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- PDB-3tib: Crystal structure of 1957 pandemic H2N2 neuraminidase complexed w... -

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Entry
Database: PDB / ID: 3tib
TitleCrystal structure of 1957 pandemic H2N2 neuraminidase complexed with laninamivir octanoate
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 6-BLADED BETA-PROPELLER / Calcium Binding / Glycosylation / antiviral / 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
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-LVO / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsVavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. ...Vavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. / Wang, J. / Liu, H. / Jiang, H. / Gao, G.F.
CitationJournal: Plos Pathog. / Year: 2011
Title: Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition
Authors: Vavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. / Wang, J. / Liu, H. / Jiang, H. / Gao, G.F.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
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_unobs_or_zero_occ_atoms / 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_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_unobs_or_zero_occ_atoms.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
Revision 2.1Nov 1, 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
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,03220
Polymers208,2894
Non-polymers6,74316
Water25,1131394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20550 Å2
ΔGint-14 kcal/mol
Surface area45690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.454, 140.180, 90.298
Angle α, β, γ (deg.)90.00, 101.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Neuraminidase /


Mass: 52072.328 Da / Num. of mol.: 4
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, 12 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.: 4
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.: 4
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-LVO / 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid / 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid / Laninamivir octanoate


Type: D-saccharide / Mass: 472.533 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N4O8

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Non-polymers , 2 types, 1398 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1394 / 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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M BIS-TRIS propane(pH 9.0), 10% v/v Jeffamine ED-2001 (pH 7.0) , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 111014 / Num. obs: 111014 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 11.77 Å2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.9

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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: PDB ENTRY 1IVG

1ivg


Resolution: 2.201→43.172 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8993 / SU ML: 0.22 / σ(F): 0.07 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.191 5184 4.99 %Random
Rwork0.1548 ---
obs0.1566 103790 93.08 %-
all-103790 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.559 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 84.08 Å2 / Biso mean: 15.7281 Å2 / Biso min: 1.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.2291 Å2-0 Å23.7623 Å2
2---3.5553 Å2-0 Å2
3---3.3262 Å2
Refinement stepCycle: LAST / Resolution: 2.201→43.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12068 0 420 1394 13882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612857
X-RAY DIFFRACTIONf_angle_d0.98417449
X-RAY DIFFRACTIONf_dihedral_angle_d24.1354757
X-RAY DIFFRACTIONf_chiral_restr0.0781911
X-RAY DIFFRACTIONf_plane_restr0.0072250
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2013-2.22630.21561200.17092756287679
2.2263-2.25250.20421610.16373126328787
2.2525-2.280.21311660.16473068323489
2.28-2.30880.22691450.17123115326088
2.3088-2.33920.2261680.17193126329489
2.3392-2.37130.20611700.16353160333089
2.3713-2.40510.20951650.15733141330690
2.4051-2.4410.21021680.15963239340790
2.441-2.47920.21051460.16243151329790
2.4792-2.51980.21351670.16583216338391
2.5198-2.56330.21541680.16583208337691
2.5633-2.60990.20711750.16333258343392
2.6099-2.660.20411890.16173258344793
2.66-2.71430.20431650.16223222338793
2.7143-2.77330.24991650.16233335350093
2.7733-2.83780.2071550.18363103325888
2.8378-2.90880.22761430.17243114325787
2.9088-2.98740.19781640.16063305346995
2.9874-3.07530.18721930.15953367356096
3.0753-3.17450.20081990.15593437363697
3.1745-3.2880.18892160.1523386360297
3.288-3.41960.16581890.14123460364998
3.4196-3.57510.17562110.13763463367499
3.5751-3.76350.16151910.13393494368599
3.7635-3.99910.15991710.12943483365498
3.9991-4.30770.14521880.12913528371698
4.3077-4.74070.14961690.123485365498
4.7407-5.42550.15171770.12673498367599
5.4255-6.83120.17741940.15833532372699
6.8312-43.18040.2041860.19393572375899
Refinement TLS params.Method: refined / Origin x: 12.1936 Å / Origin y: -0.3033 Å / Origin z: 14.8905 Å
111213212223313233
T0.0017 Å20.0009 Å2-0.0248 Å2-0.0223 Å2-0.0005 Å2---0.0081 Å2
L0.1053 °20.0075 °2-0.0651 °2-0.2189 °2-0.0037 °2--0.0867 °2
S-0.001 Å °-0.004 Å °-0.0119 Å °0.0239 Å °0.0033 Å °-0.0197 Å °-0.01 Å °0.003 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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