Reference Tables for Influenza HA and NA Antigenic Sites

tutorial
Author
Affiliation

Elgin Akin

Johns Hopkins University

Published

November 11, 2025

Overview

This page compiles reference structures, strains, numbering schema anchors, and antigenic site definitions for influenza hemagglutinin (HA) and neuraminidase (NA). The goal is to provide a standardized reference page that is easy to use for annotation.

For each protein, the tables below report:

  • Type/subtype
  • PDB reference structure
  • Reference strain
  • Starting motif or head-domain start
  • Antigenic site name
  • Epitope type
  • Residue ranges or positions
  • Reference source

Influenza B HA

Reference information

Type / subtype PDB reference structure Reference strain Starting motif Numbering schema note
Influenza B HA 4FQM B/Brisbane/60/2008 Influenza Hemagglutinin DRICT D = residue #1 in the numbering schema

Antigenic sites

Type / subtype Site Epitope type Residue(s) Reference
Influenza B HA 120 loop Linear 116–137 Wang et al., 2018; Burton et al., 1985
Influenza B HA 150 loop Linear 142–149 Wang et al., 2018; Burton et al., 1985
Influenza B HA 160 loop Linear 161–170 Wang et al., 2018; Burton et al., 1985
Influenza B HA 190 helix Linear 194–202 Wang et al., 2018; Burton et al., 1985
Influenza B HA 240 loop Linear 235–240 Wang et al., 2018

Influenza A H1 HA

Reference information

Type / subtype PDB reference structure Reference strain Starting motif Numbering schema note
Influenza A H1 HA 3LZG A/California/04/2009 DTLC D = residue #1 in the numbering schema

Antigenic sites

Type / subtype Site Epitope type Residue(s) Reference
Influenza A H1 HA Sa Conformational 124–125, 153–157, 159–164 —
Influenza A H1 HA Sb Conformational 184–195 —
Influenza A H1 HA Ca1 Conformational 166–170, 203–205, 235–237 —
Influenza A H1 HA Ca2 Conformational 137–142, 221–222 —
Influenza A H1 HA Cb Conformational 70–75 —

Influenza A H3 HA

Reference information

Type / subtype PDB reference structure Reference strain Starting motif Numbering schema note
Influenza A H3 HA 4O5N A/Victoria/361/2011 QDLP Q = residue #1 in the numbering schema

Antigenic sites

Type / subtype Site Epitope type Residue(s) Reference
Influenza A H3 HA A Linear 122–146 Palese et al., 2018
Influenza A H3 HA B Conformational 155–160, 186–198 Palese et al., 2018
Influenza A H3 HA C Conformational 44–54, 273–280 Palese et al., 2018
Influenza A H3 HA D Linear 201–219 Palese et al., 2018
Influenza A H3 HA E Conformational 62–65, 78–94, 260–265 Palese et al., 2018
Influenza A H3 HA RBD Conformational 190-helix: 183–196; 220-loop: 219–228; 130-loop: 131–140; extra: 98, 144–146, 153–159 Palese et al., 2018

Influenza A N1 NA

Reference information

Type / subtype PDB reference structure Reference strain Head domain start Numbering schema note
Influenza A N1 NA 9CYE A/California/07/2009 (A/H1N1pdm09-like), GenBank: ACQ63272.1 Position 85 May differ for nonhuman N1s

Antigenic sites

Type / subtype Site Epitope type Residue(s) (N1 numbering) Reference
Influenza A N1 NA Active site Conformational 118, 119, 151, 152, 222, 224, 276, 277, 371, 406 Stadlbauer et al., 2020
Influenza A N1 NA Family I Linear 328–335 Colman, Varghese, & Laver, 1983
Influenza A N1 NA Family II Linear 336–344 Colman, Varghese, & Laver, 1983
Influenza A N1 NA Family III (aka 370 loop) Linear 364–367 Colman, Varghese, & Laver, 1983
Influenza A N1 NA Family IV (aka 400 loop) Linear 396–399 Colman, Varghese, & Laver, 1983
Influenza A N1 NA Family V (aka 430 loop) Linear 431–434 Colman, Varghese, & Laver, 1983
Influenza A N1 NA Family VI Linear 198–200 Colman, Varghese, & Laver, 1983
Influenza A N1 NA Family VII Single residue 153 Colman, Varghese, & Laver, 1983

Influenza A N2 NA

Reference information

Type / subtype PDB reference structure Reference strain Head domain start Numbering schema note
Influenza A N2 NA 8G40 A/Hong Kong/2671/2019 (A/H3N2-like), GenBank: WMW30926.1 Position 83 May differ for nonhuman N2s

Antigenic sites

Type / subtype Site Epitope type Residue(s) (N2 numbering) Reference
Influenza A N2 NA Active site Conformational 118, 119, 151, 152, 222, 224, 276, 277, 371, 406 Stadlbauer et al., 2020
Influenza A N2 NA Family I Linear 328–336 Colman, Varghese, & Laver, 1983
Influenza A N2 NA Family II Linear 339–347 Colman, Varghese, & Laver, 1983
Influenza A N2 NA Family III (aka 370 loop) Linear 367–370 Colman, Varghese, & Laver, 1983
Influenza A N2 NA Family IV (aka 400 loop) Linear 400–403 Colman, Varghese, & Laver, 1983
Influenza A N2 NA Family V (aka 430 loop) Linear 431–434 Colman, Varghese, & Laver, 1983
Influenza A N2 NA Family VI Linear 197–199 Colman, Varghese, & Laver, 1983
Influenza A N2 NA Family VII Single residue 153 Colman, Varghese, & Laver, 1983