4N61

Crystal structure of hemagglutinin from an H7N9 influenza virus in complex with LSTa, extended soaking

PDB DOI: https://doi.org/10.2210/pdb4N61/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Shanghai/02/2013(H7N9))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2013-10-11 Released: 2013-12-18
Deposition Author(s): Xu, R., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 ?
R-Value Free: 0.262
R-Value Work: 0.216
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Preferential recognition of avian-like receptors in human influenza A H7N9 viruses.

Xu, R., de Vries, R.P., Zhu, X., Nycholat, C.M., McBride, R., Yu, W., Paulson, J.C., Wilson, I.A.

(2013) Science 342: 1230-1235

PubMed: 24311689 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1243761
Primary Citation of Related Structures:
4N5J, 4N5K, 4N60, 4N61, 4N62, 4N63, 4N64

PubMed Abstract:
The 2013 outbreak of avian-origin H7N9 influenza in eastern China has raised concerns about its ability to transmit in the human population. The hemagglutinin glycoprotein of most human H7N9 viruses carries Leu(226), a residue linked to adaptation of H2N2 and H3N2 pandemic viruses to human receptors. However, glycan array analysis of the H7 hemagglutinin reveals negligible binding to humanlike α2-6-linked receptors and strong preference for a subset of avian-like α2-3-linked glycans recognized by all avian H7 viruses. Crystal structures of H7N9 hemagglutinin and six hemagglutinin-glycan complexes have elucidated the structural basis for preferential recognition of avian-like receptors. These findings suggest that the current human H7N9 viruses are poorly adapted for efficient human-to-human transmission.

Organizational Affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 112.95 kDa
Atom Count: 7,760
Modelled Residue Count: 974
Deposited Residue Count: 1,000
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C	321	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0 Gene Names: HA, hemagglutinin
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21 Go to UniProtKB: R4NN21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R4NN21
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D	179	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0 Gene Names: HA, hemagglutinin
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21 Go to UniProtKB: R4NN21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R4NN21
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	F	2		N/A	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G30207PZ GlyCosmos: G30207PZ GlyGen: G30207PZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 ?
R-Value Free: 0.262
R-Value Work: 0.216
R-Value Observed: 0.218
Space Group: P 2₁ 3

Unit Cell:

Length ( ? )	Angle ( ? )
a = 153.913	α = 90
b = 153.913	β = 90
c = 153.913	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-12-18

Deposition Author(s):

Xu, R.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2013-12-18
Type: Initial release
Version 1.1: 2017-11-15
Changes: Advisory, 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: 2024-10-30
Changes: Data collection, Database references, Structure summary