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

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Basic information

Entry
Database: PDB / ID: 4cpn
TitleStructure of the Neuraminidase from the B/Brisbane/60/2008 virus in complex with Zanamivir
ComponentsNEURAMINIDASE
KeywordsHYDROLASE / NEURAMINIDASE INHIBITOR / RELENZA
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
ZANAMIVIR / Neuraminidase
Similarity search - Component
Biological speciesINFLUENZA B VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 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 / 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_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_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.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)105,52517
Polymers102,3652
Non-polymers3,16015
Water4,342241
1
A: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,04934
Polymers204,7294
Non-polymers6,32030
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area25620 Å2
ΔGint13.6 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.561, 159.561, 90.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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 , 5 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-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.: 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
#4: 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
#6: Sugar ChemComp-ZMR / ZANAMIVIR / 4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / 4-guanidino-Neu5Ac2en / MODIFIED SIALIC ACID


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication, inhibitor*YM
#8: 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.: 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 , 3 types, 250 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.94 Å3/Da / Density % sol: 68.79 % / 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: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→46.06 Å / Num. obs: 51600 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 41.47 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 / % possible all: 99.1

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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 4CPL

4cpl


Resolution: 2.4→45.176 Å / SU ML: 0.32 / σ(F): 0.43 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 4892 5.1 %
Rwork0.1553 --
obs0.1574 51575 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 207 241 6482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086406
X-RAY DIFFRACTIONf_angle_d1.1738640
X-RAY DIFFRACTIONf_dihedral_angle_d14.1032335
X-RAY DIFFRACTIONf_chiral_restr0.052938
X-RAY DIFFRACTIONf_plane_restr0.0051097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.42740.34341430.32622735X-RAY DIFFRACTION86
2.4274-2.45590.35151640.30262788X-RAY DIFFRACTION88
2.4559-2.48590.30581500.30072737X-RAY DIFFRACTION88
2.4859-2.51730.29651530.28452816X-RAY DIFFRACTION88
2.5173-2.55050.36571750.28992865X-RAY DIFFRACTION90
2.5505-2.58540.28151640.27042918X-RAY DIFFRACTION92
2.5854-2.62230.3191860.25953066X-RAY DIFFRACTION98
2.6223-2.66150.31531960.24973151X-RAY DIFFRACTION99
2.6615-2.70310.28331600.2433145X-RAY DIFFRACTION99
2.7031-2.74740.31671590.23393107X-RAY DIFFRACTION99
2.7474-2.79470.28521630.2193137X-RAY DIFFRACTION98
2.7947-2.84550.23621530.20233103X-RAY DIFFRACTION98
2.8455-2.90030.23991810.18883184X-RAY DIFFRACTION99
2.9003-2.95950.24391390.18233119X-RAY DIFFRACTION98
2.9595-3.02380.24551390.1743065X-RAY DIFFRACTION97
3.0238-3.09410.2031360.16373050X-RAY DIFFRACTION95
3.0941-3.17150.2031700.16253159X-RAY DIFFRACTION99
3.1715-3.25720.24181650.15763139X-RAY DIFFRACTION99
3.2572-3.3530.18691690.15063100X-RAY DIFFRACTION99
3.353-3.46120.20791430.14233176X-RAY DIFFRACTION98
3.4612-3.58490.17791500.13813146X-RAY DIFFRACTION98
3.5849-3.72830.19981930.13013058X-RAY DIFFRACTION97
3.7283-3.89790.18371400.1253037X-RAY DIFFRACTION95
3.8979-4.10330.15781790.11623108X-RAY DIFFRACTION99
4.1033-4.36020.14541740.10833115X-RAY DIFFRACTION98
4.3602-4.69650.14462100.10563066X-RAY DIFFRACTION98
4.6965-5.16860.14751610.10593025X-RAY DIFFRACTION97
5.1686-5.9150.16441680.11873145X-RAY DIFFRACTION98
5.915-7.44690.13011420.12443136X-RAY DIFFRACTION98
7.4469-45.18360.14321670.15013125X-RAY DIFFRACTION98
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)
10.6493-0.23130.05870.9587-0.1020.7665-0.029-0.0771-0.07340.0882-0.0108-0.01980.0960.01930.02750.2846-0.00510.0080.23840.01610.285976.997-21.2977-11.8809
20.39470.09120.06150.99710.05410.726-0.0498-0.05430.11730.1339-0.0006-0.0623-0.08550.02050.05670.27790.0201-0.0240.2325-0.02470.276876.987718.1287-8.5776
30.9679-0.0174-0.37310.16520.20750.70090.08120.08330.00440.21850.21240.0752-0.0986-0.0987-0.30.4640.11750.10780.53770.10550.769774.09176.3436-16.4046
40.23820.1612-0.00240.2849-0.08970.3341-0.0353-0.08180.06970.0455-0.00870.0702-0.0217-0.050.04560.20560.0144-0.02460.2333-0.02370.261675.0854-1.7893-9.5074
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 C AND RESID 1:200)
4X-RAY DIFFRACTION4(CHAIN W AND RESID 1:600)

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