6VV5

Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.2 of the entry. See complete history


Literature

Structure and immune recognition of the porcine epidemic diarrhea virus spike protein.

Kirchdoerfer, R.N.Bhandari, M.Martini, O.Sewall, L.M.Bangaru, S.Yoon, K.J.Ward, A.B.

(2021) Structure 29: 385-392.e5

  • DOI: https://doi.org/10.1016/j.str.2020.12.003
  • Primary Citation of Related Structures:  
    6VV5

  • PubMed Abstract: 

    Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components, including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.


  • 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 glycoprotein
A, B, C
1,356Porcine epidemic diarrhea virusMutation(s): 0 
UniProt
Find proteins for S5RJN4 (Porcine epidemic diarrhea virus)
Explore S5RJN4 
Go to UniProtKB:  S5RJN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS5RJN4
Glycosylation
Glycosylation Sites: 15
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, N, X
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G59621EZ
GlyCosmos:  G59621EZ
GlyGen:  G59621EZ
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-glucopyranoseBA [auth b],
H,
R
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAM
Query on PAM

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
MA [auth A]
NA [auth A]
TA [auth B]
AB [auth C],
BB [auth C],
MA [auth A],
NA [auth A],
TA [auth B],
UA [auth B]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
HA [auth A]
IA [auth A]
JA [auth A]
KA [auth A]
LA [auth A]
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta3.10
MODEL REFINEMENTPHENIX1.17rc2-3619
RECONSTRUCTIONRELION3.0

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 StatesAI123498
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI127521

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2020-11-04
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Structure summary
  • Version 3.1: 2021-01-20
    Changes: Database references
  • Version 3.2: 2021-04-14
    Changes: Database references