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- PDB-4wef: Structure of the Hemagglutinin-neuraminidase from Human parainflu... -

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Basic information

Entry
Database: PDB / ID: 4wef
TitleStructure of the Hemagglutinin-neuraminidase from Human parainfluenza virus type III: complex with difluorosialic acid
ComponentsHemagglutinin-neuraminidase glycoprotein
KeywordsVIRAL PROTEIN / neuraminidase / hPIV3 HN / complex / difluorosialic acid / covalent inhibitor / second receptor binding site
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / plasma membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-DF4 / Chem-FSI / Chem-SFJ / Hemagglutinin-neuraminidase glycoprotein
Similarity search - Component
Biological speciesHuman parainfluenza virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsStreltsov, V.A. / Pilling, P. / Barrett, S. / McKimm-Breschkin, J.
CitationJournal: Antiviral Res. / Year: 2015
Title: Catalytic mechanism and novel receptor binding sites of human parainfluenza virus type 3 hemagglutinin-neuraminidase (hPIV3 HN)
Authors: Streltsov, V.A. / Pilling, P. / Barrett, S. / McKimm-Breschkin, J.L.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references / Experimental preparation
Revision 1.3Jan 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_mod_residue / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin-neuraminidase glycoprotein
B: Hemagglutinin-neuraminidase glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,82630
Polymers96,1552
Non-polymers6,67128
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-162 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.668, 218.668, 109.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hemagglutinin-neuraminidase glycoprotein


Mass: 48077.688 Da / Num. of mol.: 2 / Fragment: UNP residues 142-572 / Mutation: S408G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parainfluenza virus 3 / Gene: HN / Cell line (production host): HIGH FIVE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6WJ03

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Sugars , 5 types, 11 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 2 / Source method: obtained synthetically / 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
#5: Sugar ChemComp-FSI / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 3-FLUOROSIALIC ACID / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid


Type: D-saccharide, beta linking / Mass: 327.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18FNO9
IdentifierTypeProgram
b-D-Neup5Ac3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#7: Sugar ChemComp-SFJ / (2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid / (2R,3R,4R,5R,6R)-5-(acetylamino)-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxy lic acid / 2,3-difluoro-sialic acid / 5-acetamido-2,3-difluoro-3-hydroxy-6-[1,2,3-trihydroxypropyl]oxane-2-carboxylic acid


Type: D-saccharide / Mass: 329.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H17F2NO8

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Non-polymers , 4 types, 608 molecules

#6: Chemical ChemComp-DF4 / (3R,4R,5R,6R)-5-(acetylamino)-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-3,4,5,6-tetrahydropyranium-2-carboxylate


Mass: 309.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16FNO8
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 591 / 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: 68.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 1.0M (NH4)2SO4, 1.0M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→188.98 Å / Num. obs: 50876 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 8 % / Rmerge(I) obs: 0.292 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data processing
PHASERphasing
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
SCALEPACKdata reduction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V3C

1v3c


Resolution: 2.5→77.46 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.646 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 2666 5 %RANDOM
Rwork0.18944 ---
obs0.19282 50876 99.91 %-
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: 36.063 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→77.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 421 591 7762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197367
X-RAY DIFFRACTIONr_bond_other_d0.0020.026795
X-RAY DIFFRACTIONr_angle_refined_deg1.82.02210077
X-RAY DIFFRACTIONr_angle_other_deg0.973.00415632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6235860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26624.077287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7461538
X-RAY DIFFRACTIONr_chiral_restr0.0880.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217930
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021564
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 181 -
Rwork0.322 3685 -
obs--99.72 %

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