9dio

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

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemagglutinin HA1

Influenza A virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 其他Polymer 6	Hemagglutinin HA2 × 3 （A0A6B7HQ27） ;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 6	Consistent with protein count
2	Other combination	Heteromer	Protein 6 其他Polymer 5	Hemagglutinin HA2 × 3 （A0A6B7HQ27） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 6	Consistent with protein count
3	Other combination	Heteromer	Protein 6 其他Polymer 3	Hemagglutinin HA2 × 3 （A0A6B7HQ27） ;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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8E4ZAK5_9INFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–325； UniProt 17–337 Author chain C； PDBConstruct 5–325； UniProt 17–337 Author chain E； PDBConstruct 5–325； UniProt 17–337 Author chain G； PDBConstruct 5–325； UniProt 17–337 Author chain I； PDBConstruct 5–325； UniProt 17–337 Author chain K； PDBConstruct 5–325； UniProt 17–337 Author chain M； PDBConstruct 5–325； UniProt 17–337 Author chain O； PDBConstruct 5–325； UniProt 17–337 Author chain Q； PDBConstruct 5–325； UniProt 17–337

Hemagglutinin HA2

Influenza A virus

UniProt A0A6B7HQ27

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 其他Polymer 6	Hemagglutinin HA1 × 3 （A0A8E4ZAK5） ;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 6	Consistent with protein count
2	Other combination	Heteromer	Protein 6 其他Polymer 5	Hemagglutinin HA1 × 3 （A0A8E4ZAK5） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 6	Consistent with protein count
3	Other combination	Heteromer	Protein 6 其他Polymer 3	Hemagglutinin HA1 × 3 （A0A8E4ZAK5） ;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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6B7HQ27_9INFA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–174； UniProt 330–503 Author chain D； PDBConstruct 1–174； UniProt 330–503 Author chain F； PDBConstruct 1–174； UniProt 330–503 Author chain H； PDBConstruct 1–174； UniProt 330–503 Author chain J； PDBConstruct 1–174； UniProt 330–503 Author chain L； PDBConstruct 1–174； UniProt 330–503 Author chain N； PDBConstruct 1–174； UniProt 330–503 Author chain P； PDBConstruct 1–174； UniProt 330–503 Author chain R； PDBConstruct 1–174； UniProt 330–503

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9dio
Deposition date deposition_date	2024-09-05
Structure title title	Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/Texas/37/2024 (H5N1) with LSTc
Keywords keywords	H1N1, Antibody, Hemagglutinin, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9dio__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9dio__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dio__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	42.80 Å
Rg (electron density)	42.47 Å
Total Rg	42.50 Å
Atom count	12190
Residues	1491
Excluded volume	215020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dio__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9dio__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9dio__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin HA1
Molecular weight formula_weight	36520.4 kDa
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O,Q
Atom count atom_count	36829

ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKIQIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGLRGRMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSP

Source Source

Source organism organism	Influenza A virus
NCBI taxonomy ID ncbi_taxonomy_id	11320
Host organism host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 2 Entity 2 polymer

Description description	Hemagglutinin HA2
Molecular weight formula_weight	20257.3 kDa
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P,R

GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSG

Source Source

Source organism organism	Influenza A virus
NCBI taxonomy ID ncbi_taxonomy_id	11320
Host organism host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 3 Entity 3 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose ;
Molecular weight formula_weight	836.7 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	7

Entity 6 Entity 6 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	674.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 branched

Description description	;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 ;
Molecular weight formula_weight	998.9 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose ;
Molecular weight formula_weight	836.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	265

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Unit-cell length a length_a	254.381 Å
Unit-cell length b length_b	214.467 Å
Unit-cell length c length_c	136.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	45.330 Å
R factor r_factor	0.2181
R_work r_work	0.2161
R_free r_free	0.2564

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemagglutinin HA1

State in the Current Structure

Other States of the Same Protein in the Database

Hemagglutinin HA2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9dio__assembly_2__model_1

9dio__assembly_2__model_1 | I(q)

9dio__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemagglutinin HA1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemagglutinin HA2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9dio__assembly_2__model_1

9dio__assembly_2__model_1 | I(q)

9dio__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)