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- PDB-3k36: Crystal Structure of B/Perth Neuraminidase -

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Basic information

Entry
Database: PDB / ID: 3k36
TitleCrystal Structure of B/Perth Neuraminidase
ComponentsNeuraminidase
KeywordsHYDROLASE / INFLUENZA / NEURAMINIDASE / MUTATION / RESISTANCE / Cell membrane / Glycosidase / Membrane / Transmembrane / Virion
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: 2.2 Å
AuthorsOakley, A.J. / McKimm-Breschkin, J.L.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses.
Authors: Oakley, A.J. / Barrett, S. / Peat, T.S. / Newman, J. / Streltsov, V.A. / Waddington, L. / Saito, T. / Tashiro, M. / McKimm-Breschkin, J.L.
History
DepositionOct 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_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.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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)90,56014
Polymers87,6502
Non-polymers2,91112
Water5,693316
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,75224
Polymers175,2994
Non-polymers5,45320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area15430 Å2
ΔGint-77 kcal/mol
Surface area45800 Å2
MethodPISA
2
B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,48932
Polymers175,2994
Non-polymers6,19028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15300 Å2
ΔGint-77 kcal/mol
Surface area45690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.640, 87.640, 197.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

21A-584-

HOH

31A-598-

HOH

41A-600-

HOH

51B-546-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 78 - 466 / Label seq-ID: 9 - 397

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Neuraminidase


Mass: 43824.836 Da / Num. of mol.: 2 / Fragment: UNP residues 70-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Perth/211/2001 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3S340, exo-alpha-sialidase
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 326 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Na2SO4, 20% w/v PEG3350, 0.1M bis-Tris propane, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95361 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 28, 2007 / Details: BEAMLINE OPTICS
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95361 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. all: 34306 / Num. obs: 34306 / % possible obs: 91.5 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 4.5 % / Biso Wilson estimate: 20.979 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.7 / Num. unique all: 12265 / % possible all: 77.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7NN9

7nn9


Resolution: 2.2→98.53 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.133 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23929 1726 5 %RANDOM
Rwork0.1823 ---
obs0.18511 32580 91.32 %-
all-32580 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.369 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20 Å2
2---1.54 Å20 Å2
3---3.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→98.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 188 316 6516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216439
X-RAY DIFFRACTIONr_bond_other_d0.0020.024441
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9828740
X-RAY DIFFRACTIONr_angle_other_deg0.921310776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9425802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07323.509265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.274151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1631538
X-RAY DIFFRACTIONr_chiral_restr0.0910.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021292
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_it0.5841.53881
X-RAY DIFFRACTIONr_mcbond_other0.1371.51621
X-RAY DIFFRACTIONr_mcangle_it1.05326245
X-RAY DIFFRACTIONr_scbond_it1.70732558
X-RAY DIFFRACTIONr_scangle_it2.5814.52482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2272medium positional0.080.5
2861loose positional0.175
2272medium thermal0.722
2861loose thermal1.1810
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 122 -
Rwork0.227 2000 -
obs--76.19 %

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