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- PDB-3ti3: Crystal structure of 2009 pandemic H1N1 neuraminidase complexed w... -

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Basic information

Entry
Database: PDB / ID: 3ti3
TitleCrystal structure of 2009 pandemic H1N1 neuraminidase complexed with laninamivir
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 6-BLADED BETA-PROPELLER / Calcium Binding / Glycosylation / antiviral / HYDROLASE-HYDROLASE INHIBITOR complex
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 / identical protein binding / membrane
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
ACETATE ION / Chem-LNV / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Atomic model / Data collection ...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_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_auth_seq_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_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
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
Revision 2.2Oct 16, 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)87,66918
Polymers85,4552
Non-polymers2,21316
Water22,8611269
1
A: Neuraminidase
B: Neuraminidase
hetero molecules

A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,33736
Polymers170,9114
Non-polymers4,42732
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area17480 Å2
ΔGint-160 kcal/mol
Surface area43880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.260, 137.089, 118.482
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
11A-603-

CA

21A-1302-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase


Mass: 42727.629 Da / Num. of mol.: 2 / Fragment: UNP residues 82-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009(H1N1) / Gene: NA / Plasmid: pAcGP67-B / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C3W5S3

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Sugars , 3 types, 5 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.: 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
#3: 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.: 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 / 5-(acetylamino)-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.: 2 / Source method: obtained synthetically / Formula: C13H22N4O7

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Non-polymers , 4 types, 1280 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1269 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16M calcium acetate hydrate, 0.08M sodium cacodylate trihydrate, 14.4% polyethylene glycol 8000, 20% glycerol , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 6, 2010
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. all: 89057 / Num. obs: 89057 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.98 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata 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 3NSS

3nss


Resolution: 1.8→34.599 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8777 / SU ML: 0.21 / σ(F): 0.13 / Phase error: 19.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 4305 4.99 %RANDOM
Rwork0.1938 ---
obs0.1948 86190 96.67 %-
all-86190 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.309 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 59.34 Å2 / Biso mean: 12.888 Å2 / Biso min: 1.06 Å2
Baniso -1Baniso -2Baniso -3
1--2.5834 Å20 Å2-0 Å2
2--4.6482 Å20 Å2
3----2.0648 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 139 1269 7390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046368
X-RAY DIFFRACTIONf_angle_d0.9358651
X-RAY DIFFRACTIONf_dihedral_angle_d21.3242319
X-RAY DIFFRACTIONf_chiral_restr0.063924
X-RAY DIFFRACTIONf_plane_restr0.0051118
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 (%)
1.799-1.81940.24381170.20472514263190
1.8194-1.84080.23721250.19342540266590
1.8408-1.86320.22561200.19412577269792
1.8632-1.88680.19071260.19222649277593
1.8868-1.91170.23441270.18762613274093
1.9117-1.93780.18131330.18552609274294
1.9378-1.96550.22191390.18862683282295
1.9655-1.99490.21781580.1822616277496
1.9949-2.0260.20761370.17882664280195
2.026-2.05920.20751370.17242754289197
2.0592-2.09470.19581460.17872681282796
2.0947-2.13280.20711530.17712698285197
2.1328-2.17380.21491480.17342697284597
2.1738-2.21820.19961330.18092744287797
2.2182-2.26640.20421410.18422752289397
2.2664-2.31910.21221330.19462747288097
2.3191-2.37710.23321260.19392751287798
2.3771-2.44140.22391480.19442760290898
2.4414-2.51320.22521520.19182769292198
2.5132-2.59430.23481510.19442762291398
2.5943-2.6870.19391610.19432740290198
2.687-2.79450.22371520.19372778293099
2.7945-2.92160.17741570.18822820297799
2.9216-3.07560.19951420.18612783292599
3.0756-3.26810.20751510.18892819297099
3.2681-3.52030.20671470.177528322979100
3.5203-3.87410.16771440.177328552999100
3.8741-4.43370.19371620.176728533015100
4.4337-5.58220.19731650.20082874303999
5.5822-34.60590.2651740.26372951312599

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