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- PDB-4qn6: Crystal structure of Neuraminidase N6 complexed with Laninamivir -

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Entry
Database: PDB / ID: 4qn6
TitleCrystal structure of Neuraminidase N6 complexed with Laninamivir
ComponentsNeuraminidase
KeywordsHYDROLASE / 6-BLADED BETA-PROPELLER / CALCIUM BINDING / GLYCOSYLATION
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-LNV / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 Å
AuthorsSun, X. / Li, Q. / Wu, Y. / Liu, Y. / Qi, J. / Vavricka, C.J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2014
Title: Structure of influenza virus N7: the last piece of the neuraminidase "jigsaw" puzzle.
Authors: Sun, X. / Li, Q. / Wu, Y. / Wang, M. / Liu, Y. / Qi, J. / Vavricka, C.J. / Gao, G.F.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,48110
Polymers86,3892
Non-polymers4,0928
Water15,241846
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,96320
Polymers172,7794
Non-polymers8,18416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,-y-1,z1
crystal symmetry operation3_535-y+1/2,x-3/2,z1
crystal symmetry operation4_655y+3/2,-x+1/2,z1
Buried area24290 Å2
ΔGint26 kcal/mol
Surface area47190 Å2
MethodPISA
2
B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,96320
Polymers172,7794
Non-polymers8,18416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,-y-1,z1
crystal symmetry operation3_535-y+1/2,x-3/2,z1
crystal symmetry operation4_655y+3/2,-x+1/2,z1
Buried area24290 Å2
ΔGint23 kcal/mol
Surface area46710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.919, 137.919, 148.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-916-

HOH

21A-994-

HOH

31B-760-

HOH

41B-881-

HOH

51B-999-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase /


Mass: 43194.707 Da / Num. of mol.: 2 / Fragment: UNP residues 80-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Nanchang/7-010/2000(H3N6))
Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2FCL6

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Sugars , 3 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...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


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-LNV / 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-D-glycero-D-galacto-non-2-enonic acid / 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-D-glycero-D-galacto-non-2-enonic acid / Laninamivir / Laninamivir


Type: D-saccharide / Mass: 346.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N4O7 / Comment: inhibitor*YM

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Non-polymers , 2 types, 848 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 846 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.97 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 8
Details: 0.1M sodium chloride, 0.1M Tris, 8%(w/v) PEG 20000, pH 8.0, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.945→50 Å / Num. all: 105174 / Num. obs: 105174 / % possible obs: 99.78 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.78 Å2
Reflection shellResolution: 1.95→2.02 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V0Z

1v0z


Resolution: 1.945→47.483 Å / FOM work R set: 0.9057 / SU ML: 0.13 / σ(F): 1.34 / Phase error: 15.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1611 5255 5 %Random
Rwork0.1451 ---
all0.1459 105174 --
obs0.1459 105174 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.31 Å2 / Biso mean: 22.08 Å2 / Biso min: 9.88 Å2
Refinement stepCycle: LAST / Resolution: 1.945→47.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6008 0 272 846 7126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086466
X-RAY DIFFRACTIONf_angle_d1.1838786
X-RAY DIFFRACTIONf_chiral_restr0.094992
X-RAY DIFFRACTIONf_plane_restr0.0051106
X-RAY DIFFRACTIONf_dihedral_angle_d23.1842476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9445-1.96660.2251610.1713230339198
1.9666-1.98980.18481600.163733133473100
1.9898-2.0140.18391750.147132903465100
2.014-2.03950.1561860.138832723458100
2.0395-2.06640.17061700.141732833453100
2.0664-2.09470.16611830.143733013484100
2.0947-2.12460.16721710.144732993470100
2.1246-2.15630.17481550.138633153470100
2.1563-2.190.16811960.134132803476100
2.19-2.22590.16081830.146732933476100
2.2259-2.26430.16231550.138433073462100
2.2643-2.30550.18071960.140832963492100
2.3055-2.34980.18921720.145732793451100
2.3498-2.39780.17451560.149933143470100
2.3978-2.44990.15791850.145133423527100
2.4499-2.50690.17181770.139633213498100
2.5069-2.56960.15911590.144333073466100
2.5696-2.6390.15281670.142433373504100
2.639-2.71670.15751650.145733333498100
2.7167-2.80440.14981820.136133213503100
2.8044-2.90460.16211920.146833153507100
2.9046-3.02090.14261650.135933463511100
3.0209-3.15830.15521660.130233543520100
3.1583-3.32480.16081810.128333633544100
3.3248-3.5330.12731840.12533343518100
3.533-3.80570.13551990.127933443543100
3.8057-4.18850.13731710.12763377354899
4.1885-4.79410.14221580.13353420357899
4.7941-6.03810.16411950.17734463641100
6.0381-47.49760.22361900.21323587377798
Refinement TLS params.Method: refined / Origin x: 156.5872 Å / Origin y: -48.5948 Å / Origin z: 185.8646 Å
111213212223313233
T0.1207 Å2-0.0082 Å20.0106 Å2-0.12 Å2-0.0002 Å2--0.1344 Å2
L0.0389 °20.0089 °20.0264 °2-0.0499 °20.0229 °2--0.1073 °2
S0.0034 Å °0.0106 Å °0.0111 Å °-0.0099 Å °0.012 Å °-0.0272 Å °-0.0248 Å °0.0218 Å °0 Å °
Refinement TLS groupSelection details: ALL

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