8GPU | pdb_00008gpu

YFV_E_YD6Fab_prefusion

• PDB DOI: https://doi.org/10.2210/pdb8GPU/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Yellow fever virus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2022-08-27 Released: 2022-11-02 
• Deposition Author(s): Li, Y., Wu, L., Qi, J., Yan, J., Gao, G.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.279 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

A neutralizing-protective supersite of human monoclonal antibodies for yellow fever virus.

Li, Y., Chen, Z., Wu, L., Dai, L., Qi, J., Chai, Y., Li, S., Wang, Q., Tong, Z., Ma, S., Duan, X., Ren, S., Song, R., Liang, M., Liu, W., Yan, J., Gao, G.F.

(2022) Innovation (Camb) 3: 100323-100323

• PubMed: 36199277 
• DOI: https://doi.org/10.1016/j.xinn.2022.100323
• Primary Citation Related Structures: 
  8GPT, 8GPU, 8GPX


• PubMed Abstract: 
  

  The yellow fever virus (YFV) is a life-threatening human pathogen. Owing to the lack of available therapeutics, non-vaccinated individuals are at risk. Here, we isolated eight human monoclonal antibodies that neutralize YFV infection. Five recognized overlapping epitopes and exhibited potent neutralizing activity. Two (YD6 and YD73) were ultra-potent and conferred complete protection against the lethal challenge of YFV as both prophylactics and therapeutics in a mouse model. Crystal structures revealed that YD6 engaged the YFV envelope protein in both pre- and post-fusion states, suggesting viral inhibition by a "double-lock" mechanism. The recognition determinants for YD6 and YD73 are clustered at the premembrane (prM)-binding site. Notably, antibodies targeting this site were present in minute traces in YFV-infected individuals but contributed significantly to neutralization, suggesting a vulnerable supersite of YFV. We provide two promising candidates for immunotherapy against YFV, and the supersite represents an ideal target for epitope-based vaccine design.

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Organizational Affiliation: 
• CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Center of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China.
Key Laboratory of Tropical Translational Medicine of Ministry of Education and School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China.
College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Hetero 18-mer - A6B6C6 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 18-mer - A7B6C4D1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 537.27 kDa 
• Atom Count: 37,132 
• Modeled Residue Count: 4,914 
• Deposited Residue Count: 4,992 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein	A, D [auth E], G [auth B], J [auth I], M, P	398	Yellow fever virus	Mutation(s): 0
UniProt
Find proteins for Q89292 (Yellow fever virus) Explore Q89292  Go to UniProtKB:  Q89292

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YD6Fab_H	B [auth H], E [auth F], H [auth C], K [auth J], N, Q	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
YD6Fab_L	C [auth L], F [auth G], I [auth D], L [auth K], O, R	217	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.279 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.259	α = 90
b = 278.003	β = 90
c = 354.657	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Li, Y., Wu, L., Qi, J., Yan, J., Gao, G.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary