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- PDB-5b2d: Crystal structure of Mumps virus hemagglutinin-neuraminidase boun... -

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Basic information

Entry
Database: PDB / ID: 5b2d
TitleCrystal structure of Mumps virus hemagglutinin-neuraminidase bound to 3-sialyllactose
ComponentsHN protein
KeywordsVIRAL PROTEIN / glycoprotein / beta-propeller / receptor binding / sugar
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / 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
3'-sialyl-alpha-lactose / Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesMumps virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.177 Å
AuthorsKubota, M. / Takeuchi, K. / Watanabe, S. / Ohno, S. / Matsuoka, R. / Kohda, D. / Hiramatsu, H. / Suzuki, Y. / Nakayama, T. / Terada, T. ...Kubota, M. / Takeuchi, K. / Watanabe, S. / Ohno, S. / Matsuoka, R. / Kohda, D. / Hiramatsu, H. / Suzuki, Y. / Nakayama, T. / Terada, T. / Shimizu, K. / Shimizu, N. / Yanagi, Y. / Hashiguchi, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Trisaccharide containing alpha 2,3-linked sialic acid is a receptor for mumps virus
Authors: Kubota, M. / Takeuchi, K. / Watanabe, S. / Ohno, S. / Matsuoka, R. / Kohda, D. / Nakakita, S.I. / Hiramatsu, H. / Suzuki, Y. / Nakayama, T. / Terada, T. / Shimizu, K. / Shimizu, N. / ...Authors: Kubota, M. / Takeuchi, K. / Watanabe, S. / Ohno, S. / Matsuoka, R. / Kohda, D. / Nakakita, S.I. / Hiramatsu, H. / Suzuki, Y. / Nakayama, T. / Terada, T. / Shimizu, K. / Shimizu, N. / Shiroishi, M. / Yanagi, Y. / Hashiguchi, T.
History
DepositionJan 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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 / software
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HN protein
B: HN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,11115
Polymers108,5362
Non-polymers3,57513
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-0 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.875, 136.875, 177.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HN protein / Hemagglutinin-neuraminidase


Mass: 54267.961 Da / Num. of mol.: 2 / Fragment: UNP residues 106-582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mumps virus / Strain: Hoshino / Gene: HN / Cell line (production host): 293SGnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9WAF5, exo-alpha-sialidase
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: 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.: 10
Source method: isolated from a genetically manipulated 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.42 Å3/Da / Density % sol: 72.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium acetate, ammonium sulfate, glycerol, 3-sialyllactose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.177→177.274 Å / Num. obs: 98249 / % possible obs: 100 % / Redundancy: 10 % / Net I/σ(I): 10.9
Reflection shellResolution: 2.177→2.184 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.083 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
autoPROCdata processing
XDSdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E8V

1e8v


Resolution: 2.177→118.537 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1906 4907 5 %
Rwork0.1765 --
obs0.1783 98172 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.177→118.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7036 0 231 234 7501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067490
X-RAY DIFFRACTIONf_angle_d1.10910250
X-RAY DIFFRACTIONf_dihedral_angle_d13.4952568
X-RAY DIFFRACTIONf_chiral_restr0.191190
X-RAY DIFFRACTIONf_plane_restr0.0051296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1771-2.21470.27632500.24484641X-RAY DIFFRACTION95
2.2147-2.25490.25392520.23864629X-RAY DIFFRACTION95
2.2549-2.29830.29142360.24044643X-RAY DIFFRACTION95
2.2983-2.34520.21272370.22854686X-RAY DIFFRACTION95
2.3452-2.39620.23522270.2284651X-RAY DIFFRACTION95
2.3962-2.4520.24122440.2214673X-RAY DIFFRACTION95
2.452-2.51330.23272400.20684655X-RAY DIFFRACTION95
2.5133-2.58120.20852670.20984634X-RAY DIFFRACTION95
2.5812-2.65720.2062150.20074663X-RAY DIFFRACTION96
2.6572-2.74290.19872570.19544673X-RAY DIFFRACTION95
2.7429-2.8410.21032430.18714651X-RAY DIFFRACTION95
2.841-2.95470.19572530.18324627X-RAY DIFFRACTION95
2.9547-3.08920.18452350.17774691X-RAY DIFFRACTION95
3.0892-3.2520.19342440.18124682X-RAY DIFFRACTION95
3.252-3.45580.18642790.16664607X-RAY DIFFRACTION94
3.4558-3.72250.17732330.15914679X-RAY DIFFRACTION95
3.7225-4.09710.16772580.15424668X-RAY DIFFRACTION95
4.0971-4.68960.1562560.13854674X-RAY DIFFRACTION95
4.6896-5.90740.17162330.1464707X-RAY DIFFRACTION95
5.9074-56.2290.18042460.17914728X-RAY DIFFRACTION95

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