2FK0 | pdb_00002fk0

Crystal Structure of a H5N1 influenza virus hemagglutinin.

PDB DOI: https://doi.org/10.2210/pdb2FK0/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2006-01-03 Released: 2006-05-02
Deposition Author(s): Stevens, J., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.319 (Depositor), 0.314 (DCC)
R-Value Work:
0.268 (Depositor), 0.266 (DCC)
R-Value Observed:
0.269 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structure and Receptor Specificity of the Hemagglutinin from an H5N1 Influenza Virus.

Stevens, J., Blixt, O., Tumpey, T.M., Taubenberger, J.K., Paulson, J.C., Wilson, I.A.

(2006) Science 312: 404-410

PubMed: 16543414 Search on PubMed
DOI: https://doi.org/10.1126/science.1124513
Primary Citation Related Structures:
2FK0

PubMed Abstract:
The hemagglutinin (HA) structure at 2.9 angstrom resolution, from a highly pathogenic Vietnamese H5N1 influenza virus, is more related to the 1918 and other human H1 HAs than to a 1997 duck H5 HA. Glycan microarray analysis of this Viet04 HA reveals an avian alpha2-3 sialic acid receptor binding preference. Introduction of mutations that can convert H1 serotype HAs to human alpha2-6 receptor specificity only enhanced or reduced affinity for avian-type receptors. However, mutations that can convert avian H2 and H3 HAs to human receptor specificity, when inserted onto the Viet04 H5 HA framework, permitted binding to a natural human alpha2-6 glycan, which suggests a path for this H5N1 virus to gain a foothold in the human population.

Organizational Affiliation

Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. jstevens@scripps.edu

Macromolecule Content

Total Structure Weight: 536.74 kDa
Atom Count: 36,202
Modeled Residue Count: 4,473
Deposited Residue Count: 4,635
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemagglutinin	A, C, E, G, I A, C, E, G, I, K, M, O, Q	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for Q1KHJ8 (Influenza A virus) Explore Q1KHJ8 Go to UniProtKB: Q1KHJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1KHJ8
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C Focus chain E Focus chain G Focus chain I Focus chain K Focus chain M Focus chain O
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hemagglutinin	B, D, F, H, J B, D, F, H, J, L, N, P, R	181	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for Q1KHG8 (Influenza A virus) Explore Q1KHG8 Go to UniProtKB: Q1KHG8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1KHG8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], S, U, V, W, Y	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain S Focus chain U Focus chain V Focus chain W Focus chain Y Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain S Focus chain U Focus chain V Focus chain W Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	T, X, Z	3		N-Glycosylation	Interactions Focus chain T Focus chain X Focus chain Z Interactions & Density Focus chain T Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.319 (Depositor), 0.314 (DCC)
R-Value Work: 0.268 (Depositor), 0.266 (DCC)
R-Value Observed: 0.269 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.943	α = 90
b = 197.943	β = 90
c = 134.688	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-05-02

Deposition Author(s):

Stevens, J.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2006-05-02
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary