8US0 | pdb_00008us0

Human antibody S8V1-157 in complex with the A/American black duck/New Brunswick/00464/2010(H4N6) HA head domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.293 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface.

Simmons, H.C.Finney, J.Kotaki, R.Adachi, Y.Park Moseman, A.Watanabe, A.Song, S.Robinson-McCarthy, L.R.Le Sage, V.Kuraoka, M.Moseman, E.A.Kelsoe, G.Takahashi, Y.McCarthy, K.R.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2023.12.13.571543
  • Primary Citation of Related Structures:  
    8US0

  • PubMed Abstract: 

    Influenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal influenza infection in mice. Antibody isotypes that direct clearance of infected cells enhance this protection. Head-stem interface antibodies bind to most influenza A serotypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to "universal" influenza immunity.


  • Organizational Affiliation
    • Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin292Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for M1UPL4 (Influenza A virus)
Explore M1UPL4 
Go to UniProtKB:  M1UPL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1UPL4
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
human antibody S8V1-157 light chain221Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
human antibody S8V1-157 heavy chain231Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
CA [auth c],
S,
T,
U,
AA [auth a],
CA [auth c],
S,
T,
U,
V,
W,
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b],
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
HA [auth M]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
DA [auth A]
EA [auth D]
FA [auth G]
GA [auth J]
IA [auth M]
DA [auth A],
EA [auth D],
FA [auth G],
GA [auth J],
IA [auth M],
JA [auth P]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.293 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.92α = 90
b = 241.54β = 101.619
c = 144.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2P01AI089618-11A1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references