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- PDB-4b7j: H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neura... -

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Basic information

Entry
Database: PDB / ID: 4b7j
TitleH1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis
ComponentsNEURAMINIDASE
KeywordsHYDROLASE / NEURAMINIDASE INHIBITOR / NAI / NAIS / OSELTAMIVIR / ZANAMIVIR / ANTIVIRAL RESISTANCE / IMMUNOCOMPROMISED / H275Y
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-G39 / Neuraminidase
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.417 Å
Authorsvan der Vries, E. / Vachieri, S.G. / Xiong, X. / Liu, J. / Collins, P.J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. ...van der Vries, E. / Vachieri, S.G. / Xiong, X. / Liu, J. / Collins, P.J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. / Martin, S.R. / Boucher, C.A.B. / Skehel, J.J. / Gamblin, S.J.
CitationJournal: Plos Pathog. / Year: 2012
Title: H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis
Authors: Van Der Vries, E. / Collins, P.J. / Vachieri, S.G. / Xiong, X. / Liu, J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. / Martin, S.R. / Boucher, C.A.B. / ...Authors: Van Der Vries, E. / Collins, P.J. / Vachieri, S.G. / Xiong, X. / Liu, J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. / Martin, S.R. / Boucher, C.A.B. / Skehel, J.J. / Gamblin, S.J.
History
DepositionAug 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Jul 17, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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 / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_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)52,6876
Polymers51,6991
Non-polymers9885
Water4,161231
1
A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,74724
Polymers206,7954
Non-polymers3,95220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17530 Å2
ΔGint-80.3 kcal/mol
Surface area45310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.550, 118.550, 67.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-2091-

HOH

21A-2131-

HOH

31A-2132-

HOH

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Components

#1: Protein NEURAMINIDASE / 2009 N1 NEURAMINIDASE


Mass: 51698.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: OSELTAMIVIR LIGAND BOUND / Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/NETHERLANDS/2631_1202/2010 / Description: PATIENT ISOLATE / Variant: H1N1 / Plasmid: PHW2000 / Production host: GALLUS GALLUS (chicken) / References: UniProt: F8UU09
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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.: 1 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication, antivirus*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.8 Å3/Da / Density % sol: 56.13 % / Description: NONE
Crystal growDetails: 15% PEG3350, 0.1M BIS-TRIS PROPANE, 0.1M SODIUM ACETATE BUFFER (PH 4.6)

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.42→83.83 Å / Num. obs: 19102 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.4
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.417→83.828 Å / SU ML: 0.61 / σ(F): 1.37 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 931 5.1 %
Rwork0.1892 --
obs0.1914 18127 95.16 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.23 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2907 Å20 Å20 Å2
2---0.2907 Å20 Å2
3---0.5814 Å2
Refinement stepCycle: LAST / Resolution: 2.417→83.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 63 231 3292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033150
X-RAY DIFFRACTIONf_angle_d0.8344268
X-RAY DIFFRACTIONf_dihedral_angle_d12.2551131
X-RAY DIFFRACTIONf_chiral_restr0.056451
X-RAY DIFFRACTIONf_plane_restr0.003552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4173-2.54470.2779970.23951628X-RAY DIFFRACTION65
2.5447-2.70410.28971540.24612531X-RAY DIFFRACTION100
2.7041-2.91290.28121460.21582522X-RAY DIFFRACTION100
2.9129-3.20610.22631570.18942529X-RAY DIFFRACTION100
3.2061-3.670.20191360.16282575X-RAY DIFFRACTION100
3.67-4.62380.18911130.14972632X-RAY DIFFRACTION100
4.6238-83.87790.22511280.19422779X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2676-0.0057-0.06870.3491-0.0390.2029-0.03580.08940.0459-0.0810.03130.1386-0.0399-0.0140.00990.0845-0.0255-0.06610.0710.0159-0.004341.0666-0.35919.2582
20.2294-00.04110.26040.00060.15220.02050.0381-0.06610.0660.00040.05050.0358-0.00160.00160.05850.015-0.0209-0.10690.02370.138930.8224-9.89327.3019
30.06550.0561-0.09770.2914-0.03610.16870.0210.21020.0718-0.16630.04090.29730.0016-0.2276-0.0587-0.21080.0496-0.19250.09680.0460.069418.76655.221619.6329
40.42890.0323-0.12820.2938-0.08570.27290.07420.13580.1845-0.1240.01930.1473-0.0637-0.00840.1532-0.00830.0178-0.07020.06890.04950.094632.59268.483717.9131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 83:156)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 157:311)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 312:376)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 377:469)

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