Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin.


Abstract

Influenza A virus hemagglutinin (HA) initiates viral entry by engaging host receptor sialylated glycans via its receptor-binding site (RBS). The amino acid sequence of the RBS naturally varies across avian and human influenza virus subtypes and is also evolvable. However, functional sequence diversity in the RBS has not been fully explored. Here, we performed a large-scale mutational analysis of the RBS of A/WSN/33 (H1N1) and A/Hong Kong/1/1968 (H3N2) HAs. Many replication-competent mutants not yet observed in nature were identified, including some that could escape from an RBS-targeted broadly neutralizing antibody. This functional sequence diversity is made possible by pervasive epistasis in the RBS 220-loop and can be buffered by avidity in viral receptor binding. Overall, our study reveals that the HA RBS can accommodate a much greater range of sequence diversity than previously thought, which has significant implications for the complex evolutionary interrelationships between receptor specificity and immune escape.

Submission Details

ID: aSy5yPFi

Submitter: Marie Ary

Submission Date: Jan. 22, 2018, 11:29 a.m.

Version: 1

Publication Details
Wu NC;Xie J;Zheng T;Nycholat CM;Grande G;Paulson JC;Lerner RA;Wilson IA,Cell Host Microbe (2017) Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin. PMID:28618270
Additional Information

Study Summary

Number of data points 20882
Proteins Hemagglutinin A/HK68 ; Hemagglutinin A/WSN/33
Unique complexes 18725
Assays/Quantities/Protocols Experimental Assay: log10 TCID50, HK68 mutants ; Experimental Assay: HA RBS function by RF index, WSN ; Experimental Assay: Kd S139/1 IgG ; Experimental Assay: Kd1 3'-SLNLN ; Experimental Assay: HA RBS function by RF index, HK68 ; Experimental Assay: log2 HA titer, WSN mutants ; Experimental Assay: log10 TCID50, WSN mutants ; Experimental Assay: Kd1 6'-SLNLN ; Experimental Assay: Kd2 6'-SLNLN ; Experimental Assay: log2 HA titer, HK68 mutants ; Experimental Assay: Kd C05 IgG ; Experimental Assay: Kd2 3'-SLNLN ; Experimental Assay: koff1 3'-SLNLN ; Experimental Assay: koff2 3'-SLNLN ; Experimental Assay: Kd 3'-SLNLN-PAA ; Experimental Assay: Kd 6'-SLNLN-PAA ; Computational Protocol: R^2 (goodness of fit), 3'-SLNLN binding ; Computational Protocol: R^2 (goodness of fit), 3'-SLNLN-PAA binding ; Computational Protocol: R^2 (goodness of fit), 6'-SLNLN binding ; Computational Protocol: R^2 (goodness of fit), 6'-SLNLN-PAA binding ; Computational Protocol: R^2 (goodness of fit), C05 IgG binding ; Computational Protocol: R^2 (goodness of fit), S139/1 IgG binding
Libraries Kds of HK68 HA WT and escape mutant for binding to bnAb S139/1 IgG (Figure S4, B-C) ; Off-rates of glycan 3'-SLNLN with WSN recombinant HA variants (Table S4_WSN) ; Kds for binding polymerized glycoconjugates (3'-SLNLN-PAA and 6'-SLNLN-PAA) to HK68 HA variants (Table S5_HK68) ; Kds for binding of glycans 3'-SLNLN and 6'-SLNLN to HK68 HA variants (Table S3_HK68) ; Kds for binding of glycans 3'-SLNLN and 6'-SLNLN to WSN HA variants (Table S3_WSN) ; Kds for binding of bnAbs C05 IgG and S139/1 IgG to WSN HA variants (Table S1) ; Validation of HK68 deep scan data by virus rescue and hemagglutination assays (log10 TCID50, log2 HA Titer) (Data S1_HK68) ; Validation of WSN deep scan data by virus rescue and hemagglutination assays (log10 TCID50, log2 HA Titer) (Data S1_WSN) ; Relative fitness index for single, double, and triple mutants in HK68 HA 220 loop (residues 225, 226, 228) by deep mutational scanning (Data S2_HK68) ; Relative fitness index for single, double, and triple mutants in WSN HA RBS (11 residues) by deep mutational scanning (Data S2)

