6PDX | pdb_00006pdx

Crystal structure of C585 Fab in complex with influenza virus hemagglutinin from A/Switzerland/9715293/2013 (H3N2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.99 Å
  • R-Value Free: 
    0.241 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Mapping of a Novel H3-Specific Broadly Neutralizing Monoclonal Antibody Targeting the Hemagglutinin Globular Head Isolated from an Elite Influenza Virus-Immunized Donor Exhibiting Serological Breadth.

Qiu, Y.Stegalkina, S.Zhang, J.Boudanova, E.Park, A.Zhou, Y.Prabakaran, P.Pougatcheva, S.Ustyugova, I.V.Vogel, T.U.Mundle, S.T.Oomen, R.Delagrave, S.Ross, T.M.Kleanthous, H.Qiu, H.

(2020) J Virol 94

  • DOI: https://doi.org/10.1128/JVI.01035-19
  • Primary Citation Related Structures: 
    6PDX

  • PubMed Abstract: 

    The discovery of potent and broadly protective influenza virus epitopes could lead to improved vaccines that are resistant to antigenic drift. Here, we describe human antibody C585, isolated from a vaccinee with remarkable serological breadth as measured by hemagglutinin inhibition (HAI). C585 binds and neutralizes multiple H3N2 strains isolated between 1968 and 2016, including strains that emerged up to 4 years after B cells were isolated from the vaccinated donor. The crystal structure of C585 Fab in complex with the HA from A/Switzerland/9715293/2013 (H3N2) shows that the antibody binds to a novel and well-conserved epitope on the globular head of H3 HA and that it differs from other antibodies not only in its epitope but in its binding geometry and hypermutated framework 3 region, thereby explaining its breadth and ability to mediate hemagglutination inhibition across decades of H3N2 strains. The existence of epitopes such as the one elucidated by C585 has implications for rational vaccine design. IMPORTANCE Influenza viruses escape immunity through continuous antigenic changes that occur predominantly on the viral hemagglutinin (HA). Induction of broadly neutralizing antibodies (bnAbs) targeting conserved epitopes following vaccination is a goal of universal influenza vaccines and advantageous in protecting hosts against virus evolution and antigenic drift. To date, most of the discovered bnAbs bind either to conserved sites in the stem region or to the sialic acid-binding pocket. Generally, antibodies targeting the stem region offer broader breadth with low potency, while antibodies targeting the sialic acid-binding pocket cover narrower breadth but usually have higher potency. In this study, we identified a novel neutralizing epitope in the head region recognized by a broadly neutralizing human antibody against a broad range of H3N2 with high potency. This epitope may provide insights for future universal vaccine design.


  • Organizational Affiliation
    • Biologics Research, Sanofi, Framingham, Massachusetts, USA Yu.Qiu@sanofi.com harry.kleanthous@gatesfoundation.org.

Macromolecule Content 

  • Total Structure Weight: 324.14 kDa 
  • Atom Count: 20,896 
  • Modeled Residue Count: 2,773 
  • Deposited Residue Count: 2,871 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HemagglutininA,
D [auth B],
G [auth C]
505Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A5J6A331 (Influenza A virus)
Explore A0A5J6A331 
Go to UniProtKB:  A0A5J6A331
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5J6A331
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
C585 Fab heavy chainB [auth H],
E [auth M],
H [auth O]
237Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
C585 Fab light chainC [auth L],
F [auth N],
I [auth P]
215Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J [auth D],
K [auth E],
M [auth G],
N [auth I],
O [auth J],
J [auth D],
K [auth E],
M [auth G],
N [auth I],
O [auth J],
P [auth K],
Q,
R,
U,
W,
X,
Y,
Z
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a],
L [auth F],
S,
T,
V
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
BA [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.99 Å
  • R-Value Free:  0.241 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 287.265α = 90
b = 287.265β = 90
c = 182.933γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2020-03-11
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary