Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.25 kDa 
• Atom Count: 1232 
• Modelled Residue Count: 143 
• Deposited Residue Count: 148 
• Unique protein chains: 2

5YL9

1.86 Angstrom crystal structure of human Coronavirus 229E fusion core

• PDB DOI: 10.2210/pdb5YL9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human coronavirus 229E
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-17 Released: 2018-09-26 
• Deposition Author(s): Yang, B., Yan, L., Meng, B., WIlson, I.A.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.206 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Crystal structure of the post-fusion core of the Human coronavirus 229E spike protein at 1.86 angstrom resolution

Yan, L., Meng, B., Xiang, J., Wilson, I.A., Yang, B.

(2018) Acta Crystallogr D Struct Biol 74: 841-851

• PubMed: 30198895 
• DOI: 10.1107/S2059798318008318
• Primary Citation of Related Structures:  
  5YL9


• PubMed Abstract: 
  

Human coronavirus 229E (HCoV-229E) usually causes mild upper respiratory infections in heathy adults, but may lead to severe complications or mortality in individuals with weakened immune systems. Virus entry of HCoV-229E is mediated by its spike (S) protein, where the S1 domain facilitates attachment to host cells and the S2 domain is involved in subsequent fusion of the virus and host membranes. During the fusion process, two heptad repeats, HR1 and HR2, in the S2 domain assemble into a six-helix membrane-fusion structure termed the fusion core. Here, the complete fusion-core structure of HCoV-229E has been determined at 1.86 Å resolution, representing the most complete post-fusion conformation thus far among published human alphacoronavirus (α-HCoV) fusion-core structures. The overall structure of the HCoV-229E fusion core is similar to those of SARS, MERS and HCoV-NL63, but the packing of its 3HR1 core differs from those of SARS and MERS in that it contains more noncanonical `x' and `da' layers. Side-by-side electrostatic surface comparisons reveal that the electrostatic surface potentials are opposite in α-HCoVs and β-HCoVs at certain positions and that the HCoV-229E surface also appears to be the most hydrophobic among the various HCoVs. In addition to the highly conserved hydrophobic interactions between HR1 and HR2, some polar and electrostatic interactions are also well preserved across different HCoVs. This study adds to the structural profiling of HCoVs to aid in the structure-based design of pan-coronavirus small molecules or peptides to inhibit viral fusion.

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Organizational Affiliation: 

Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	89	Human coronavirus 229E	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P15423 (Human coronavirus 229E) Explore P15423  Go to UniProtKB:  P15423

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	59	Human coronavirus 229E	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P15423 (Human coronavirus 229E) Explore P15423  Go to UniProtKB:  P15423

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.206 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.941	α = 90
b = 46.941	β = 90
c = 402.145	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-10-17 
• Released Date: 2018-09-26 
Deposition Author(s): Yang, B., Yan, L., Meng, B., WIlson, I.A.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31600619

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release