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- PDB-6n6b: The complex crystal structure of neuraminidase from A/Minnesota/1... -

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Basic information

Entry
Database: PDB / ID: 6n6b
TitleThe complex crystal structure of neuraminidase from A/Minnesota/11/2010 with B10 antibody.
Components
  • (B10 antibody ...) x 2
  • Neuraminidase
KeywordsVIRAL PROTEIN/Immune System / neuraminidase / influenza / antibody complex / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
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 / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsYang, H. / Stevens, J.
CitationJournal: Nat Microbiol / Year: 2019
Title: The neuraminidase of A(H3N2) influenza viruses circulating since 2016 is antigenically distinct from the A/Hong Kong/4801/2014 vaccine strain.
Authors: Wan, H. / Gao, J. / Yang, H. / Yang, S. / Harvey, R. / Chen, Y.Q. / Zheng, N.Y. / Chang, J. / Carney, P.J. / Li, X. / Plant, E. / Jiang, L. / Couzens, L. / Wang, C. / Strohmeier, S. / Wu, W. ...Authors: Wan, H. / Gao, J. / Yang, H. / Yang, S. / Harvey, R. / Chen, Y.Q. / Zheng, N.Y. / Chang, J. / Carney, P.J. / Li, X. / Plant, E. / Jiang, L. / Couzens, L. / Wang, C. / Strohmeier, S. / Wu, W.W. / Shen, R.F. / Krammer, F. / Cipollo, J.F. / Wilson, P.C. / Stevens, J. / Wan, X.F. / Eichelberger, M.C. / Ye, Z.
History
DepositionNov 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_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 / _struct_conn.ptnr2_symmetry
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
K: B10 antibody Heavy Chain Fab
L: B10 antibody Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8216
Polymers91,6493
Non-polymers1,1723
Water4,234235
1
A: Neuraminidase
K: B10 antibody Heavy Chain Fab
L: B10 antibody Light Chain Fab
hetero molecules

A: Neuraminidase
K: B10 antibody Heavy Chain Fab
L: B10 antibody Light Chain Fab
hetero molecules

A: Neuraminidase
K: B10 antibody Heavy Chain Fab
L: B10 antibody Light Chain Fab
hetero molecules

A: Neuraminidase
K: B10 antibody Heavy Chain Fab
L: B10 antibody Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,28324
Polymers366,59512
Non-polymers4,68812
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area44450 Å2
ΔGint-131 kcal/mol
Surface area118770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.471, 188.471, 136.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase


Mass: 43797.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Minnesota/11/2010(H3N2))
Strain: A/Minnesota/11/2010(H3N2) / Gene: NA, L998_47822gpNA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A075ETL7, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules KL

#2: Antibody B10 antibody Heavy Chain Fab


Mass: 24047.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: hybrid (others)
#3: Antibody B10 antibody Light Chain Fab


Mass: 23803.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: hybrid (others)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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, 236 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 6.62 Å3/Da / Density % sol: 81.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl (pH 8.5) and 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 97962 / % possible obs: 100 % / Redundancy: 5 % / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.864 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24478 5115 5 %RANDOM
Rwork0.21988 ---
obs0.22111 97962 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.445 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6383 0 76 235 6694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.026634
X-RAY DIFFRACTIONr_bond_other_d0.0020.025771
X-RAY DIFFRACTIONr_angle_refined_deg2.3081.9439039
X-RAY DIFFRACTIONr_angle_other_deg1.237313470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7045820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67323.937287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.215151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791537
X-RAY DIFFRACTIONr_chiral_restr0.1570.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217350
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021375
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7183.4013289
X-RAY DIFFRACTIONr_mcbond_other3.6963.43288
X-RAY DIFFRACTIONr_mcangle_it5.425.0874106
X-RAY DIFFRACTIONr_mcangle_other5.4195.0894107
X-RAY DIFFRACTIONr_scbond_it4.5283.7293345
X-RAY DIFFRACTIONr_scbond_other4.5263.7293345
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.625.4174934
X-RAY DIFFRACTIONr_long_range_B_refined8.48637.7936935
X-RAY DIFFRACTIONr_long_range_B_other8.49137.7866935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 270 -
Rwork0.285 6088 -
obs--82.56 %

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