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1R5I 2003-10-10T00:00:00+0000 2.6 Crystal structure of the MAM-MHC complex
2DCI 2006-01-07T00:00:00+0000 0 NMR structure of influenza HA fusion peptide mutant W14A in DPC in pH5
1DLH 1994-02-15T00:00:00+0000 2.8 CRYSTAL STRUCTURE OF THE HUMAN CLASS II MHC PROTEIN HLA-DR1 COMPLEXED WITH AN INFLUENZA VIRUS PEPTIDE
1HXY 2001-01-17T00:00:00+0000 2.6 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN H IN COMPLEX WITH HUMAN MHC CLASS II
2G9H 2006-03-06T00:00:00+0000 2.0 Crystal Structure of Staphylococcal Enterotoxin I (SEI) in Complex with a Human MHC class II Molecule
2XN9 2010-07-31T00:00:00+0000 2.3 Crystal structure of the ternary complex between human T cell receptor, staphylococcal enterotoxin H and human major histocompatibility complex class II
4WE5 2014-09-09T00:00:00+0000 2.1 The crystal structure of hemagglutinin from A/Port Chalmers/1/1973 influenza virus
4WE5 2014-09-09T00:00:00+0000 2.1 The crystal structure of hemagglutinin from A/Port Chalmers/1/1973 influenza virus
5T6N 2016-09-01T00:00:00+0000 2.54 Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in complex with the antiviral drug arbidol
6BKM 2017-11-09T00:00:00+0000 2.2 Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D mutant apo form

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.5 Hemagglutinin A/HK68 P03440 HEMA_I77A8
90.9 Hemagglutinin A/HK68 P26141 HEMA_I84A5
91.8 Hemagglutinin A/HK68 Q2VNF2 HEMA_I78A7
91.8 Hemagglutinin A/HK68 Q2VND2 HEMA_I78A8
91.8 Hemagglutinin A/HK68 Q03909 HEMA_I89A7
92.2 Hemagglutinin A/HK68 P26139 HEMA_I77A4
92.5 Hemagglutinin A/HK68 Q30NQ1 HEMA_I75A0
92.5 Hemagglutinin A/HK68 Q2RFA5 HEMA_I76A6
93.7 Hemagglutinin A/HK68 P03435 HEMA_I75A3
95.0 Hemagglutinin A/HK68 P43259 HEMA_I77A7
95.3 Hemagglutinin A/HK68 P12586 HEMA_I82A6
95.6 Hemagglutinin A/HK68 P03442 HEMA_I63A3
95.0 Hemagglutinin A/HK68 P26138 HEMA_I78A4
95.9 Hemagglutinin A/HK68 P43260 HEMA_I76AC
95.6 Hemagglutinin A/HK68 P26135 HEMA_I74A2
95.6 Hemagglutinin A/HK68 P11133 HEMA_I78A9
95.9 Hemagglutinin A/HK68 P26134 HEMA_I76A3
95.6 Hemagglutinin A/HK68 P43257 HEMA_I75A2
96.2 Hemagglutinin A/HK68 Q1PUD9 HEMA_I73A5
96.2 Hemagglutinin A/HK68 P43258 HEMA_I76AD
95.9 Hemagglutinin A/HK68 P11134 HEMA_I82A4
96.6 Hemagglutinin A/HK68 P12582 HEMA_I77A6
96.6 Hemagglutinin A/HK68 P12583 HEMA_I80A6
97.2 Hemagglutinin A/HK68 Q2ICR0 HEMA_I72A4
97.2 Hemagglutinin A/HK68 P03439 HEMA_I72A3
97.2 Hemagglutinin A/HK68 P19106 HEMA_I72A2
97.2 Hemagglutinin A/HK68 P12587 HEMA_I85A1
97.2 Hemagglutinin A/HK68 P12584 HEMA_I80A7
97.5 Hemagglutinin A/HK68 P12588 HEMA_I85A2
97.2 Hemagglutinin A/HK68 P12585 HEMA_I82A5
98.7 Hemagglutinin A/HK68 P04663 HEMA_I70A0
98.4 Hemagglutinin A/HK68 P03438 HEMA_I000X
98.7 Hemagglutinin A/HK68 P04664 HEMA_I69A0
99.1 Hemagglutinin A/HK68 P03449 HEMA_I71A1
99.4 Hemagglutinin A/HK68 P03436 HEMA_I68A6
99.7 Hemagglutinin A/HK68 P03437 HEMA_I68A0
100.0 Hemagglutinin A/HK68 Q91MA7 HEMA_I68A4
90.8 Hemagglutinin A/WSN/33 P03452 HEMA_I34A1
91.9 Hemagglutinin A/WSN/33 A4GCI6 HEMA_I36A0
92.8 Hemagglutinin A/WSN/33 A4GCL9 HEMA_I35A3
99.5 Hemagglutinin A/WSN/33 P03454 HEMA_I33A0