Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 534.06 kDa 
• Atom Count: 32115 
• Modelled Residue Count: 3735 
• Deposited Residue Count: 4404 
• Unique protein chains: 1

6JX7

Cryo-EM structure of spike protein of feline infectious peritonitis virus strain UU4

• DOI: 10.2210/pdb6JX7/pdb
• EMDataResource: EMD-9891

• Classification: VIRAL PROTEIN
• Organism(s): Feline infectious peritonitis virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-04-22 Released: 2020-01-15 
• Deposition Author(s): Hsu, S.T.D., Yang, T.J., Ko, T.P., Draczkowski, P.
• Funding Organization(s): Ministry of Science and Technology (Taiwan), Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.31 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans.

Yang, T.J., Chang, Y.C., Ko, T.P., Draczkowski, P., Chien, Y.C., Chang, Y.C., Wu, K.P., Khoo, K.H., Chang, H.W., Hsu, S.D.

(2020) Proc Natl Acad Sci U S A 117: 1438-1446

• PubMed: 31900356 
• DOI: 10.1073/pnas.1908898117
• Primary Citation of Related Structures:  
  6JX7


• PubMed Abstract: 
  

Feline infectious peritonitis virus (FIPV) is an alphacoronavirus that causes a nearly 100% mortality rate without effective treatment. Here we report a 3.3-Å cryoelectron microscopy (cryo-EM) structure of the serotype I FIPV spike (S) protein, which is responsible for host recognition and viral entry. Mass spectrometry provided site-specific compositions of densely distributed high-mannose and complex-type N - glycans that account for 1/4 of the total molecular mass; most of the N-glycans could be visualized by cryo-EM. Specifically, the N-glycans that wedge between 2 galectin-like domains within the S1 subunit of FIPV S protein result in a unique propeller-like conformation, underscoring the importance of glycosylation in maintaining protein structures. The cleavage site within the S2 subunit responsible for activation also showed distinct structural features and glycosylation. These structural insights provide a blueprint for a better molecular understanding of the pathogenesis of FIP.

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Organizational Affiliation: 

Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Feline Infectious Peritonitis Virus Spike Protein	A, B, C	1468	Feline infectious peritonitis virus	Mutation(s): 0
Find proteins for C6GHB7 (Feline coronavirus UU4) Explore C6GHB7  Go to UniProtKB:  C6GHB7
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104  Go to UniProtKB:  P10104

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	0, 4, D, F, K, M, N, Q, U, V, X, c, e, f, i, m, n, p, u, w, x	2		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, H, W, Y, Z, o, q, r	3		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	I, a, s	7		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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	J, L, O, P, b, d, g, h, t, v, y, z	4		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	1, R, j	4		N-Glycosylation

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[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	2, S, k	5		N-Glycosylation

Entity ID: 8
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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	3, T, l	7		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	A, B, C	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.31 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-04-22 
• Released Date: 2020-01-15 
Deposition Author(s): Hsu, S.T.D., Yang, T.J., Ko, T.P., Draczkowski, P.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	106-2311-B-002-028-MY3
Ministry of Science and Technology (Taiwan)	Taiwan	107-2628-M-001-005-MY3
Academia Sinica (Taiwan)	Taiwan	AS-KPQ-105-TPP

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary