7k37

Structure of full-length influenza HA with a head-binding antibody at pH 7.8

Method: ELECTRON MICROSCOPY Dmax: 183.3 Å Quality: GOOD

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

Hemagglutinin

Influenza A virus (strain A/Hong Kong/1/1968 H3N2)

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 Heteromer Protein × 12 其他Polymer 9 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 1–345 Chain C; UniProt 1–345 Chain E; UniProt 1–345 Not recorded Hemagglutinin × 3 (C7RWD9) antibody Fab light chain × 3 antibody Fab heavy chain × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;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 ; × 3 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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 ; × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 Å

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
Chains and sequence ranges Author chain A; PDBConstruct 1–345; UniProt 1–345 Author chain C; PDBConstruct 1–345; UniProt 1–345 Author chain E; PDBConstruct 1–345; UniProt 1–345

Hemagglutinin

Influenza A virus (strain A/Hong Kong/1/1968 H3N2)

UniProt C7RWD9

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 Heteromer Protein × 12 其他Polymer 9 PDB declaration: dodecameric(12) Consistent with protein copy count Chain B; UniProt 346–566 Chain D; UniProt 346–566 Chain F; UniProt 346–566 Not recorded Hemagglutinin × 3 (Q91MA7) antibody Fab light chain × 3 antibody Fab heavy chain × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;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 ; × 3 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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 ; × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 Å

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C7RWD9_I68A4
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–221; UniProt 346–566 Author chain D; PDBConstruct 1–221; UniProt 346–566 Author chain F; PDBConstruct 1–221; UniProt 346–566

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 7k37

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7k37
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7k37
Deposition date deposition_date2020-09-10
Structure title titleStructure of full-length influenza HA with a head-binding antibody at pH 7.8
Keywords keywordsinfluenza, virus, hemagglutinin, antibody, low pH, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier53.47
Radius of gyration Rg (electron density) rg_electron53.47
Forward intensity I(0) i01426850000.00
Molecular weight molecular_weight306780.0 kDa
Excluded volume excluded_volume380650 ų
Envelope volume envelope_volume539400 ų
Hydration-shell volume shell_volume86987 ų
Envelope diameter envelope_diameter179.0
Shell Rg shell_rg52.74
Envelope Rg envelope_rg54.17
Shape Rg shape_rg53.48
Total Rg total_rg53.44
Total atoms total_atoms21555
Residues n_residues2712
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 dmax183.3
Rg (real space) rg_real53.43
Rg uncertainty (real space) rg_real_error1.93
I(0) (real space) i0_real1.4270e+09
I(0) uncertainty (real space) i0_real_error2.5830e+07
Rg (reciprocal space) rg_reciprocal53.49
I(0) (reciprocal space) i0_reciprocal1427000000.0000
Solution quality estimate total_estimate0.8086
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary75.9
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha127000000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

Domain ID domain_idd7k37a_
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_idd7k37b_
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_idd7k37c_
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_idd7k37d_
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_idd7k37e_
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_idd7k37f_
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_idd7k37g1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7k37g2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7k37h_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7k37i1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7k37i2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7k37j_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7k37k1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7k37k2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7k37l_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches

CATH v4.4 (15 domains)

Domain ID domain_id7k37B01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id7k37D01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id7k37F01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id7k37G01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37G02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37I01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37I02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37J01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37J02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37K01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37K02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k37L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)