8GV5

Crystal structure of PN-SIA28 in complex with influenza hemagglutinin A/swine/Guangdong/104/2013 (H1N1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes.

Chen, Y.Wang, F.Yin, L.Jiang, H.Lu, X.Bi, Y.Zhang, W.Shi, Y.Burioni, R.Tong, Z.Song, H.Qi, J.Gao, G.F.

(2022) Nat Commun 13: 7603-7603

  • DOI: https://doi.org/10.1038/s41467-022-35236-y
  • Primary Citation of Related Structures:  
    7WVD, 7WVG, 7WVI, 8GV4, 8GV5, 8GV6, 8GV7

  • PubMed Abstract: 

    Influenza infection continues are a persistent threat to public health. The identification and characterization of human broadly neutralizing antibodies can facilitate the development of antibody drugs and the design of universal influenza vaccines. Here, we present structural information for the human antibody PN-SIA28's heterosubtypic binding of hemagglutinin (HA) from circulating and emerging potential influenza A viruses (IAVs). Aside from group 1 and 2 conventional IAV HAs, PN-SIA28 also inhibits membrane fusion mediated by bat-origin H17 and H18 HAs. Crystallographic analyses of Fab alone or in complex with H1, H14, and H18 HA proteins reveal that PN-SIA28 binds to a highly conserved epitope in the fusion domain of different HAs, with the same CDRHs but different CDRLs for different HAs tested, distinguishing it from other structurally characterized anti-stem antibodies. The binding characteristics of PN-SIA28 provides information to support the design of increasingly potent engineered antibodies, antiviral drugs, and/or universal influenza vaccines.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain330Influenza A virus (A/swine/Guangdong/104/2013(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0D3LZV1 (Influenza A virus)
Explore A0A0D3LZV1 
Go to UniProtKB:  A0A0D3LZV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D3LZV1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain173Influenza A virus (A/swine/Guangdong/104/2013(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0D3LZV1 (Influenza A virus)
Explore A0A0D3LZV1 
Go to UniProtKB:  A0A0D3LZV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D3LZV1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PN-SIA28 Heavy chain125Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PN-SIA28 Light Chain108Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.797α = 90
b = 85.797β = 90
c = 231.289γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Refinement description