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- PDB-4cpl: Structure of the Neuraminidase from the B/Brisbane/60/2008 virus. -

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Basic information

Entry
Database: PDB / ID: 4cpl
TitleStructure of the Neuraminidase from the B/Brisbane/60/2008 virus.
ComponentsNEURAMINIDASE
KeywordsHYDROLASE
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 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 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _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)104,1018
Polymers102,3652
Non-polymers1,7376
Water14,430801
1
A: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,20216
Polymers204,7294
Non-polymers3,47312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area18840 Å2
ΔGint-88.1 kcal/mol
Surface area48830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.784, 159.784, 91.592
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-2052-

HOH

21A-2055-

HOH

31A-2056-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NEURAMINIDASE /


Mass: 51182.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) INFLUENZA B VIRUS (B/BRISBANE/60/2008) / References: UniProt: C0LT34, exo-alpha-sialidase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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
#5: 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.: 1
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 , 2 types, 803 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 801 / 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: 4.02 Å3/Da / Density % sol: 69.41 % / 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: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→46.13 Å / Num. obs: 90807 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.84
Reflection shellResolution: 2→2.11 Å / Redundancy: 7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4G

1a4g


Resolution: 2→46.126 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 14.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1609 4554 5 %
Rwork0.1375 --
obs0.1387 90803 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 2→46.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 111 801 6934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076343
X-RAY DIFFRACTIONf_angle_d1.1388573
X-RAY DIFFRACTIONf_dihedral_angle_d16.1662325
X-RAY DIFFRACTIONf_chiral_restr0.083920
X-RAY DIFFRACTIONf_plane_restr0.0041098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.22351650.17482847X-RAY DIFFRACTION100
2.0227-2.04650.21071450.17612834X-RAY DIFFRACTION100
2.0465-2.07150.20281660.16622826X-RAY DIFFRACTION100
2.0715-2.09770.19441620.16272850X-RAY DIFFRACTION100
2.0977-2.12530.1861610.15392820X-RAY DIFFRACTION100
2.1253-2.15440.17611460.15492861X-RAY DIFFRACTION100
2.1544-2.18520.17721600.14672868X-RAY DIFFRACTION100
2.1852-2.21780.17461360.14012874X-RAY DIFFRACTION100
2.2178-2.25250.16891550.1422840X-RAY DIFFRACTION100
2.2525-2.28940.15871550.13832855X-RAY DIFFRACTION100
2.2894-2.32890.18381470.14162853X-RAY DIFFRACTION100
2.3289-2.37120.18241500.14612853X-RAY DIFFRACTION100
2.3712-2.41680.1641450.14282878X-RAY DIFFRACTION100
2.4168-2.46620.16731280.13792885X-RAY DIFFRACTION100
2.4662-2.51980.1511520.13612851X-RAY DIFFRACTION100
2.5198-2.57840.18881480.13822885X-RAY DIFFRACTION100
2.5784-2.64290.16421360.13842851X-RAY DIFFRACTION100
2.6429-2.71430.17621530.14462874X-RAY DIFFRACTION100
2.7143-2.79420.18051600.14162885X-RAY DIFFRACTION100
2.7942-2.88440.17741650.14622849X-RAY DIFFRACTION100
2.8844-2.98740.18821470.14382869X-RAY DIFFRACTION100
2.9874-3.1070.18991310.14132907X-RAY DIFFRACTION100
3.107-3.24840.16241410.13632890X-RAY DIFFRACTION100
3.2484-3.41960.14661520.12982886X-RAY DIFFRACTION100
3.4196-3.63380.12961480.12432900X-RAY DIFFRACTION100
3.6338-3.91420.13441460.11972901X-RAY DIFFRACTION100
3.9142-4.30780.12131720.11142873X-RAY DIFFRACTION100
4.3078-4.93060.11311350.10932923X-RAY DIFFRACTION100
4.9306-6.20960.16031650.14452946X-RAY DIFFRACTION100
6.2096-46.13790.18081820.16433015X-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)
10.51810.2453-0.00780.6494-0.08990.63340.022-0.02480.00670.0937-0.01860.02080.0032-0.0134-0.00680.1583-0.00650.02230.15960.00840.167619.9155-77.39832.8417
20.76140.14080.06230.49590.02060.46540.0356-0.05320.0350.0732-0.0311-0.04140.00840.005-0.00110.1693-0.0105-0.00270.14380.00180.166454.2676-57.5786.2506
30.66320.18260.00920.2997-0.01130.21280.0256-0.03810.02150.0764-0.0275-0.01080.0017-0.020.00530.21890.01240.01620.1727-0.00260.182536.7998-67.11145.5433
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 2001:2426) OR (CHAIN B AND RESID 2001:2375))

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