9DEZ

PDCoV S trimer bound by three copies of PD41 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses.

Rexhepaj, M.Asarnow, D.Perruzza, L.Park, Y.J.Guarino, B.Mccallum, M.Culap, K.Saliba, C.Leoni, G.Balmelli, A.Yoshiyama, C.N.Dickinson, M.S.Quispe, J.Brown, J.T.Tortorici, M.A.Sprouse, K.R.Taylor, A.L.Corti, D.Starr, T.N.Benigni, F.Veesler, D.

(2024) Immunity 

  • DOI: https://doi.org/10.1016/j.immuni.2024.10.001
  • Primary Citation of Related Structures:  
    9B2C, 9DEZ, 9DF0

  • PubMed Abstract: 

    Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,166Porcine deltacoronavirusMutation(s): 0 
UniProt
Find proteins for A0A6M5ICE2 (Porcine deltacoronavirus)
Explore A0A6M5ICE2 
Go to UniProtKB:  A0A6M5ICE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M5ICE2
Glycosylation
Glycosylation Sites: 21
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PD41 Fab variable heavy-chainD [auth H],
E [auth I],
F [auth J]
118Mus musculusMutation(s): 0 
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
PD41 Fab variable light-chainG [auth L],
H [auth M],
I [auth N]
111Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • 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],
BA [auth b],
DA [auth d],
EA [auth e],
FA [auth f],
AA [auth a],
BA [auth b],
DA [auth d],
EA [auth e],
FA [auth f],
GA [auth g],
HA [auth h],
IA [auth i],
J [auth D],
JA [auth j],
K [auth E],
KA [auth k],
L [auth F],
MA [auth m],
N [auth K],
NA [auth n],
O,
OA [auth o],
P,
Q,
S,
T,
U,
V,
W,
Y,
Z
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
CA [auth c],
LA [auth l],
M [auth G],
PA [auth p],
R,
CA [auth c],
LA [auth l],
M [auth G],
PA [auth p],
R,
X
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAM
Query on PAM

Download Ideal Coordinates CCD File 
AB [auth A],
LB [auth B],
MB [auth C]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BB [auth B]
CB [auth B]
DB [auth B]
EB [auth B]
FB [auth B]
BB [auth B],
CB [auth B],
DB [auth B],
EB [auth B],
FB [auth B],
GB [auth B],
HB [auth B],
IB [auth B],
JB [auth B],
KB [auth B],
NB [auth C],
OB [auth C],
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 A],
VB [auth C],
WA [auth A],
WB [auth C],
XA [auth A],
YA [auth A],
ZA [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: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX

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 StatesP01AI167966
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesDP1AI158186
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00036
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD032290
Burroughs Wellcome FundUnited States--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection