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- PDB-5b2c: Crystal structure of Mumps virus hemagglutinin-neuraminidase -

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Basic information

Entry
Database: PDB / ID: 5b2c
TitleCrystal structure of Mumps virus hemagglutinin-neuraminidase
ComponentsHN protein
KeywordsVIRAL PROTEIN / glycoprotein / beta-propeller / receptor binding
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 / 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
Biological speciesMumps virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.238 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,49812
Polymers108,5362
Non-polymers1,96210
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-17 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.523, 137.523, 178.269
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): HEK293GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9WAF5, exo-alpha-sialidase
#2: 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.: 8
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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 4.48 Å3/Da / Density % sol: 72.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, ammonium sulfate, glycerol

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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: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.238→119.1 Å / Num. obs: 91923 / % possible obs: 100 % / Redundancy: 10.2 % / Net I/σ(I): 14.3
Reflection shellResolution: 2.238→2.245 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.709 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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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: 2.238→119.098 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.28 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2221 4599 5.01 %
Rwork0.202 --
obs0.2036 91851 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.238→119.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7036 0 122 174 7332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047374
X-RAY DIFFRACTIONf_angle_d0.88810078
X-RAY DIFFRACTIONf_dihedral_angle_d12.4582568
X-RAY DIFFRACTIONf_chiral_restr0.0351148
X-RAY DIFFRACTIONf_plane_restr0.0051288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2378-2.27640.30562300.28424338X-RAY DIFFRACTION95
2.2764-2.31780.2892390.28394347X-RAY DIFFRACTION95
2.3178-2.36230.29842150.26864346X-RAY DIFFRACTION95
2.3623-2.41060.30362440.27514367X-RAY DIFFRACTION95
2.4106-2.4630.2992380.27264331X-RAY DIFFRACTION95
2.463-2.52030.30462330.26254323X-RAY DIFFRACTION95
2.5203-2.58330.30392210.25514406X-RAY DIFFRACTION95
2.5833-2.65310.25152400.2564317X-RAY DIFFRACTION95
2.6531-2.73120.24992480.24894317X-RAY DIFFRACTION95
2.7312-2.81930.26452240.23714354X-RAY DIFFRACTION95
2.8193-2.920.26192390.22854365X-RAY DIFFRACTION95
2.92-3.03690.21972410.21424331X-RAY DIFFRACTION95
3.0369-3.17510.22541850.21674411X-RAY DIFFRACTION96
3.1751-3.34240.23082380.20674345X-RAY DIFFRACTION95
3.3424-3.55170.20692190.19394360X-RAY DIFFRACTION95
3.5517-3.82580.21412330.18124375X-RAY DIFFRACTION95
3.8258-4.21050.18762220.16814358X-RAY DIFFRACTION95
4.2105-4.8190.16782190.15014391X-RAY DIFFRACTION95
4.819-6.06850.18362390.16124388X-RAY DIFFRACTION95
6.0685-42.07040.18532320.18614419X-RAY DIFFRACTION95

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