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Basic information

Entry
Database: PDB / ID: 4mwy
TitleShanghai N9-laninamivir
ComponentsNeuraminidase
KeywordsHYDROLASE / 6-BLADED BETA-PROPELLER / Glycosylation
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-LNV / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWu, Y. / Qi, J.X. / Gao, F. / Gao, G.F.
CitationJournal: Cell Res. / Year: 2013
Title: Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses
Authors: Wu, Y. / Bi, Y.H. / Vavricka, C.J. / Sun, X.M. / Zhang, Y.F. / Gao, F. / Zhao, M. / Xiao, H.X. / Qin, C.F. / He, J.H. / Liu, W.J. / Yan, J.H. / Qi, J.X. / Gao, G.F.
History
DepositionSep 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Oct 21, 2015Group: Database references / Source and taxonomy
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
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_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 / _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

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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)45,9146
Polymers43,5261
Non-polymers2,3885
Water10,719595
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,65524
Polymers174,1024
Non-polymers9,55320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation23_555-z,y,x1
Buried area26020 Å2
ΔGint87 kcal/mol
Surface area46180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.516, 181.516, 181.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-720-

HOH

21A-840-

HOH

31A-924-

HOH

41A-1003-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase


Mass: 43525.500 Da / Num. of mol.: 1 / Fragment: UNP residues 78-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/1/2013(H7N9) / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A067Y7N7*PLUS

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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-LNV / 5-acetamido-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

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Non-polymers , 2 types, 596 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5%(v/v)(+/-)-2-Methyl-2,4-pentanediol, 0.1M HEPES, 10% Polyethylene glycol 10000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 47220 / Num. obs: 47220 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Biso Wilson estimate: 12.46 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.784 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.9222 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 13.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1537 2389 5.06 %
Rwork0.1368 --
all0.1377 47217 -
obs0.1377 47217 99.98 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.69 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 61.71 Å2 / Biso mean: 14.2917 Å2 / Biso min: 4.09 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 158 595 3806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063342
X-RAY DIFFRACTIONf_angle_d1.1414562
X-RAY DIFFRACTIONf_chiral_restr0.082512
X-RAY DIFFRACTIONf_plane_restr0.005574
X-RAY DIFFRACTIONf_dihedral_angle_d22.9691249
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7999-1.83670.2091300.182926272757100
1.8367-1.87660.21561450.165525832728100
1.8766-1.92030.1691270.147826072734100
1.9203-1.96830.16491360.13726002736100
1.9683-2.02150.18191320.127226172749100
2.0215-2.0810.14581390.1297259127301.01
2.081-2.14810.16971560.129825882744100
2.1481-2.22490.18091280.134926182746100
2.2249-2.3140.14231490.128726132762100
2.314-2.41930.15241340.13226322766100
2.4193-2.54680.17261510.136725912742100
2.5468-2.70640.17741490.143926302779100
2.7064-2.91530.13831350.137426502785100
2.9153-3.20860.14781450.135326522797100
3.2086-3.67270.15021430.131426702813100
3.6727-4.62630.1151460.119227052851100
4.6263-42.79580.13881440.152528542998100
Refinement TLS params.Method: refined / Origin x: 20.0076 Å / Origin y: -54.618 Å / Origin z: 20.0142 Å
111213212223313233
T0.0508 Å2-0.0075 Å2-0.005 Å2-0.0514 Å20.0022 Å2--0.0448 Å2
L0.1831 °20.0052 °2-0.0204 °2-0.0616 °2-0.0209 °2--0.265 °2
S0.0134 Å °-0.0258 Å °0.0025 Å °0.0226 Å °-0.0175 Å °-0.012 Å °-0.0192 Å °0.0354 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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