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- PDB-5kv9: Crystal structure of a hPIV haemagglutinin-neuraminidase-inhibito... -

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Basic information

Entry
Database: PDB / ID: 5kv9
TitleCrystal structure of a hPIV haemagglutinin-neuraminidase-inhibitor complex
ComponentsHemagglutinin-neuraminidase
KeywordsHYDROLASE/INHIBITOR / haemagglutinin-neuraminidase / hyrdrolase / viral protein / host cell surface receptor binding / HYDROLASE-INHIBITOR 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 / metabolic process / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane ...exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / metabolic process / 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-I57 / Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesHuman parainfluenza virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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: Atomic model / Data collection / Structure summary / Category: atom_site / chem_comp / entity
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _entity.src_method
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_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_unobs_or_zero_occ_atoms / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.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_type.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

Downloads & links

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Assembly

Deposited unit
B: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3868
Polymers49,0681
Non-polymers1,3187
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin-neuraminidase
hetero molecules

B: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,77216
Polymers98,1352
Non-polymers2,63714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5700 Å2
ΔGint-22 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.098, 107.373, 94.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Hemagglutinin-neuraminidase /


Mass: 49067.660 Da / Num. of mol.: 1
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 , 3 types, 3 molecules

#2: 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.: 1 / Source method: isolated from a natural 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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural 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
#5: Sugar ChemComp-I57 / 2,6-anhydro-3,4,5-trideoxy-5-[(2-methylpropanoyl)amino]-4-(4-phenyl-1H-1,2,3-triazol-1-yl)-D-glycero-D-galacto-non-2-en onic acid / (2~{R},3~{R},4~{S})-3-(2-methylpropanoylamino)-4-(4-phenyl-1,2,3-triazol-1-yl)-2-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)pro pyl]-3,4-dihydro-2~{H}-pyran-6-carboxylic acid


Type: D-saccharide / Mass: 446.454 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H26N4O7

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Non-polymers , 3 types, 251 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.11 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M citrate buffer, 0.2 M ammonium sulfate, 20 % PEG 3000

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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 315r / Detector: CCD / Date: Jan 24, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40.05 Å / Num. obs: 24135 / % possible obs: 87.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.033 / Rrim(I) all: 0.07 / Net I/σ(I): 17.8 / Num. measured all: 98693 / Scaling rejects: 64
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.053.20.259497015430.9070.1520.3035.276.3
8.94-40.054.10.02511312760.9990.0140.02940.878.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å38.05 Å
Translation2 Å38.05 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.17data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XJQ

4xjq


Resolution: 2→36.874 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 1249 5.18 %RANDOM
Rwork0.1616 22883 --
obs0.1639 24132 86.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.07 Å2 / Biso mean: 22.0506 Å2 / Biso min: 9.21 Å2
Refinement stepCycle: final / Resolution: 2→36.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 87 247 3707
Biso mean--34.3 25.23 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093557
X-RAY DIFFRACTIONf_angle_d1.2864852
X-RAY DIFFRACTIONf_chiral_restr0.167558
X-RAY DIFFRACTIONf_plane_restr0.007611
X-RAY DIFFRACTIONf_dihedral_angle_d16.3671329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.08010.24331290.17372245237478
2.0801-2.17480.24861420.17042622276490
2.1748-2.28940.21881330.17372614274790
2.2894-2.43280.22771550.17422600275590
2.4328-2.62060.24261180.16642626274489
2.6206-2.88420.21391530.15982579273288
2.8842-3.30140.17951580.15552544270287
3.3014-4.15850.17541380.14522530266885
4.1585-36.880.19721230.16462523264682

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