4K64 | pdb_00004k64

Structure of an avian influenza H5 hemagglutinin from the influenza virus complexed with human receptor analog LSTc

PDB DOI: https://doi.org/10.2210/pdb4K64/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Indonesia/5/2005(H5N1))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2013-04-15 Released: 2013-05-22
Deposition Author(s): Zhang, W., Shi, Y., Lu, X., Shu, Y., Qi, J., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.280 (Depositor), 0.273 (DCC)
R-Value Work:
0.221 (Depositor), 0.216 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

An airborne transmissible avian influenza H5 hemagglutinin seen at the atomic level.

Zhang, W., Shi, Y., Lu, X., Shu, Y., Qi, J., Gao, G.F.

(2013) Science 340: 1463-1467

PubMed: 23641058 Search on PubMed
DOI: https://doi.org/10.1126/science.1236787
Primary Citation Related Structures:
4K62, 4K63, 4K64, 4K65, 4K66, 4K67

PubMed Abstract:
Recent studies have identified several mutations in the hemagglutinin (HA) protein that allow the highly pathogenic avian H5N1 influenza A virus to transmit between mammals by airborne route. Here, we determined the complex structures of wild-type and mutant HAs derived from an Indonesia H5N1 virus bound to either avian or human receptor sialic acid analogs. A cis/trans conformational change in the glycosidic linkage of the receptor analog was observed, which explains how the H5N1 virus alters its receptor-binding preference. Furthermore, the mutant HA possessed low affinities for both avian and human receptors. Our findings provide a structural and biophysical basis for the H5N1 adaptation to acquire human, but maintain avian, receptor-binding properties.

Organizational Affiliation

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content

Total Structure Weight: 222.25 kDa
Atom Count: 15,829
Modeled Residue Count: 1,940
Deposited Residue Count: 1,940
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	321	Influenza A virus (A/Indonesia/5/2005(H5N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A8HWY8 (Influenza A virus) Explore A8HWY8 Go to UniProtKB: A8HWY8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8HWY8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C Focus chain E Focus chain G
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F, H	164	Influenza A virus (A/Indonesia/5/2005(H5N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A8HWY8 (Influenza A virus) Explore A8HWY8 Go to UniProtKB: A8HWY8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8HWY8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose	I, J	2		N/A	Interactions Focus chain I Focus chain J Interactions & Density Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G63069TR GlyCosmos: G63069TR GlyGen: G63069TR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth C] SDF format, chain M [auth E] SDF format, chain N [auth G] MOL2 format, chain K [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth E] MOL2 format, chain N [auth G] mmCIF format, chain K [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth E] mmCIF format, chain N [auth G]	K [auth A], L [auth C], M [auth E], N [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth C] Focus chain M [auth E] Focus chain N [auth G] Interactions & Density Focus chain K [auth A] Focus chain L [auth C] Focus chain M [auth E] Focus chain N [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.280 (Depositor), 0.273 (DCC)
R-Value Work: 0.221 (Depositor), 0.216 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.336	α = 90
b = 70.336	β = 90
c = 491.793	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-22
Type: Initial release
Version 1.1: 2013-05-29
Changes: Refinement description
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: 2022-08-24
Changes: Database references, Structure summary
Version 2.2: 2023-11-08
Changes: Data collection, Refinement description
Version 2.3: 2024-10-30
Changes: Structure summary