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- PDB-4hzz: Crystal structure of influenza neuraminidase N3-H274Y complexed w... -

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Basic information

Entry
Database: PDB / ID: 4hzz
TitleCrystal structure of influenza neuraminidase N3-H274Y complexed with oseltamivir
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / neuraminidase / 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
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-G39 / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 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 16, 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 / chem_comp ...atom_site / 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 / _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

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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)44,7116
Polymers43,2061
Non-polymers1,5065
Water8,827490
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,84524
Polymers172,8224
Non-polymers6,02220
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 area21490 Å2
ΔGint-11 kcal/mol
Surface area47120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.113, 108.113, 62.226
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-686-

HOH

31A-896-

HOH

41A-1052-

HOH

51A-1058-

HOH

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Components

#1: Protein Neuraminidase /


Mass: 43205.535 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 83-469 / Mutation: H274Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Cell: Hi5 / Gene: NA / 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: Chemical ChemComp-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate / Oseltamivir


Mass: 284.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication, antivirus*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 46695 / Num. obs: 46695 / % possible obs: 99.6 % / 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
GUGIdata 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: 1.601→34.188 Å / SU ML: 0.13 / σ(F): 0.15 / Phase error: 14.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1647 2363 5.06 %
Rwork0.1377 --
obs0.139 46695 98.61 %
all-46695 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.291 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8309 Å2-0 Å20 Å2
2---0.8309 Å2-0 Å2
3---1.6619 Å2
Refinement stepCycle: LAST / Resolution: 1.601→34.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 98 490 3618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073231
X-RAY DIFFRACTIONf_angle_d1.1914385
X-RAY DIFFRACTIONf_dihedral_angle_d23.1641205
X-RAY DIFFRACTIONf_chiral_restr0.085475
X-RAY DIFFRACTIONf_plane_restr0.005562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6005-1.63320.16661310.1291254196
1.6332-1.66870.14621360.1228254297
1.6687-1.70750.16231360.1219257398
1.7075-1.75020.14841410.1206258598
1.7502-1.79750.161430.1158259799
1.7975-1.85040.16631310.1215258799
1.8504-1.91010.151470.1282262499
1.9101-1.97840.18861280.1318261699
1.9784-2.05760.14941600.1272258299
2.0576-2.15120.15631380.12952646100
2.1512-2.26460.16741440.13172625100
2.2646-2.40650.16171460.13612638100
2.4065-2.59220.17831460.14432643100
2.5922-2.8530.1771320.15152658100
2.853-3.26550.16731230.14652650100
3.2655-4.11310.16191490.1291257697
4.1131-34.19610.15061320.1431264997
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2487-0.0205-0.03350.13270.01650.133500.01670.0191-0.01490.0084-0.0151-0.0180.00200.0817-0.00310.00190.0743-0.00720.0717-0.12717.47430.902
20.1245-0.04290.03510.0724-0.07840.06660.02880.04570.13710.00450.0216-0.0642-0.04890.035700.1179-0.0090.01640.09160.00450.137610.35517.58526.641
30.2926-0.00820.00930.11540.04390.11020.00650.00930.14270.00140.01340.0216-0.0656-0.01300.11210.00570.01150.08230.00580.13628.75833.81222.314
40.23740.1132-0.0110.1514-0.03090.0184-0.0012-0.00290.06030.00090.01210.0249-0.0122-0.0035-0.00070.09080.00840.00620.0854-0.00280.0794-7.5441.61229.209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 83:165)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 166:201)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 202:326)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 327:390)

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