Skip to main content

 9EI9 | pdb_00009ei9

Cryo-EM structure of 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9EI9

This is version 1.2 of the entry. See complete history. 

Literature

The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody.

Rawi, R., Morano, N.C., Cheung, C.S., Du, H., Gorman, J., Prabhakaran, M., Becker, J.E., Bylund, T., Charaf, S., Chen, X., Lee, M., Harris, D.R., Olia, A.S., Ou, L., Wang, L., Wang, S., Zhang, B., Kanekiyo, M., McDermott, A.B., Zhou, T., Shapiro, L., Kwong, P.D.

(2025) Structure 33: 1820

  • DOI: https://doi.org/10.1016/j.str.2025.07.015
  • Primary Citation Related Structures: 
    9E69, 9EI8, 9EI9

  • PubMed Abstract: 

    The N terminus of the H3 subtype of influenza virus hemagglutinin is ∼10 residues longer than the N termini of most other hemagglutinins. As conserved, exposed, and linear regions may be good vaccine targets, we investigated the vaccine utility of the extended H3-N terminus. First, we identified antibody 5E10, for which structure and binding analyses revealed recognition of the H3-N terminus. Second, we immunized mice with immunogens incorporating the H3-N terminus, boosted with hemagglutinin trimer, and isolated antibodies from immunogen-elicited B cells that bound both H3-N terminus and hemagglutinin trimer. However, hemagglutinin-complex structures of two such antibodies, 3864-6 and 3864-10, that neutralized H3-influenza strains, revealed only peripheral recognition of the hemagglutinin N terminus. Collectively, these results reveal the N terminus of H3 hemagglutinin to be a suboptimal vaccine target and suggest that-in addition to being conserved, flexible, and accessible-other factors influence the elicitation of potent broadly neutralizing responses.


  • Organizational Affiliation: 
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: reda.rawi@nih.gov.

Macromolecule Content 

  • Total Structure Weight: 246.38 kDa 
  • Atom Count: 14,564 
  • Modeled Residue Count: 1,954 
  • Deposited Residue Count: 2,136 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1A [auth B],
B [auth C],
E [auth G]
334Influenza A virus (A/Victoria/361/2011(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A5P1MU07 (Influenza A virus)
Explore A0A5P1MU07 
Go to UniProtKB:  A0A5P1MU07
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P1MU07
Glycosylation
Glycosylation Sites: 8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2C [auth E],
D [auth F],
F [auth I]
222Influenza A virus (A/Victoria/361/2011(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A3G2CC79 (Influenza A virus)
Explore A0A3G2CC79 
Go to UniProtKB:  A0A3G2CC79
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G2CC79
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
5E10 Fab Heavy chainG [auth A],
I [auth H]
123Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
5E10 Fab Light chainH [auth D],
J
111Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, M, N, P
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
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
L, O, Q
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth E]
DA [auth F]
EA [auth G]
AA [auth C],
BA [auth C],
CA [auth E],
DA [auth F],
EA [auth G],
FA [auth G],
GA [auth G],
HA [auth G],
IA [auth G],
JA [auth G],
KA [auth I],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Simons FoundationUnited StatesSF349247

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references
  • Version 1.2: 2025-11-19
    Changes: Data collection, Database references