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- PDB-5nzn: Complex of H275Y/S247N mutant variant of neuraminidase from H1N1 ... -

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Basic information

Entry
Database: PDB / ID: 5nzn
TitleComplex of H275Y/S247N mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / neuraminidase / influenza / complex / inhibitor
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
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / 6 Propeller / Neuraminidase / Sialidase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-G39 / Neuraminidase / Neuraminidase
Similarity search - Component
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPachl, P. / Pokorna, J.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic13-19561S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLO1302 Czech Republic
Czech Academy of Sciences61388963 Czech Republic
Czech Academy of Sciences68378050 Czech Republic
CitationJournal: Viruses / Year: 2018
Title: Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus.
Authors: Pokorna, J. / Pachl, P. / Karlukova, E. / Hejdanek, J. / Rezacova, P. / Machara, A. / Hudlicky, J. / Konvalinka, J. / Kozisek, M.
History
DepositionMay 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 2.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 2.2Nov 6, 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
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,62828
Polymers171,1194
Non-polymers4,50924
Water24,5361362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.778, 127.538, 96.773
Angle α, β, γ (deg.)90.00, 93.24, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 5 / Auth seq-ID: 88 - 700 / Label seq-ID: 7

Dom-IDAuth asym-IDLabel asym-ID
1AA - CA
2BB - DA
3CC - EA
4DD - FA

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.589309, -0.639213, -0.494087), (0.64661, 0.00652, 0.762792), (-0.484365, -0.769002, 0.417164)38.00786, -3.79636, 45.45171
3given(0.18197, 0.000473, -0.983304), (0.000631, -1, -0.000364), (-0.983304, -0.000554, -0.181971)40.1546, 55.79044, 48.29309
4given(0.592161, 0.640323, -0.489215), (-0.632752, -0.006437, -0.774327), (-0.498969, 0.768079, 0.401354)2.13021, 59.36474, 3.25467

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Neuraminidase


Mass: 42779.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Gene: NA / Production host: Escherichia coli (E. coli) / References: UniProt: W5R8B8, UniProt: C3W6G3*PLUS

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Sugars , 3 types, 10 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 1
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
#6: 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.: 8
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

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Non-polymers , 4 types, 1376 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate


Mass: 284.351 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication, antivirus*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1362 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES pH 7.5, 5% PEG 8000,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.73→48.31 Å / Num. obs: 214537 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.38 % / Biso Wilson estimate: 22.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.11 / Net I/σ(I): 9.41
Reflection shellResolution: 1.73→1.84 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.554 / Num. unique obs: 34153 / CC1/2: 0.732 / Rrim(I) all: 0.664 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NWE

5nwe


Resolution: 1.73→48.31 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.035 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26138 2253 1.1 %RANDOM
Rwork0.22896 ---
obs0.2293 212283 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0.79 Å2
2---0.26 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.73→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11984 0 285 1362 13631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212676
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211290
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.94617256
X-RAY DIFFRACTIONr_angle_other_deg1.125326092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63851554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18624.159565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.301151917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3361569
X-RAY DIFFRACTIONr_chiral_restr0.1170.21823
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114507
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2951.6096207
X-RAY DIFFRACTIONr_mcbond_other1.2931.6096206
X-RAY DIFFRACTIONr_mcangle_it1.7842.4087758
X-RAY DIFFRACTIONr_mcangle_other1.7842.4087759
X-RAY DIFFRACTIONr_scbond_it1.8211.816469
X-RAY DIFFRACTIONr_scbond_other1.8211.816469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6322.6629497
X-RAY DIFFRACTIONr_long_range_B_refined3.83820.11614896
X-RAY DIFFRACTIONr_long_range_B_other3.68419.76514616
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A2212medium positional0.070.5
B2212medium positional0.070.5
C2212medium positional0.080.5
D2212medium positional0.070.5
A3424loose positional0.285
B3424loose positional0.35
C3424loose positional0.295
D3424loose positional0.295
A2212medium thermal1.972
B2212medium thermal1.822
C2212medium thermal1.542
D2212medium thermal1.62
A3424loose thermal1.9910
B3424loose thermal1.8610
C3424loose thermal1.8110
D3424loose thermal1.8310
LS refinement shellResolution: 1.731→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 161 -
Rwork0.304 15185 -
obs--96.4 %

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