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- PDB-3san: Crystal structure of influenza A virus neuraminidase N5 complexed... -

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Basic information

Entry
Database: PDB / ID: 3san
TitleCrystal structure of influenza A virus neuraminidase N5 complexed with Zanamivir
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 6-BLADED BETA-PROPELLER / HYDROLASE / CALCIUM BINDING / GLYCOSYLATION / HYDROLASE-HYDROLASE INHIBITOR complex
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
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
ZANAMIVIR / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, M.Y. / Qi, J.X. / Liu, Y. / Vavricka, C.J. / Wu, Y. / Li, Q. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2011
Title: Influenza a virus n5 neuraminidase has an extended 150-cavity
Authors: Wang, M.Y. / Qi, J.X. / Liu, Y. / Vavricka, C.J. / Wu, Y. / Li, Q. / Gao, G.F.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,46814
Polymers87,0642
Non-polymers2,40412
Water19,8531102
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,93628
Polymers174,1284
Non-polymers4,80924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area20600 Å2
ΔGint-66 kcal/mol
Surface area46530 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)178,93628
Polymers174,1284
Non-polymers4,80924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area20910 Å2
ΔGint-68 kcal/mol
Surface area46060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.110, 112.110, 66.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11B-520-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase


Mass: 43531.934 Da / Num. of mol.: 2 / Fragment: UNP residues 79-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/duck/Alberta/60/1976(H12N5) / Gene: NA / Plasmid: pFastBac1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A1ILL9, exo-alpha-sialidase

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Sugars , 3 types, 6 molecules

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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-ZMR / ZANAMIVIR / 4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / 4-guanidino-Neu5Ac2en / MODIFIED SIALIC ACID


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication, inhibitor*YM

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Non-polymers , 3 types, 1108 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1102 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 12% w/v Polyethylene glycol 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 109012 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.66 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NSS

3nss


Resolution: 1.6→35.452 Å / FOM work R set: 0.9326 / SU ML: 0.16 / σ(F): 2 / Phase error: 13.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1572 5287 5.01 %RANDOM
Rwork0.1205 ---
all0.1223 109012 --
obs0.1223 105577 96.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.17 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 16.421 Å2
Baniso -1Baniso -2Baniso -3
1--0.6945 Å2-0 Å20 Å2
2---0.6945 Å2-0 Å2
3---1.3891 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 156 1102 7342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056491
X-RAY DIFFRACTIONf_angle_d1.048801
X-RAY DIFFRACTIONf_dihedral_angle_d22.7292374
X-RAY DIFFRACTIONf_chiral_restr0.074965
X-RAY DIFFRACTIONf_plane_restr0.0051124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6005-1.61860.19081690.12533101X-RAY DIFFRACTION91
1.6186-1.63770.17781890.12153116X-RAY DIFFRACTION91
1.6377-1.65770.16551610.11053190X-RAY DIFFRACTION93
1.6577-1.67860.15741670.10823178X-RAY DIFFRACTION93
1.6786-1.70070.16311710.1073230X-RAY DIFFRACTION93
1.7007-1.7240.16922010.11183197X-RAY DIFFRACTION94
1.724-1.74870.17991860.10743226X-RAY DIFFRACTION95
1.7487-1.77480.15221720.10153284X-RAY DIFFRACTION95
1.7748-1.80250.15221570.09593305X-RAY DIFFRACTION96
1.8025-1.8320.15871850.09693284X-RAY DIFFRACTION96
1.832-1.86360.13561680.09633337X-RAY DIFFRACTION97
1.8636-1.89750.16191580.10563342X-RAY DIFFRACTION96
1.8975-1.9340.16121750.1163246X-RAY DIFFRACTION94
1.934-1.97350.14241430.10113375X-RAY DIFFRACTION97
1.9735-2.01640.14541600.10113383X-RAY DIFFRACTION98
2.0164-2.06330.14421780.10493336X-RAY DIFFRACTION98
2.0633-2.11490.15211600.10563424X-RAY DIFFRACTION98
2.1149-2.17210.15991740.10743411X-RAY DIFFRACTION99
2.1721-2.2360.16031690.10913391X-RAY DIFFRACTION98
2.236-2.30810.16291880.11843335X-RAY DIFFRACTION98
2.3081-2.39060.15182050.11663425X-RAY DIFFRACTION99
2.3906-2.48630.17221780.12253418X-RAY DIFFRACTION99
2.4863-2.59940.16981890.12663430X-RAY DIFFRACTION99
2.5994-2.73640.16461920.13253413X-RAY DIFFRACTION99
2.7364-2.90780.15271860.1223464X-RAY DIFFRACTION100
2.9078-3.13220.1351780.12473462X-RAY DIFFRACTION100
3.1322-3.44710.14631910.12093467X-RAY DIFFRACTION100
3.4471-3.94540.12741660.11583487X-RAY DIFFRACTION100
3.9454-4.96860.13791750.11363496X-RAY DIFFRACTION100
4.9686-35.4610.1791960.1613537X-RAY DIFFRACTION99

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