8F38 | pdb_00008f38

Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural basis for the broad antigenicity of the computationally optimized influenza hemagglutinin X6.

Nagashima, K.A.Dzimianski, J.V.Yang, M.Abendroth, J.Sautto, G.A.Ross, T.M.DuBois, R.M.Edwards, T.E.Mousa, J.J.

(2024) Structure 32: 1079

  • DOI: https://doi.org/10.1016/j.str.2024.05.001
  • Primary Citation Related Structures: 
    8F38, 8GHK, 8SJ9, 8V7O

  • PubMed Abstract: 

    Influenza causes significant morbidity and mortality. As an alternative approach to current seasonal vaccines, the computationally optimized broadly reactive antigen (COBRA) platform has been previously applied to hemagglutinin (HA). This approach integrates wild-type HA sequences into a single immunogen to expand the breadth of accessible antibody epitopes. Adding to previous studies of H1, H3, and H5 COBRA HAs, we define the structural features of another H1 subtype COBRA, X6, that incorporates HA sequences from before and after the 2009 H1N1 influenza pandemic. We determined structures of this antigen alone and in complex with COBRA-specific as well as broadly reactive and functional antibodies, analyzing its antigenicity. We found that X6 possesses features representing both historic and recent H1 HA strains, enabling binding to both head- and stem-reactive antibodies. Overall, these data confirm the integrity of broadly reactive antibody epitopes of X6 and contribute to design efforts for a next-generation vaccine.


  • Organizational Affiliation
    • Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA; Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.

Macromolecule Content 

  • Total Structure Weight: 340.73 kDa 
  • Atom Count: 16,952 
  • Modeled Residue Count: 2,121 
  • Deposited Residue Count: 3,054 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CR6261 Fab light chainA [auth G],
H,
I
221Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CR6261 Fab heavy chainB [auth D],
C [auth E],
D [auth F]
232Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
hemagglutininE [auth A],
F [auth B],
G [auth C]
565synthetic constructMutation(s): 0 
UniProt
Find proteins for Q289M7 (Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1))
Explore Q289M7 
Go to UniProtKB:  Q289M7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ289M7
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
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Reference Sequence

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-glucopyranoseJ [auth K],
L,
N
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-glucopyranoseK [auth J],
M,
O
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
AA [auth B]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth B],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.2.0
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700059C

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary