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- PDB-4cpo: Structure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 virus -

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Basic information

Entry
Database: PDB / ID: 4cpo
TitleStructure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 virus
ComponentsNEURAMINIDASE
KeywordsHYDROLASE / INFLUENZA / NEURAMINIDASE
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 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesINFLUENZA B VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVachieri, S.G. / Collins, P.J. / Escuret, V. / Casalegno, J.S. / Cattle, N. / Ferraris, O. / Sabatier, M. / Frobert, E. / Caro, V. / Skehel, J.J. ...Vachieri, S.G. / Collins, P.J. / Escuret, V. / Casalegno, J.S. / Cattle, N. / Ferraris, O. / Sabatier, M. / Frobert, E. / Caro, V. / Skehel, J.J. / Gamblin, S.J. / Valla, F. / Valette, M. / Ottmann, M. / McCauley, J.W. / Daniels, R.S. / Lina, B.
CitationJournal: J.Infect.Dis. / Year: 2014
Title: A Novel I221 L Substitution in Neuraminidase Confers High Level Resistance to Oseltamivir in Influenza B Viruses.
Authors: Escuret, V. / Collins, P.J. / Casalegno, J. / Vachieri, S.G. / Cattle, N. / Ferraris, O. / Sabatier, M. / Frobert, E. / Caro, V. / Skehel, J.J. / Gamblin, S. / Valla, F. / Valette, M. / ...Authors: Escuret, V. / Collins, P.J. / Casalegno, J. / Vachieri, S.G. / Cattle, N. / Ferraris, O. / Sabatier, M. / Frobert, E. / Caro, V. / Skehel, J.J. / Gamblin, S. / Valla, F. / Valette, M. / Ottmann, M. / Mccauley, J.W. / Daniels, R.S. / Lina, B.
History
DepositionFeb 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 9, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag
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.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_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_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.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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,08128
Polymers102,4682
Non-polymers2,61326
Water11,025612
1
A: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,16256
Polymers204,9374
Non-polymers5,22552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area26560 Å2
ΔGint31 kcal/mol
Surface area46770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.490, 159.490, 89.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

21A-2037-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NEURAMINIDASE /


Mass: 51234.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) INFLUENZA B VIRUS / Strain: B/LYON/CHU/15.216/2011 / References: UniProt: U5XBU0*PLUS, exo-alpha-sialidase

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Sugars , 2 types, 4 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: 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 / N-Acetylglucosamine


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

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Non-polymers , 3 types, 634 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE FOR B/LYON/CHU/15.216/2011 NEURAMINIDASE IS AVAILABLE THROUGH THE GLOBAL INITIATIVE ON ...THE SEQUENCE FOR B/LYON/CHU/15.216/2011 NEURAMINIDASE IS AVAILABLE THROUGH THE GLOBAL INITIATIVE ON SHARING ALL INFLUENZA DATABASE.THE ACCESSION NUMBER IS EPI498043

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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: 3.21 Å3/Da / Density % sol: 61.66 % / Description: NONE
Crystal growDetails: 25% PEG 1500, 0.1M SUCCINIC ACID PH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.2→46.04 Å / Num. obs: 64990 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 16.02 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CPL

4cpl


Resolution: 2.2→46.041 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 3301 5.1 %
Rwork0.1526 --
obs0.1546 64970 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 166 612 6812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076348
X-RAY DIFFRACTIONf_angle_d1.1498524
X-RAY DIFFRACTIONf_dihedral_angle_d15.5132314
X-RAY DIFFRACTIONf_chiral_restr0.079902
X-RAY DIFFRACTIONf_plane_restr0.0041090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23140.28861330.2142589X-RAY DIFFRACTION99
2.2314-2.26470.30071310.21562547X-RAY DIFFRACTION98
2.2647-2.30010.26711670.20242538X-RAY DIFFRACTION98
2.3001-2.33780.24981270.18792557X-RAY DIFFRACTION98
2.3378-2.37820.24121450.18632560X-RAY DIFFRACTION98
2.3782-2.42140.20461280.18162540X-RAY DIFFRACTION96
2.4214-2.4680.20971480.18052401X-RAY DIFFRACTION93
2.468-2.51830.24431320.18032473X-RAY DIFFRACTION96
2.5183-2.57310.22871530.18222593X-RAY DIFFRACTION99
2.5731-2.63290.22361310.16912613X-RAY DIFFRACTION99
2.6329-2.69880.20721280.16142603X-RAY DIFFRACTION99
2.6988-2.77170.17311440.15532598X-RAY DIFFRACTION99
2.7717-2.85330.20971260.16022607X-RAY DIFFRACTION99
2.8533-2.94540.21511310.16272592X-RAY DIFFRACTION99
2.9454-3.05060.20381190.16432615X-RAY DIFFRACTION99
3.0506-3.17270.17551430.14842568X-RAY DIFFRACTION98
3.1727-3.31710.21311550.14872593X-RAY DIFFRACTION98
3.3171-3.49190.1751240.1382514X-RAY DIFFRACTION96
3.4919-3.71060.16371140.13392456X-RAY DIFFRACTION92
3.7106-3.9970.16361450.12072635X-RAY DIFFRACTION99
3.997-4.39890.15811380.11222627X-RAY DIFFRACTION99
4.3989-5.03480.10251500.10242621X-RAY DIFFRACTION98
5.0348-6.34060.15791580.13092587X-RAY DIFFRACTION96
6.3406-46.05090.15621310.16672642X-RAY DIFFRACTION95
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)
10.2746-0.01250.08080.4830.01810.4715-0.0055-0.02470.02380.0915-0.0076-0.0452-0.03730.02050.01470.1263-0.0019-0.00330.0997-0.00840.1008-78.727119.2628-9.4831
20.1348-0.0752-0.08380.41670.0060.507-0.0075-0.0191-0.02880.0641-0.0131-0.02850.07170.01450.01240.1266-0.0118-0.01140.09210.00260.1099-78.8208-20.2295-10.4234
30.1729-0.00110.01070.7577-0.00640.23170.0171-0.0396-0.00590.0685-0.0286-0.0422-0.00390.00820.00610.1227-0.00680.00170.1348-0.00580.0882-79.47750.6877-8.9768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 76:700)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 76:700)
3X-RAY DIFFRACTION3((CHAIN A AND RESID 2001:2315) OR (CHAIN B AND RESID 2001:2297))

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