8TP2 | pdb_00008tp2

H2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeting 1-1-1F05


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8TP2

This is version 1.4 of the entry. See complete history

Literature

Immune memory shapes human polyclonal antibody responses to H2N2 vaccination.

Yang, Y.R.Han, J.Perrett, H.R.Richey, S.T.Rodriguez, A.J.Jackson, A.M.Gillespie, R.A.O'Connell, S.Raab, J.E.Cominsky, L.Y.Chopde, A.Kanekiyo, M.Houser, K.V.Chen, G.L.McDermott, A.B.Andrews, S.F.Ward, A.B.

(2024) Cell Rep 43: 114171-114171

  • DOI: https://doi.org/10.1016/j.celrep.2024.114171
  • Primary Citation Related Structures: 
    8TP2, 8TP3, 8TP4, 8TP5, 8TP6, 8TP7, 8TP9, 8TPA

  • PubMed Abstract: 

    Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase 1 clinical trial investigating a ferritin nanoparticle vaccine displaying H2 hemagglutinin (HA) in H2-naive and H2-exposed adults enabled us to perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited. We temporally map the epitopes targeted by serum antibodies after vaccine prime and boost, revealing that previous H2 exposure results in higher responses to the variable HA head domain. In contrast, initial responses in H2-naive participants are dominated by antibodies targeting conserved epitopes. We use cryoelectron microscopy and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the HA head, including the receptor-binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses post-vaccination.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Chinese Academy of Sciences Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.

Macromolecule Content 

  • Total Structure Weight: 200.47 kDa 
  • Atom Count: 13,485 
  • Modeled Residue Count: 1,678 
  • Deposited Residue Count: 1,751 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of Fab 1-1-1F05A [auth H]126Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of Fab 1-1-1F05B [auth L]107Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
HemagglutininC,
D [auth A],
E [auth B]
506Homo sapiensMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q67333 (Influenza A virus (strain A/Singapore/1/1957 H2N2))
Explore Q67333 
Go to UniProtKB:  Q67333
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ67333
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D],
G [auth E],
H [auth F]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
I [auth C]
J [auth C]
K [auth C]
L [auth C]
M [auth A]
I [auth C],
J [auth C],
K [auth C],
L [auth C],
M [auth A],
N [auth A],
O [auth A],
P [auth B],
Q [auth B],
R [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: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2 T32 AI007244-36
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1F31Al172358

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-02-19
    Changes: Data collection, Database references
  • Version 1.3: 2025-02-26
    Changes: Data collection, Database references
  • Version 1.4: 2025-05-14
    Changes: Data collection