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- PDB-5kv8: Crystal structure of a hPIV haemagglutinin-neuraminidase-inhibito... -

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Entry
Database: PDB / ID: 5kv8
TitleCrystal structure of a hPIV haemagglutinin-neuraminidase-inhibitor complex
ComponentsHemagglutinin-neuraminidase
KeywordsHYDROLASE/INHIBITOR / haemagglutinin-neuraminidase / hydrolase / viral protein / host cell surface receptor binding / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


metabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane ...metabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / 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-6Y6 / beta-D-mannopyranose / CITRIC ACID / alpha-D-mannopyranose / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesHuman parainfluenza virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.949 Å
AuthorsDirr, L. / El-Deeb, I.M. / Chavas, L.M.G. / Guillon, P. / von Itzstein, M.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP1094549 Australia
National Health and Medical Research Council (NHMRC, Australia)ID1047824 Australia
National Health and Medical Research Council (NHMRC, Australia)ID1071659 Australia
CitationJournal: Sci Rep / Year: 2017
Title: The impact of the butterfly effect on human parainfluenza virus haemagglutinin-neuraminidase inhibitor design.
Authors: Dirr, L. / El-Deeb, I.M. / Chavas, L.M.G. / Guillon, P. / Itzstein, M.V.
History
DepositionJul 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Apr 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Jul 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_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_conn.pdbx_dist_value / _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 3.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,79326
Polymers97,8212
Non-polymers3,97224
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-35 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.570, 98.612, 103.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hemagglutinin-neuraminidase


Mass: 48910.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parainfluenza virus 3 / Cell line (production host): Sf9 cells / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G8G134, exo-alpha-sialidase

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Sugars , 4 types, 13 molecules

#2: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-6Y6 / 2,6-anhydro-3,4,5-trideoxy-4-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]-5-[(2-methylpropanoyl)amino]-D-glycero-D-galacto -non-2-enonic acid / (2~{R},3~{R},4~{S})-4-[4-(methoxymethyl)-1,2,3-triazol-1-yl]-3-(2-methylpropanoylamino)-2-[(1~{R},2~{R})-1,2,3-tris(oxi danyl)propyl]-3,4-dihydro-2~{H}-pyran-6-carboxylic acid


Type: D-saccharide / Mass: 414.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C17H26N4O8
#9: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 656 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
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H8O7
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M citrate buffer, 0.2 M ammonium sulphate, 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 6, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.949→45.784 Å / Num. obs: 61585 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.95-25.60.793199.1
8.93-45.7846.30.025199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.59 Å45.78 Å
Translation7.59 Å45.78 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.6data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XJQ

4xjq


Resolution: 1.949→45.784 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 19.41
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 6008 5.11 %RANDOM
Rwork0.161 ---
obs0.163 61585 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.21 Å2 / Biso mean: 27.14 Å2 / Biso min: 12.29 Å2
Refinement stepCycle: final / Resolution: 1.949→45.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6692 0 253 647 7592
Biso mean--45.22 33.51 -
Num. residues----854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097131
X-RAY DIFFRACTIONf_angle_d1.2239690
X-RAY DIFFRACTIONf_chiral_restr0.0531122
X-RAY DIFFRACTIONf_plane_restr0.0051211
X-RAY DIFFRACTIONf_dihedral_angle_d13.7662624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9488-1.9710.30351750.26353699387498
1.971-1.99420.28212360.24537153951100
1.9942-2.01850.27032170.219736253842100
2.0185-2.04410.25732210.216137423963100
2.0441-2.0710.28672140.214536843898100
2.071-2.09930.23851990.237813980100
2.0993-2.12930.24432090.194436703879100
2.1293-2.16110.24911690.195537983967100
2.1611-2.19490.25191890.189437513940100
2.1949-2.23080.24211580.183337013859100
2.2308-2.26930.21432000.184137533953100
2.2693-2.31060.2582040.181437103914100
2.3106-2.3550.25711850.180137243909100
2.355-2.40310.24911930.175637223915100
2.4031-2.45530.20162020.172737323934100
2.4553-2.51240.23862200.164536883908100
2.5124-2.57530.1712210.159536953916100
2.5753-2.64490.19572080.160537443952100
2.6449-2.72270.20772110.155537183929100
2.7227-2.81060.19322070.153737013908100
2.8106-2.9110.18591940.148137073901100
2.911-3.02760.20441940.15537043898100
3.0276-3.16530.19262040.146937633967100
3.1653-3.33210.19551830.147137083891100
3.3321-3.54080.172200.140737123932100
3.5408-3.81410.17572140.139137093923100
3.8141-4.19770.14721630.135837543917100
4.1977-4.80450.15052240.124236923916100
4.8045-6.0510.17681810.144637483929100
6.051-45.79640.19241930.176637173910100

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