4WE6 | pdb_00004we6

The crystal structure of hemagglutinin HA1 domain from influenza virus A/Perth/142/2007(H3N2)

PDB DOI: https://doi.org/10.2210/pdb4WE6/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Perth/142/2007(H3N2))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2014-09-09 Released: 2015-02-11
Deposition Author(s): Yang, H., Carney, P.J., Chang, J.C., Guo, Z., Villanueva, J.M., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.201 (Depositor), 0.202 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins.

Yang, H., Carney, P.J., Chang, J.C., Guo, Z., Villanueva, J.M., Stevens, J.

(2015) Virology 477C: 18-31

PubMed: 25617824 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.virol.2014.12.024
Primary Citation Related Structures:
4WE4, 4WE5, 4WE6, 4WE7, 4WE8, 4WE9, 4WEA

PubMed Abstract:
A(H3N2) influenza viruses have circulated in humans since 1968, and antigenic drift of the hemagglutinin (HA) protein continues to be a driving force that allows the virus to escape the human immune response. Since the major antigenic sites of the HA overlap into the receptor binding site (RBS) of the molecule, the virus constantly struggles to effectively adapt to host immune responses, without compromising its functionality. Here, we have structurally assessed the evolution of the A(H3N2) virus HA RBS, using an established recombinant expression system. Glycan binding specificities of nineteen A(H3N2) influenza virus HAs, each a component of the seasonal influenza vaccine between 1968 and 2012, were analyzed. Results suggest that while its receptor-binding site has evolved from one that can bind a broad range of human receptor analogs to one with a more restricted binding profile for longer glycans, the virus continues to circulate and transmit efficiently among humans.

Organizational Affiliation

Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.

Macromolecule Content

Total Structure Weight: 63.62 kDa
Atom Count: 4,954
Modeled Residue Count: 546
Deposited Residue Count: 558
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, B	279	Influenza A virus (A/Perth/142/2007(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for B2VNP1 (Influenza A virus) Explore B2VNP1 Go to UniProtKB: B2VNP1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2VNP1
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	E [auth A], F [auth A], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.201 (Depositor), 0.202 (DCC)
R-Value Work: 0.170 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.472	α = 90
b = 50.567	β = 90.08
c = 182.256	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-02-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-11
Type: Initial release
Version 1.1: 2017-09-27
Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Structure summary
Version 1.4: 2024-10-30
Changes: Structure summary