1rd8

Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)

Method: X-RAY DIFFRACTION

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Other combination	Heteromer	6 / 0 / 0 / 3	Consistent with protein count

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	1rd8
Deposition date deposition_date	2003-11-05
Structure title title	Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)
Keywords keywords	GLYCOPROTEIN, MEMBRANE-FUSION PRECURSOR, VIRUS/VIRAL PROTEIN, 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.

1rd8__assembly_1__model_1

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

Download this curve (.dat)

1rd8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rd8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.28 Å
Rg (electron density)	42.02 Å
Total Rg	42.10 Å
Atom count	12082
Residues	1509
Excluded volume	212530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rd8__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	hemagglutinin
Molecular weight formula_weight	36971.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	12082

ADPGYLLEDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPSIQSR

Source Source

Source organism organism	Influenza A virus
NCBI taxonomy ID ncbi_taxonomy_id	11320
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	hemagglutinin
Molecular weight formula_weight	20804.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVRSLVPR

Source Source

Source organism organism	Influenza A virus
NCBI taxonomy ID ncbi_taxonomy_id	11320
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 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	2

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-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	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1rd8a1
Class class	b — All beta proteins
Fold Fold fold	b.19 — Viral protein domain
Superfamily Superfamily superfamily	b.19.1 — Viral protein domain
Family Family family	b.19.1.2 — Influenza hemagglutinin headpiece

Domain ID domain_id	d1rd8a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1rd8b_
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
Family Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

Domain ID domain_id	d1rd8c1
Class class	b — All beta proteins
Fold Fold fold	b.19 — Viral protein domain
Superfamily Superfamily superfamily	b.19.1 — Viral protein domain
Family Family family	b.19.1.2 — Influenza hemagglutinin headpiece

Domain ID domain_id	d1rd8c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1rd8d_
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
Family Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

Domain ID domain_id	d1rd8e1
Class class	b — All beta proteins
Fold Fold fold	b.19 — Viral protein domain
Superfamily Superfamily superfamily	b.19.1 — Viral protein domain
Family Family family	b.19.1.2 — Influenza hemagglutinin headpiece

Domain ID domain_id	d1rd8e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1rd8f_
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
Family Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

CATH v4.4 (9 domains)

Domain ID domain_id	1rd8A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

Domain ID domain_id	1rd8A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	1rd8B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1rd8C01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

Domain ID domain_id	1rd8C02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	1rd8D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1rd8E01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

Domain ID domain_id	1rd8E02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	1rd8F00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	190.529 Å
Unit-cell length b length_b	109.953 Å
Unit-cell length c length_c	136.238 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	49.390 Å
R factor r_factor	0.2713
R_work r_work	0.2700
R_free r_free	0.2952

Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)

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

Assembly Composition of the Current Entry

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1rd8__assembly_1__model_1

1rd8__assembly_1__model_1 | I(q)

1rd8__assembly_1__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 (6)

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 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)