9DIO

Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/Texas/37/2024 (H5N1) with LSTc

PDB DOI: https://doi.org/10.2210/pdb9DIO/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): Yes

Deposited: 2024-09-05 Released: 2024-12-04
Deposition Author(s): Lin, T.H., Zhu, Y., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256
R-Value Work: 0.216
R-Value Observed: 0.218

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors

Lin, T.H., Zhu, X., Wang, W., Zhang, D., McBride, R., Yu, W., Babarinde, S., Paulson, J.C., Wilson, I.A.

(2024) Science

DOI: https://doi.org/10.1126/science.adt0180

Macromolecule Content

Total Structure Weight: 524.09 kDa
Atom Count: 36,829
Modelled Residue Count: 4,477
Deposited Residue Count: 4,509
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, E, G, I A, C, E, G, I, K, M, O, Q	325	Influenza A virus	Mutation(s): 1 Gene Names: HA
UniProt
Find proteins for A0A8E4ZAK5 (Influenza A virus) Explore A0A8E4ZAK5 Go to UniProtKB: A0A8E4ZAK5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8E4ZAK5
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 Focus chain Q
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, F, H, J B, D, F, H, J, L, N, P, R	176	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A6B7HQ27 (Influenza A virus) Explore A0A6B7HQ27 Go to UniProtKB: A0A6B7HQ27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6B7HQ27
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain J Focus chain P
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	DA [auth d], S, W	4		N/A	Interactions Focus chain DA [auth d] Focus chain S Focus chain W Interactions & Density Focus chain DA [auth d] Focus chain S Focus chain W

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	T	2		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], FA [auth f], U, V, BA [auth b], CA [auth c], FA [auth f], U, V, X, Z	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain FA [auth f] Focus chain U Focus chain V Focus chain X Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain FA [auth f] Focus chain U Focus chain V Focus chain X Focus chain Z

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Y	3		N/A	Interactions Focus chain Y Interactions & Density Focus chain Y

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	AA [auth a]	5		N/A	Interactions Focus chain AA [auth a] Interactions & Density Focus chain AA [auth a]

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	EA [auth e]	4		N/A	Interactions Focus chain EA [auth e] Interactions & Density Focus chain EA [auth e]

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth B] SDF format, chain JA [auth C] SDF format, chain KA [auth E] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain NA [auth I] SDF format, chain OA [auth I] SDF format, chain PA [auth K] SDF format, chain QA [auth M] SDF format, chain RA [auth M] SDF format, chain SA [auth O] SDF format, chain TA [auth O] SDF format, chain UA [auth P] SDF format, chain VA [auth Q] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth I] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth K] MOL2 format, chain QA [auth M] MOL2 format, chain RA [auth M] MOL2 format, chain SA [auth O] MOL2 format, chain TA [auth O] MOL2 format, chain UA [auth P] MOL2 format, chain VA [auth Q] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth I] mmCIF format, chain OA [auth I] mmCIF format, chain PA [auth K] mmCIF format, chain QA [auth M] mmCIF format, chain RA [auth M] mmCIF format, chain SA [auth O] mmCIF format, chain TA [auth O] mmCIF format, chain UA [auth P] mmCIF format, chain VA [auth Q]	GA [auth A] HA [auth A] IA [auth B] JA [auth C] KA [auth E] GA [auth A], HA [auth A], IA [auth B], JA [auth C], KA [auth E], LA [auth G], MA [auth G], NA [auth I], OA [auth I], PA [auth K], QA [auth M], RA [auth M], SA [auth O], TA [auth O], UA [auth P], VA [auth Q]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth B] Focus chain JA [auth C] Focus chain KA [auth E] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain PA [auth K] Focus chain QA [auth M] Focus chain RA [auth M] Focus chain SA [auth O] Focus chain TA [auth O] Focus chain UA [auth P] Focus chain VA [auth Q] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth B] Focus chain JA [auth C] Focus chain KA [auth E] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain PA [auth K] Focus chain QA [auth M] Focus chain RA [auth M] Focus chain SA [auth O] Focus chain TA [auth O] Focus chain UA [auth P] Focus chain VA [auth Q]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046 Query on PRD_900046	Y	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component		Interactions Focus chain Y Interactions & Density Focus chain Y

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256
R-Value Work: 0.216
R-Value Observed: 0.218
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 254.381	α = 90
b = 214.467	β = 115.08
c = 136.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Lin, T.H.

Zhu, Y.

Wilson, I.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93021C00015

Revision History (Full details and data files)

Version 1.0: 2024-12-04
Type: Initial release
Version 1.1: 2024-12-11
Changes: Structure summary

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Help and Resources

9DIO

Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/Texas/37/2024 (H5N1) with LSTc

A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

Entity ID: 4

Entity ID: 5

Entity ID: 6

Entity ID: 7