4fnk

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin

Method: X-RAY DIFFRACTION Dmax: 139.1 Å Quality: GOOD

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

Hemagglutinin HA1 chain

Influenza A virus

UniProt Q91MA7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 6 其他Polymer 9 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 27–345 Chain B; UniProt 346–519 Chain C; UniProt 27–345 Chain D; UniProt 346–519 Chain E; UniProt 27–345 Chain F; UniProt 346–519 Fragment:UNP residues 27-345 Fragment:UNP residues 346-519 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 SO4 SULFATE ION × 6 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;2.0 M ammonium sulfate, 100 mM sodium cacodylate, pH 6.5, 200 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.90 Å R-free 0.189

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

46 other PDB entries and 90 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEMA_I68A4
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 5–323; UniProt 27–345 Author chain C; PDBConstruct 5–323; UniProt 27–345 Author chain E; PDBConstruct 5–323; UniProt 27–345 Author chain B; PDBConstruct 1–174; UniProt 346–519 Author chain D; PDBConstruct 1–174; UniProt 346–519 Author chain F; PDBConstruct 1–174; UniProt 346–519

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4fnk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fnk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fnk
Deposition date deposition_date2012-06-19
Structure title titleCrystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin
Keywords keywordsviral fusion protein, virus attachment and entry, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.52
Radius of gyration Rg (electron density) rg_electron40.94
Forward intensity I(0) i0466731000.00
Molecular weight molecular_weight170350.0 kDa
Excluded volume excluded_volume210390 ų
Envelope volume envelope_volume270900 ų
Hydration-shell volume shell_volume56937 ų
Envelope diameter envelope_diameter139.0
Shell Rg shell_rg44.72
Envelope Rg envelope_rg40.60
Shape Rg shape_rg40.93
Total Rg total_rg41.14
Total atoms total_atoms11960
Residues n_residues1467
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax139.1
Rg (real space) rg_real41.74
Rg uncertainty (real space) rg_real_error1.36
I(0) (real space) i0_real4.6670e+08
I(0) uncertainty (real space) i0_real_error8.0670e+06
Rg (reciprocal space) rg_reciprocal41.52
I(0) (reciprocal space) i0_reciprocal466600000.0000
Solution quality estimate total_estimate0.8424
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.3
Skewness Skewness skewness0.491
Kurtosis Kurtosis kurtosis-0.451
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha50720000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.746; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.739

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd4fnka1
Class classb — All beta proteins
Fold Fold foldb.19 — Viral protein domain
Superfamily Superfamily superfamilyb.19.1 — Viral protein domain
Family Family familyb.19.1.2 — Influenza hemagglutinin headpiece
Domain ID domain_idd4fnka2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4fnkb_
Class classh — Coiled coil proteins
Fold Fold foldh.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamilyh.3.1 — Influenza hemagglutinin (stalk)
Family Family familyh.3.1.1 — Influenza hemagglutinin (stalk)
Domain ID domain_idd4fnkc1
Class classb — All beta proteins
Fold Fold foldb.19 — Viral protein domain
Superfamily Superfamily superfamilyb.19.1 — Viral protein domain
Family Family familyb.19.1.2 — Influenza hemagglutinin headpiece
Domain ID domain_idd4fnkc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4fnkd_
Class classh — Coiled coil proteins
Fold Fold foldh.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamilyh.3.1 — Influenza hemagglutinin (stalk)
Family Family familyh.3.1.1 — Influenza hemagglutinin (stalk)
Domain ID domain_idd4fnke1
Class classb — All beta proteins
Fold Fold foldb.19 — Viral protein domain
Superfamily Superfamily superfamilyb.19.1 — Viral protein domain
Family Family familyb.19.1.2 — Influenza hemagglutinin headpiece
Domain ID domain_idd4fnke2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4fnkf_
Class classh — Coiled coil proteins
Fold Fold foldh.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamilyh.3.1 — Influenza hemagglutinin (stalk)
Family Family familyh.3.1.1 — Influenza hemagglutinin (stalk)

CATH v4.4 (6 domains)

Domain ID domain_id4fnkA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id4fnkB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id4fnkC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id4fnkD00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id4fnkE01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id4fnkF00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)