5wko

Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1) influenza virus

Method: X-RAY DIFFRACTION Dmax: 276.9 Å Quality: GOOD

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

Antibody 27F3 heavy chain

Homo sapiens

UniProt Q6N089

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 135–244 Chain E; UniProt 135–244 Chain I; UniProt 135–244 Not recorded Antibody 27F3 light chain × 3 (Q9UL78,Q6P5S8) Hemagglutinin × 3 (C3W5S1) Hemagglutinin × 3 (A0A023ZYH9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268
2 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain C; UniProt 135–244 Chain G; UniProt 135–244 Chain K; UniProt 135–244 Not recorded Antibody 27F3 light chain × 3 (Q9UL78,Q6P5S8) Hemagglutinin × 3 (C3W5S1) Hemagglutinin × 3 (A0A023ZYH9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268

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.

17 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6N089_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 116–225; UniProt 135–244 Author chain C; PDBConstruct 116–225; UniProt 135–244 Author chain E; PDBConstruct 116–225; UniProt 135–244 Author chain G; PDBConstruct 116–225; UniProt 135–244 Author chain I; PDBConstruct 116–225; UniProt 135–244 Author chain K; PDBConstruct 116–225; UniProt 135–244

Antibody 27F3 light chain

Homo sapiens

UniProt Q6P5S8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain B; UniProt 126–234 Chain F; UniProt 126–234 Chain J; UniProt 126–234 Not recorded Antibody 27F3 heavy chain × 3 (Q6N089) Hemagglutinin × 3 (C3W5S1) Hemagglutinin × 3 (A0A023ZYH9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268
2 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain D; UniProt 126–234 Chain H; UniProt 126–234 Chain L; UniProt 126–234 Not recorded Antibody 27F3 heavy chain × 3 (Q6N089) Hemagglutinin × 3 (C3W5S1) Hemagglutinin × 3 (A0A023ZYH9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268

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.

16 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6P5S8_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 105–213; UniProt 126–234 Author chain D; PDBConstruct 105–213; UniProt 126–234 Author chain F; PDBConstruct 105–213; UniProt 126–234 Author chain H; PDBConstruct 105–213; UniProt 126–234 Author chain J; PDBConstruct 105–213; UniProt 126–234 Author chain L; PDBConstruct 105–213; UniProt 126–234

Antibody 27F3 light chain

Homo sapiens

UniProt Q9UL78

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain B; UniProt 1–104 Chain F; UniProt 1–104 Chain J; UniProt 1–104 Not recorded Antibody 27F3 heavy chain × 3 (Q6N089) Hemagglutinin × 3 (C3W5S1) Hemagglutinin × 3 (A0A023ZYH9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268
2 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain D; UniProt 1–104 Chain H; UniProt 1–104 Chain L; UniProt 1–104 Not recorded Antibody 27F3 heavy chain × 3 (Q6N089) Hemagglutinin × 3 (C3W5S1) Hemagglutinin × 3 (A0A023ZYH9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q9UL78_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–104; UniProt 1–104 Author chain D; PDBConstruct 1–104; UniProt 1–104 Author chain F; PDBConstruct 1–104; UniProt 1–104 Author chain H; PDBConstruct 1–104; UniProt 1–104 Author chain J; PDBConstruct 1–104; UniProt 1–104 Author chain L; PDBConstruct 1–104; UniProt 1–104

Hemagglutinin

Influenza A virus

UniProt C3W5S1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain M; UniProt 18–344 Chain N; UniProt 18–344 Chain O; UniProt 18–344 Not recorded Antibody 27F3 heavy chain × 3 (Q6N089) Antibody 27F3 light chain × 3 (Q9UL78,Q6P5S8) Hemagglutinin × 3 (A0A023ZYH9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268
2 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain S; UniProt 18–344 Chain T; UniProt 18–344 Chain U; UniProt 18–344 Not recorded Antibody 27F3 heavy chain × 3 (Q6N089) Antibody 27F3 light chain × 3 (Q9UL78,Q6P5S8) Hemagglutinin × 3 (A0A023ZYH9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268

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.

