, N.Zhan, X.Torres, J.L.Copps, J.de la Pena, A.T.Crowe Jr., J.E.Ward, A.B.

(2022) Sci Adv 8: eabn2911-eabn2911

  • DOI: https://doi.org/10.1126/sciadv.abn2911
  • Primary Citation of Related Structures:  
    7SB3, 7SB4, 7SB5, 7SBV, 7SBW, 7SBX, 7SBY

  • PubMed Abstract: 

    Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based polyclonal epitope mapping (EMPEM) to characterize the antibody specificities against β-CoV spike proteins in prepandemic (PP) sera or SARS-CoV-2 convalescent (SC) sera. We observed that most PP sera had antibodies specific to seasonal human CoVs (HCoVs) OC43 and HKU1 spike proteins while the SC sera showed reactivity across all human β-CoVs. Detailed molecular mapping of spike-antibody complexes revealed epitopes that were differentially targeted by preexisting antibodies and SC serum antibodies. Our studies provide an antigenic landscape to β-HCoV spikes in the general population serving as a basis for cross-reactive epitope analyses in SARS-CoV-2-infected individuals.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike proteinA,
B [auth C],
C [auth B]
1,367Human coronavirus OC43Mutation(s): 0 
UniProt
Find proteins for A0A0B4N7I3 (Human coronavirus OC43)
Explore A0A0B4N7I3 
Go to UniProtKB:  A0A0B4N7I3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4N7I3
Glycosylation
Glycosylation Sites: 14
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Human polyclonal Fab model with polyalanine backbone - Heavy chainD [auth H],
E [auth L]
113Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F [auth D],
H [auth F],
I [auth G],
J [auth I],
K [auth J],
F [auth D],
H [auth F],
I [auth G],
J [auth I],
K [auth J],
M,
N,
O,
P
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E],
L [auth K]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8Z9
Query on 8Z9

Download Ideal Coordinates CCD File 
BA [auth A],
MA [auth C],
XA [auth B]
Sapienic acid
C16 H30 O2
NNNVXFKZMRGJPM-KHPPLWFESA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
AA [auth A],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
NA [auth B],
OA [auth B],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
X [auth A],
Y [auth A],
Z [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: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary