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- PDB-6hfc: Influenza A Virus N9 Neuraminidase Native (Tern). -

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Basic information

Entry
Database: PDB / ID: 6hfc
TitleInfluenza A Virus N9 Neuraminidase Native (Tern).
ComponentsNeuraminidase
KeywordsHYDROLASE / Complex / Native / Neuraminidase / N9 / Influenza / Virus / Enzyme
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 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
CARBON DIOXIDE / : / PHOSPHATE ION / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsSalinger, M.T. / Hobbs, J.R. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Garman, E.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: To Be Published
Title: High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (In preparation)
Authors: Salinger, M.T. / Hobbs, J.R. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Garman, E.F.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _citation_author.identifier_ORCID / _citation_author.name
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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_symmetry / _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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,23617
Polymers43,7241
Non-polymers3,51216
Water10,611589
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,94468
Polymers174,8954
Non-polymers14,04964
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area24540 Å2
ΔGint-20 kcal/mol
Surface area46550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.000, 180.000, 180.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-515-

CA

21A-817-

HOH

31A-1095-

HOH

41A-1189-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase /


Mass: 43723.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)
Strain: A/Tern/Australia/G70C/1975 H11N9 / References: UniProt: P03472, exo-alpha-sialidase

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+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.: 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

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Non-polymers , 6 types, 602 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: N9 crystals were grown by-hanging drop vapour diffusion against a reservoir of 1.9M potassium phosphate, pH 6.8, starting with equal volumes of N9 NA solution (10 to 15 mg/ml in water) and ...Details: N9 crystals were grown by-hanging drop vapour diffusion against a reservoir of 1.9M potassium phosphate, pH 6.8, starting with equal volumes of N9 NA solution (10 to 15 mg/ml in water) and potassium phosphate buffer 1.4M KH2PO4: 3M K2HPO4 in ratio 8:4, pH 6.6 at 20 degrees celsius. Large rhombic dodecahedral crystals grew within a few days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.83 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 1.29→30.89 Å / Num. obs: 122339 / % possible obs: 100 % / Redundancy: 20.5 % / Rsym value: 0.105 / Net I/σ(I): 11.7
Reflection shellResolution: 1.29→1.32 Å / Redundancy: 19.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5993 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NN9

7nn9


Resolution: 1.29→30.89 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.929 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16367 6189 5.1 %RANDOM
Rwork0.14127 ---
obs0.14238 116150 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.271 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.29→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 226 589 3882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0143680
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183035
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.7475067
X-RAY DIFFRACTIONr_angle_other_deg1.1931.7197229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.9975.525467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72621.189185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33715542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3551529
X-RAY DIFFRACTIONr_chiral_restr0.1210.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024572
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02680
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_it1.3411.7081712
X-RAY DIFFRACTIONr_mcbond_other1.3231.7071711
X-RAY DIFFRACTIONr_mcangle_it1.8762.5642189
X-RAY DIFFRACTIONr_mcangle_other1.8792.5652190
X-RAY DIFFRACTIONr_scbond_it2.9842.1441968
X-RAY DIFFRACTIONr_scbond_other2.9472.1361962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2933.0982872
X-RAY DIFFRACTIONr_long_range_B_refined6.31624.7324552
X-RAY DIFFRACTIONr_long_range_B_other6.00523.3374356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.293→1.327 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 506 -
Rwork0.377 8406 -
obs--99.99 %

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