21 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C3W5S1_I09A0
Isoform
PDB entities 3
Chains and sequence ranges Author chain M; PDBConstruct 5–331; UniProt 18–344 Author chain N; PDBConstruct 5–331; UniProt 18–344 Author chain O; PDBConstruct 5–331; UniProt 18–344 Author chain S; PDBConstruct 5–331; UniProt 18–344 Author chain T; PDBConstruct 5–331; UniProt 18–344 Author chain U; PDBConstruct 5–331; UniProt 18–344

Hemagglutinin

Influenza A virus

UniProt A0A023ZYH9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain P; UniProt 345–518 Chain Q; UniProt 345–518 Chain R; UniProt 345–518 Not recorded Antibody 27F3 heavy chain × 3 (Q6N089) Antibody 27F3 light chain × 3 (Q9UL78,Q6P5S8) Hemagglutinin × 3 (C3W5S1) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268
2 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain V; UniProt 345–518 Chain W; UniProt 345–518 Chain X; UniProt 345–518 Not recorded Antibody 27F3 heavy chain × 3 (Q6N089) Antibody 27F3 light chain × 3 (Q9UL78,Q6P5S8) Hemagglutinin × 3 (C3W5S1) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 Resolution 3.49 Å R-free 0.268

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A023ZYH9_9INFA
Isoform
PDB entities 4
Chains and sequence ranges Author chain P; PDBConstruct 1–174; UniProt 345–518 Author chain Q; PDBConstruct 1–174; UniProt 345–518 Author chain R; PDBConstruct 1–174; UniProt 345–518 Author chain V; PDBConstruct 1–174; UniProt 345–518 Author chain W; PDBConstruct 1–174; UniProt 345–518 Author chain X; PDBConstruct 1–174; UniProt 345–518

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 5wko

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wko
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5wko
Deposition date deposition_date2017-07-25
Structure title titleCrystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1) influenza virus
Keywords keywords27F3 H1 HA A/California/04/2009, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier83.36
Radius of gyration Rg (electron density) rg_electron83.36
Forward intensity I(0) i05349720000.00
Molecular weight molecular_weight614890.0 kDa
Excluded volume excluded_volume766310 ų
Envelope volume envelope_volume1315200 ų
Hydration-shell volume shell_volume134830 ų
Envelope diameter envelope_diameter274.6
Shell Rg shell_rg76.09
Envelope Rg envelope_rg80.15
Shape Rg shape_rg83.34
Total Rg total_rg83.34
Total atoms total_atoms43322
Residues n_residues5494
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 dmax276.9
Rg (real space) rg_real87.30
Rg uncertainty (real space) rg_real_error1.58
I(0) (real space) i0_real5.3500e+09
I(0) uncertainty (real space) i0_real_error1.0640e+08
Rg (reciprocal space) rg_reciprocal81.72
I(0) (reciprocal space) i0_reciprocal5324000000.0000
Solution quality estimate total_estimate0.8849
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary87.4
Skewness Skewness skewness0.406
Kurtosis Kurtosis kurtosis-0.514
Angular range angular_range— – 0.0950 −1
Current regularization parameter α current_alpha1.6680
Highest regularization parameter α highest_alpha139900000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.965; Stabil: 0.881; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.014

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

Domain ID domain_id5wkoA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wkoM01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Hemagglutinin Chain A, Domain 2
Domain ID domain_id5wkoM02
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_id5wkoN01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Hemagglutinin Chain A, Domain 2
Domain ID domain_id5wkoN02
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_id5wkoO01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Hemagglutinin Chain A, Domain 2
Domain ID domain_id5wkoO02
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_id5wkoP01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id5wkoQ01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id5wkoR01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id5wkoS01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Hemagglutinin Chain A, Domain 2
Domain ID domain_id5wkoS02
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_id5wkoT01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Hemagglutinin Chain A, Domain 2
Domain ID domain_id5wkoT02
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_id5wkoU01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology77 — Hemagglutinin; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Hemagglutinin Chain A, Domain 2
Domain ID domain_id5wkoU02
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_id5wkoV01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id5wkoW01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id5wkoX01
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)