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- PDB-4cpz: Structure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 vi... -

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Basic information

Entry
Database: PDB / ID: 4cpz
TitleStructure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 virus in complex with Zanamivir
ComponentsNEURAMINIDASE
KeywordsHYDROLASE / NEURAMINIDASE INHIBITOR / RELENZA
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / 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: 2.2 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 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Apr 1, 2015Group: Derived calculations
Revision 1.3Oct 2, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...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_oper_list.matrix[1][1] ..._pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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_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_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_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEURAMINIDASE
B: NEURAMINIDASE
C: NEURAMINIDASE
D: NEURAMINIDASE
E: NEURAMINIDASE
F: NEURAMINIDASE
G: NEURAMINIDASE
H: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)418,83140
Polymers409,8748
Non-polymers8,95832
Water22,9511274
1
E: NEURAMINIDASE
F: NEURAMINIDASE
hetero molecules

G: NEURAMINIDASE
hetero molecules

H: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,27419
Polymers204,9374
Non-polymers4,33715
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
crystal symmetry operation2_757-x+2,y+1/2,-z+21
Buried area21190 Å2
ΔGint-71 kcal/mol
Surface area47910 Å2
MethodPISA
2
A: NEURAMINIDASE
B: NEURAMINIDASE
C: NEURAMINIDASE
D: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,55721
Polymers204,9374
Non-polymers4,62017
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21640 Å2
ΔGint-67 kcal/mol
Surface area48240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.344, 163.255, 123.451
Angle α, β, γ (deg.)90.00, 108.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
NEURAMINIDASE


Mass: 51234.223 Da / Num. of mol.: 8 / 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 , 4 types, 23 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.: 6
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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
#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.: 8 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication, inhibitor*YM

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Non-polymers , 3 types, 1283 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 2.54 Å3/Da / Density % sol: 51.68 % / 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: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→48.5 Å / Num. obs: 164411 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 34.21 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.9 / % possible all: 93.6

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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 4CPO

4cpo


Resolution: 2.2→48.503 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 8204 5 %
Rwork0.1533 --
obs0.1556 164328 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24126 0 584 1274 25984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725386
X-RAY DIFFRACTIONf_angle_d1.12634267
X-RAY DIFFRACTIONf_dihedral_angle_d17.0759260
X-RAY DIFFRACTIONf_chiral_restr0.0793682
X-RAY DIFFRACTIONf_plane_restr0.0044371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.31662720.25465144X-RAY DIFFRACTION96
2.225-2.25120.27652300.25514644X-RAY DIFFRACTION87
2.2512-2.27860.32872600.24644934X-RAY DIFFRACTION91
2.2786-2.30750.26462550.22185249X-RAY DIFFRACTION98
2.3075-2.33780.29682690.21245298X-RAY DIFFRACTION98
2.3378-2.36990.28142800.20715275X-RAY DIFFRACTION99
2.3699-2.40370.25322840.19465296X-RAY DIFFRACTION98
2.4037-2.43960.25172940.19025261X-RAY DIFFRACTION99
2.4396-2.47770.22572860.17875316X-RAY DIFFRACTION99
2.4777-2.51830.2442630.17865267X-RAY DIFFRACTION98
2.5183-2.56180.26492920.18995304X-RAY DIFFRACTION98
2.5618-2.60830.25122500.1915261X-RAY DIFFRACTION98
2.6083-2.65850.27422630.19325341X-RAY DIFFRACTION99
2.6585-2.71280.25922940.18275234X-RAY DIFFRACTION98
2.7128-2.77170.24772630.16865318X-RAY DIFFRACTION98
2.7717-2.83620.24912790.16725235X-RAY DIFFRACTION98
2.8362-2.90710.22532860.16155291X-RAY DIFFRACTION98
2.9071-2.98570.23382760.16945259X-RAY DIFFRACTION98
2.9857-3.07360.24122570.175211X-RAY DIFFRACTION98
3.0736-3.17280.22982990.16755184X-RAY DIFFRACTION96
3.1728-3.28610.21722430.16214691X-RAY DIFFRACTION87
3.2861-3.41770.22693050.15265209X-RAY DIFFRACTION97
3.4177-3.57320.17952800.14035294X-RAY DIFFRACTION98
3.5732-3.76150.16142930.1325255X-RAY DIFFRACTION98
3.7615-3.9970.14672730.12475278X-RAY DIFFRACTION98
3.997-4.30550.15992870.11635263X-RAY DIFFRACTION98
4.3055-4.73840.14272950.10985247X-RAY DIFFRACTION98
4.7384-5.42330.14392440.11025257X-RAY DIFFRACTION97
5.4233-6.82980.17432620.13174918X-RAY DIFFRACTION91
6.8298-48.5150.15072700.15355390X-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)
10.6302-0.02320.06280.7277-0.12460.43130.05520.0680.16540.0034-0.04240.0985-0.0093-0.0426-0.01320.12510.0080.04580.1601-0.03150.2342-7.294236.307648.6862
20.74880.12130.13730.9073-0.0610.2260.0899-0.0627-0.17280.1882-0.05290.16670.0348-0.0391-0.03320.2228-0.05580.0380.1567-0.01220.2318-10.41360.723766.4491
30.80440.0733-0.09380.7349-0.060.23890.06640.09610.15380.0371-0.0573-0.40840.02070.02120.00060.14460.00640.01560.1713-0.0270.427132.519534.455752.218
40.8135-0.09050.05840.7438-0.03790.15040.1162-0.1273-0.37550.2158-0.0383-0.41080.08910.0311-0.04540.2949-0.0129-0.17120.1760.0160.484929.2026-1.080870.0673
50.5681-0.1127-0.0680.56340.51930.9116-0.12540.0738-0.1762-0.0572-0.29060.35480.3348-0.48060.00860.5226-0.30070.07170.6852-0.18630.118815.382455.3041101.1138
60.8615-0.1584-0.28960.63660.48230.5181-0.0745-0.1342-0.20250.0110.09-0.31210.29360.15750.01480.50.02330.04830.44790.05290.235855.099750.8963103.957
70.9347-0.0796-0.07420.8151-0.22870.69310.07350.18490.44920.037-0.1787-0.3179-0.14360.27140.07260.36570.03770.01620.60040.19420.4283-6.28359.2607115.4277
80.57230.0487-0.19330.8498-0.31760.48980.12330.43070.4283-0.03670.10330.4675-0.0467-0.3765-0.16180.32720.1580.01010.78060.25520.422943.50324.6607112.4321
90.1485-0.0183-0.02110.05750.0180.08620.0379-0.0258-0.02720.0275-0.0156-0.02260.0165-0.0068-0.01450.2225-0.0163-0.00160.2046-0.0120.272812.848423.023769.4104
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 76:700)
4X-RAY DIFFRACTION4(CHAIN D AND RESID 76:700)
5X-RAY DIFFRACTION5(CHAIN E AND RESID 76:700)
6X-RAY DIFFRACTION6(CHAIN F AND RESID 76:700)
7X-RAY DIFFRACTION7(CHAIN G AND RESID 76:700)
8X-RAY DIFFRACTION8(CHAIN H AND RESID 76:700)
9X-RAY DIFFRACTION9((CHAIN A AND RESID 2001:2314) OR (CHAIN B AND RESID 2001:2251) OR (CHAIN C AND RESID 2001:2255) OR (CHAIN D AND RESID 2001:2188) OR (CHAIN E AND RESID 2001:2102) OR (CHAIN F AND RESID 2001:2050) OR (CHAIN G AND RESID 2001:2058) OR (CHAIN H AND RESID 2001:2056))

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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