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- PDB-4hzw: Crystal structure of influenza A neuraminidase N3 complexed with ... -

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Basic information

Entry
Database: PDB / ID: 4hzw
TitleCrystal structure of influenza A neuraminidase N3 complexed with laninamivir
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Neuraminidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / 6 Propeller / Neuraminidase / Sialidase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-LNV / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsLi, Q. / Qi, J. / Vavricka, C.J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2013
Title: Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance.
Authors: Li, Q. / Qi, J. / Wu, Y. / Kiyota, H. / Tanaka, K. / Suhara, Y. / Ohrui, H. / Suzuki, Y. / Vavricka, C.J. / Gao, G.F.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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 2.1Nov 8, 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8956
Polymers43,3281
Non-polymers1,5685
Water8,017445
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,58124
Polymers173,3114
Non-polymers6,27020
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 area19020 Å2
ΔGint-17 kcal/mol
Surface area46950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.977, 105.977, 66.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-508-

CA

21A-647-

HOH

31A-696-

HOH

41A-921-

HOH

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Components

#1: Protein Neuraminidase


Mass: 43327.680 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 83-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: 2006(H2N3) / Gene: NA / Cell (production host): Hi5 / References: UniProt: A9YN63
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: 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


Type: D-saccharide / Mass: 346.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N4O7 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 20mM Tris, pH 8.0, 50mM NaCl, 0.1M BIS-TRIS propane (pH 9.0), 10% v/v Jeffamine ED-2001 (pH 7.0), VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 39081 / Num. obs: 39081 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BAT

2bat


Resolution: 1.701→33.513 Å / SU ML: 0.13 / σ(F): 0.08 / Phase error: 13.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1586 1961 5.02 %
Rwork0.1367 --
all0.1378 39081 -
obs0.1378 39081 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.303 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7082 Å2-0 Å20 Å2
2---1.7082 Å2-0 Å2
3---3.4163 Å2
Refinement stepCycle: LAST / Resolution: 1.701→33.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 102 445 3586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073236
X-RAY DIFFRACTIONf_angle_d1.144390
X-RAY DIFFRACTIONf_dihedral_angle_d23.0661210
X-RAY DIFFRACTIONf_chiral_restr0.122477
X-RAY DIFFRACTIONf_plane_restr0.006561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7011-1.74360.17711310.1346245689
1.7436-1.79070.16721370.1261255694
1.7907-1.84340.16851360.1309256594
1.8434-1.90290.17231590.1338249592
1.9029-1.97090.19921630.1436253093
1.9709-2.04980.15781160.1281267496
2.0498-2.14310.14241440.1289264497
2.1431-2.25610.17431190.1324269397
2.2561-2.39740.16981440.142268197
2.3974-2.58240.17181450.1423274699
2.5824-2.84220.15851520.1481272399
2.8422-3.25320.15231250.1383273999
3.2532-4.09750.12921390.12232797100
4.0975-33.51940.13631510.1362282199
Refinement TLS params.Method: refined / Origin x: -0.2372 Å / Origin y: -28.0443 Å / Origin z: 26.8902 Å
111213212223313233
T0.0323 Å2-0.0003 Å2-0.002 Å2-0.0231 Å20.0011 Å2--0.0251 Å2
L0.2015 °2-0.0181 °20.0075 °2-0.2248 °20.0306 °2--0.1062 °2
S-0.0022 Å °0.0106 Å °-0.0304 Å °-0.0103 Å °0.0104 Å °0.0012 Å °0.0193 Å °0.0009 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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