8H3C

Crystal structure of M2e Influenza peptide in complex with antibody scFv

• PDB DOI: https://doi.org/10.2210/pdb8H3C/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens, Influenza A virus (A/New York/392/2004(H3N2))
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-08 Released: 2023-08-02 
• Deposition Author(s): Kumar, U., Madni, Z.K., Gaur, V., Salunke, D.M.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free: 0.235 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

A structure and knowledge-based combinatorial approach to engineering universal scFv antibodies against influenza M2 protein.

Kumar, U., Goyal, P., Madni, Z.K., Kamble, K., Gaur, V., Rajala, M.S., Salunke, D.M.

(2023) J Biomed Sci 30: 56-56

• PubMed: 37491224 
• DOI: https://doi.org/10.1186/s12929-023-00950-2
• Primary Citation of Related Structures:  
  8H3B, 8H3C, 8H73


• PubMed Abstract: 
  

  The influenza virus enters the host via hemagglutinin protein binding to cell surface sialic acid. Receptor-mediated endocytosis is followed by viral nucleocapsid uncoating for replication aided by the transmembrane viral M2 proton ion channel. M2 ectodomain (M2e) is a potential universal candidate for monoclonal antibody therapy owing to its conserved nature across influenza virus subtypes and its importance in viral propagation.

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Organizational Affiliation: 

International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Macromolecule Content

• Total Structure Weight: 139.14 kDa 
• Atom Count: 8,520 
• Modelled Residue Count: 1,128 
• Deposited Residue Count: 1,295 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single Chain Variable Fragment	A, B, C, D, E	253	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein 2	F, G	15	Influenza A virus (A/New York/392/2004(H3N2))	Mutation(s): 0
UniProt
Find proteins for Q464B8 (Influenza A virus) Explore Q464B8  Go to UniProtKB:  Q464B8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free: 0.235 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.818	α = 90
b = 120.398	β = 90
c = 176.858	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Kumar, U., Madni, Z.K., Gaur, V., Salunke, D.M.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Source and taxonomy