6crd

INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk

Method: X-RAY DIFFRACTION Dmax: 210.8 Å Quality: GOOD

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

Tetrabrachion,Neuraminidase

Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)

UniProt P03472

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 Homooligomer Protein × 4 其他Polymer 11 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 83–470 Chain B; UniProt 83–470 Chain E; UniProt 83–470 Chain H; UniProt 83–470 Not recorded ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 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 ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;100 mM HEPES buffer at pH7.0 with 10% PEG6000 Resolution 2.57 Å R-free 0.306
2 Insufficient information Homooligomer Protein × 4 其他Polymer 12 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 83–470 Chain D; UniProt 83–470 Chain F; UniProt 83–470 Chain G; UniProt 83–470 Not recorded ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;100 mM HEPES buffer at pH7.0 with 10% PEG6000 Resolution 2.57 Å R-free 0.306

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.

47 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRAM_I75A5
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 86–473; UniProt 83–470 Author chain B; PDBConstruct 86–473; UniProt 83–470 Author chain C; PDBConstruct 86–473; UniProt 83–470 Author chain D; PDBConstruct 86–473; UniProt 83–470 Author chain E; PDBConstruct 86–473; UniProt 83–470 Author chain F; PDBConstruct 86–473; UniProt 83–470 Author chain G; PDBConstruct 86–473; UniProt 83–470 Author chain H; PDBConstruct 86–473; UniProt 83–470

Tetrabrachion,Neuraminidase

Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)

UniProt Q54436

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 Homooligomer Protein × 4 其他Polymer 11 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1251–1285 Chain B; UniProt 1251–1285 Chain E; UniProt 1251–1285 Chain H; UniProt 1251–1285 Not recorded ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 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 ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;100 mM HEPES buffer at pH7.0 with 10% PEG6000 Resolution 2.57 Å R-free 0.306
2 Insufficient information Homooligomer Protein × 4 其他Polymer 12 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1251–1285 Chain D; UniProt 1251–1285 Chain F; UniProt 1251–1285 Chain G; UniProt 1251–1285 Not recorded ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;100 mM HEPES buffer at pH7.0 with 10% PEG6000 Resolution 2.57 Å R-free 0.306

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.

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q54436_STAMA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 51–85; UniProt 1251–1285 Author chain B; PDBConstruct 51–85; UniProt 1251–1285 Author chain C; PDBConstruct 51–85; UniProt 1251–1285 Author chain D; PDBConstruct 51–85; UniProt 1251–1285 Author chain E; PDBConstruct 51–85; UniProt 1251–1285 Author chain F; PDBConstruct 51–85; UniProt 1251–1285 Author chain G; PDBConstruct 51–85; UniProt 1251–1285 Author chain H; PDBConstruct 51–85; UniProt 1251–1285

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 6crd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6crd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6crd
Deposition date deposition_date2018-03-16
Structure title titleINFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk
Keywords keywords;NEURAMINIDASE, SIALIDASE, HYDROLASE(O-GLUCOSYL), HYDROLASE-HYDROLASE, ARTIFICIAL STALK, Tetrabrachion, HYDROLASE, viral protein-hydrolase complex ;; viral protein/hydrolase
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier56.58
Radius of gyration Rg (electron density) rg_electron56.93
Forward intensity I(0) i02630840000.00
Molecular weight molecular_weight414220.0 kDa
Excluded volume excluded_volume510910 ų
Envelope volume envelope_volume684200 ų
Hydration-shell volume shell_volume100190 ų
Envelope diameter envelope_diameter222.0
Shell Rg shell_rg59.42
Envelope Rg envelope_rg56.26
Shape Rg shape_rg56.92
Total Rg total_rg57.05
Total atoms total_atoms29042
Residues n_residues3468
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 dmax210.8
Rg (real space) rg_real56.81
Rg uncertainty (real space) rg_real_error2.55
I(0) (real space) i0_real2.6310e+09
I(0) uncertainty (real space) i0_real_error5.4150e+07
Rg (reciprocal space) rg_reciprocal56.38
I(0) (reciprocal space) i0_reciprocal2629000000.0000
Solution quality estimate total_estimate0.8419
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary60.2
Skewness Skewness skewness0.451
Kurtosis Kurtosis kurtosis-0.196
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha122400000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.695; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.927

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6crdA00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10
Domain ID domain_id6crdB00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10
Domain ID domain_id6crdC00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10
Domain ID domain_id6crdD00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10
Domain ID domain_id6crdE00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10
Domain ID domain_id6crdF00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10
Domain ID domain_id6crdG00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10
Domain ID domain_id6crdH00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)