7VN9 | pdb_00007vn9

Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab

• PDB DOI: https://doi.org/10.2210/pdb7VN9/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human coronavirus 229E
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2021-10-10 Released: 2022-10-26 
• Deposition Author(s): Xiang, J.C., Yang, B.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.49 Å
• R-Value Free: 
  0.288 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.273 (Depositor), 0.288 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Starting Models: experimental

Literature

Antigenic mapping reveals sites of vulnerability on alpha-HCoV spike protein.

Xiang, J., Su, J., Lan, Q., Zhao, W., Zhou, Y., Xu, Y., Niu, J., Xia, S., Qi, Q., Sidhu, S., Lu, L., Miersch, S., Yang, B.

(2022) Commun Biol 5: 1179-1179

• PubMed: 36333470 
• DOI: https://doi.org/10.1038/s42003-022-04160-8
• Primary Citation Related Structures: 
  7VMZ, 7VN9, 7VNG


• PubMed Abstract: 
  

  Understanding the antigenic signatures of all human coronaviruses (HCoVs) Spike (S) proteins is imperative for pan-HCoV epitopes identification and broadly effective vaccine development. To depict the currently elusive antigenic signatures of α-HCoVs S proteins, we isolated a panel of antibodies against the HCoV-229E S protein and characterized their epitopes and neutralizing potential. We found that the N-terminal domain of HCoV-229E S protein is antigenically dominant wherein an antigenic supersite is present and appears conserved in HCoV-NL63, which holds potential to serve as a pan-α-HCoVs epitope. In the receptor binding domain, a neutralizing epitope is captured in the end distal to the receptor binding site, reminiscent of the locations of the SARS-CoV-2 RBD cryptic epitopes. We also identified a neutralizing antibody that recognizes the connector domain, thus representing the first S2-directed neutralizing antibody against α-HCoVs. The unraveled HCoVs S proteins antigenic similarities and variances among genera highlight the challenges faced by pan-HCoV vaccine design while supporting the feasibility of broadly effective vaccine development against a subset of HCoVs.

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Organizational Affiliation: 
• School of Life Science and Technology and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China.
CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China.
University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China.
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, 130 Dong An Road, 200032, Shanghai, China.
The Anvil Institute, School of Pharmacy, University of Waterloo, 151 Charles St. W, Kitchener, ON, N2G 1H6, Canada.
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, 130 Dong An Road, 200032, Shanghai, China. [e-mail].
The Anvil Institute, School of Pharmacy, University of Waterloo, 151 Charles St. W, Kitchener, ON, N2G 1H6, Canada. [e-mail].
School of Life Science and Technology and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China. [e-mail].
Shanghai Clinical Research and Trial Center, 201210, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance, gel filtration, electron microscopy

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 129.5 kDa 
• Atom Count: 8,541 
• Modeled Residue Count: 1,113 
• Deposited Residue Count: 1,188 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C04 Fab heavy chain	A [auth H], D [auth A]	231	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C04 Fab light chain	B [auth L], E [auth B]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein S1	C [auth E], F [auth C]	148	Human coronavirus 229E	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P15423 (Human coronavirus 229E) Explore P15423  Go to UniProtKB:  P15423
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D], I [auth G]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.49 Å
• R-Value Free:  0.288 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.273 (Depositor), 0.288 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.732	α = 90
b = 183.732	β = 90
c = 255.988	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Xiang, J.C., Yang, B.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32070170

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 1.1: 2022-11-23
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary