9OFP | pdb_00009ofp

HCoV-229E S2P bound by two DH1533 Fabs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A neutralizing human antibody induces movement of the HCoV-229E receptor binding domain.

Liccione, M.F.Scobey, T.Froggatt, H.M.Pajon, C.Yount, B.L.Yin, Q.Spence, T.N.Walter, E.B.Saunders, K.O.Edwards, R.J.Baric, R.S.Haynes, B.F.Cain, D.W.Sheahan, T.P.Wrapp, D.

(2025) Commun Biol 

  • DOI: https://doi.org/10.1038/s42003-025-09446-1
  • Primary Citation of Related Structures:  
    9OFP, 9OFQ

  • PubMed Abstract: 

    HCoV-229E is an endemic Alphacoronavirus that typically causes common cold-like disease in most healthy adults, but can also cause severe respiratory disease in the very young and the elderly. Although the virus was discovered over sixty years ago and undergoes continuous antigenic drift, remarkably little is known about the humoral immune response to HCoV-229E infection. Here we report the isolation of two receptor binding domain-targeting neutralizing human antibodies raised in response to natural HCoV-229E infection. One of these, DH1533, potently neutralizes HCoV-229E, binds to spike with sub-nanomolar affinity and prevents the association between the RBD and the host cell receptor aminopeptidase N. Structural characterization of this antibody bound to HCoV-229E spike delineated a neutralization-sensitive epitope on the RBD and revealed that DH1533 induces conformational flexibility in neighboring RBDs, reminiscent of the "up-and-down" kinetics observed in the related Betacoronavirus spikes. These findings provide insight into the humoral immune response to HCoV-229E infection and will serve as a guide for the design of future therapeutic interventions.


  • Organizational Affiliation
    • Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Surface glycoprotein
A, B, C
1,134Human coronavirus 229EMutation(s): 0 
UniProt
Find proteins for A0A1B3TN99 (Human coronavirus 229E)
Explore A0A1B3TN99 
Go to UniProtKB:  A0A1B3TN99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B3TN99
Glycosylation
Glycosylation Sites: 24
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH1533 heavy chainD [auth H],
F [auth M]
239Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DH1533 light chainE [auth L],
G [auth N]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

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-glucopyranose
AA [auth a],
CA [auth c],
H [auth D],
I [auth E],
K [auth G],
AA [auth a],
CA [auth c],
H [auth D],
I [auth E],
K [auth G],
P,
Q,
R,
T,
U,
V
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
DA [auth d],
EA [auth e],
J [auth F],
L [auth I],
BA [auth b],
DA [auth d],
EA [auth e],
J [auth F],
L [auth I],
M [auth J],
N [auth K],
O,
S,
W,
X,
Y,
Z
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 
AB [auth B]
BB [auth B]
CB [auth B]
DB [auth B]
EB [auth B]
AB [auth B],
BB [auth B],
CB [auth B],
DB [auth B],
EB [auth B],
FA [auth A],
FB [auth B],
GA [auth A],
GB [auth B],
HA [auth A],
HB [auth B],
IA [auth A],
IB [auth B],
JA [auth A],
JB [auth C],
KA [auth A],
KB [auth C],
LA [auth A],
LB [auth C],
MA [auth A],
MB [auth C],
NA [auth A],
NB [auth C],
OA [auth A],
OB [auth C],
PA [auth A],
PB [auth C],
QA [auth A],
QB [auth C],
RA [auth A],
RB [auth C],
SA [auth A],
SB [auth C],
TA [auth A],
TB [auth C],
UA [auth A],
UB [auth C],
VA [auth B],
VB [auth C],
WA [auth B],
WB [auth C],
XA [auth B],
XB [auth C],
YA [auth B],
ZA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4.6.2
MODEL REFINEMENTISOLDE

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-12-03 
  • Deposition Author(s): Wrapp, D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States3P01AI158571-01A1S1

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Data collection, Database references