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- PDB-4h52: Wild-type influenza N2 neuraminidase covalent complex with 3-fluo... -

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Basic information

Entry
Database: PDB / ID: 4h52
TitleWild-type influenza N2 neuraminidase covalent complex with 3-fluoro-Neu5Ac
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / NEURAMINIDASE / INFLUENZA SURFACE GLYCOPROTEIN / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


: / : / : / 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
Chem-FSI / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsVavricka, C.J. / Liu, Y. / Kiyota, H. / Sriwilaijaroen, N. / Qi, J. / Tanaka, K. / Wu, Y. / Li, Q. / Li, Y. / Yan, J. ...Vavricka, C.J. / Liu, Y. / Kiyota, H. / Sriwilaijaroen, N. / Qi, J. / Tanaka, K. / Wu, Y. / Li, Q. / Li, Y. / Yan, J. / Suzuki, Y. / Gao, G.F.
CitationJournal: Nat Commun / Year: 2013
Title: Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors
Authors: Vavricka, C.J. / Liu, Y. / Kiyota, H. / Sriwilaijaroen, N. / Qi, J. / Tanaka, K. / Wu, Y. / Li, Q. / Li, Y. / Yan, J. / Suzuki, Y. / Gao, G.F.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Structure summary
Revision 1.2Jul 31, 2013Group: Database references / Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / 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 / _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.mon_nstd_flag / _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_atom_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_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.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 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 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,19010
Polymers86,1102
Non-polymers3,0818
Water16,700927
1
A: Neuraminidase
B: Neuraminidase
hetero molecules

A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,38120
Polymers172,2194
Non-polymers6,16216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area23740 Å2
ΔGint6 kcal/mol
Surface area44630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.698, 139.704, 140.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-705-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase


Mass: 43054.773 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, UNP residues 82-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/RI/5+/1957(H2N2) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q194T1

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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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-FSI / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 3-FLUOROSIALIC ACID / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid


Type: D-saccharide, beta linking / Mass: 327.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18FNO9
IdentifierTypeProgram
b-D-Neup5Ac3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 929 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


Mass: 18.015 Da / Num. of mol.: 927 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9
Details: 0.1M BIS-TRIS PROPANE (pH 9.0), 0.1% JEFFAMINE ED-2001 (pH 7.0), VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 93 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: 1.8→50 Å / Num. obs: 103214 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 15.2 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIA

3tia


Resolution: 1.803→38.817 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8973 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 5156 5 %RANDOM
Rwork0.1513 ---
all0.1525 103136 --
obs0.1525 103136 99.81 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.113 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 68.48 Å2 / Biso mean: 19.5113 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1-11.4079 Å2-0 Å2-0 Å2
2---4.2808 Å20 Å2
3----7.1271 Å2
Refinement stepCycle: LAST / Resolution: 1.803→38.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 200 927 7161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076462
X-RAY DIFFRACTIONf_angle_d1.1998788
X-RAY DIFFRACTIONf_dihedral_angle_d20.4982358
X-RAY DIFFRACTIONf_chiral_restr0.082964
X-RAY DIFFRACTIONf_plane_restr0.0051133
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.803-1.82350.25231230.2149310696
1.8235-1.8450.23351680.1963295100
1.845-1.86750.22351490.18353226100
1.8675-1.89110.18211470.17813284100
1.8911-1.9160.21491740.17113245100
1.916-1.94220.19731660.15723237100
1.9422-1.970.17951760.15523242100
1.97-1.99940.19571780.15093219100
1.9994-2.03060.17571670.1453250100
2.0306-2.06390.18751910.14083239100
2.0639-2.09950.16822000.14693228100
2.0995-2.13770.18081620.14673252100
2.1377-2.17880.18151500.1423267100
2.1788-2.22330.17421700.14733254100
2.2233-2.27160.18351670.14553243100
2.2716-2.32440.19811870.15333265100
2.3244-2.38260.1812060.14423253100
2.3826-2.4470.17961740.14753252100
2.447-2.5190.18721720.15083245100
2.519-2.60030.18251760.14783251100
2.6003-2.69320.18111960.14623252100
2.6932-2.8010.17011340.13923323100
2.801-2.92840.18461440.14433300100
2.9284-3.08270.15181760.14613282100
3.0827-3.27580.16741900.15013264100
3.2758-3.52860.15251950.14293266100
3.5286-3.88340.16761610.14113349100
3.8834-4.44460.14881890.13233288100
4.4446-5.5970.13912000.13893335100
5.597-38.82610.2141680.2053468100
Refinement TLS params.Method: refined / Origin x: 38.2757 Å / Origin y: 2.8413 Å / Origin z: -19.5365 Å
111213212223313233
T0.0624 Å2-0.0061 Å2-0.0064 Å2-0.093 Å2-0.0011 Å2--0.0882 Å2
L0.031 °20.029 °2-0.0017 °2-0.2201 °2-0.0118 °2--0.2788 °2
S-0.0215 Å °0.01 Å °0.0004 Å °-0.0685 Å °0.0182 Å °0.0067 Å °-0.0096 Å °-0.0447 Å °-0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA82 - 469
2X-RAY DIFFRACTION1allA501 - 508
3X-RAY DIFFRACTION1allB82 - 469
4X-RAY DIFFRACTION1allB501 - 508
5X-RAY DIFFRACTION1allA601 - 1065
6X-RAY DIFFRACTION1allA - B601 - 1062

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