5XHV | pdb_00005xhv

Crystal Structure Of Fab S40 In Complex With Influenza Hemagglutinin, HA1 subunit.

• PDB DOI: https://doi.org/10.2210/pdb5XHV/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/California/07/2009(H1N1)), Homo sapiens
• Expression System: Insect cell expression vector pTIE1, Homo sapiens
• Mutation(s): No 


• Deposited: 2017-04-24 Released: 2017-11-15 
• Deposition Author(s): Lee, C.C., Wang, A.H.J., Yu, C.M., Yang, A.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.275 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Models: experimental

Literature

High throughput discovery of influenza virus neutralizing antibodies from phage-displayed synthetic antibody libraries.

Chen, I.C., Chiu, Y.K., Yu, C.M., Lee, C.C., Tung, C.P., Tsou, Y.L., Huang, Y.J., Lin, C.L., Chen, H.S., Wang, A.H., Yang, A.S.

(2017) Sci Rep 7: 14455-14455

• PubMed: 29089574 
• DOI: https://doi.org/10.1038/s41598-017-14823-w
• Primary Citation Related Structures: 
  5XHV


• PubMed Abstract: 
  

  Pandemic and epidemic outbreaks of influenza A virus (IAV) infection pose severe challenges to human society. Passive immunotherapy with recombinant neutralizing antibodies can potentially mitigate the threats of IAV infection. With a high throughput neutralizing antibody discovery platform, we produced artificial anti-hemagglutinin (HA) IAV-neutralizing IgGs from phage-displayed synthetic scFv libraries without necessitating prior memory of antibody-antigen interactions or relying on affinity maturation essential for in vivo immune systems to generate highly specific neutralizing antibodies. At least two thirds of the epitope groups of the artificial anti-HA antibodies resemble those of natural protective anti-HA antibodies, providing alternatives to neutralizing antibodies from natural antibody repertoires. With continuing advancement in designing and constructing synthetic scFv libraries, this technological platform is useful in mitigating not only the threats of IAV pandemics but also those from other newly emerging viral infections.

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Organizational Affiliation: 
• Genomics Research Center, Academia Sinica, 115, Taipei, Taiwan.
Institute of Biological Chemistry, Academia Sinica, 115, Taipei, Taiwan.
Genomics Research Center, Academia Sinica, 115, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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: 168.1 kDa 
• Atom Count: 11,100 
• Modeled Residue Count: 1,440 
• Deposited Residue Count: 1,534 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B [auth E]	324	Influenza A virus (A/California/07/2009(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for C3W5X2 (Influenza A virus) Explore C3W5X2  Go to UniProtKB:  C3W5X2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S40 heavy chain	C [auth H], E [auth P]	229	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S40 light chain	D [auth L], F [auth Q]	214	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.275 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.395	α = 90
b = 133.64	β = 110.47
c = 133.136	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Lee, C.C., Wang, A.H.J., Yu, C.M., Yang, A.S.

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary