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- PDB-9qd0: Structure of Beilong paramyxovirus receptor binding protein -

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Basic information

Entry
Database: PDB / ID: 9qd0
TitleStructure of Beilong paramyxovirus receptor binding protein
ComponentsAttachment glycoprotein
KeywordsVIRAL PROTEIN / Receptor binding protein / glycoprotein / attachment protein
Function / homology
Function and homology information


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 / Sialidase superfamily
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-mannopyranose / Attachment glycoprotein
Similarity search - Component
Biological speciesJeilongvirus beilongi
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsStelfox, A.J. / Bowden, T.A.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K503113/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L505031/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/M50659X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/M508111/1 United Kingdom
Wellcome Trust203141/Z/16Z United Kingdom
CitationJournal: To Be Published
Title: Structure of the Jeilongvirus Receptor Binding Receptor Protein Provides a Molecular Basis for Elongation of the Paramyxoviral C-terminus
Authors: Stelfox, A.J. / Javorsky, A. / Stass, R. / Sutton, G. / El Omari, K. / Bowden, T.A.
History
DepositionMar 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Attachment glycoprotein
A: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0078
Polymers121,0722
Non-polymers1,9356
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-1 kcal/mol
Surface area42340 Å2
Unit cell
Length a, b, c (Å)87.980, 162.380, 226.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Attachment glycoprotein


Mass: 60535.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jeilongvirus beilongi / Production host: Homo (humans) / References: UniProt: Q287X2
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}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.: 3 / 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
#4: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / 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-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: obtained synthetically / 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
Has ligand of interestN
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: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals grew in 0.2 M potassium thiocynate, 0.1 M sodium cacodylate pH 6.5, 8% w/v poly-gamma-glutamic acid polymer (PGA), 6% 1,5-diaminopentance di-HCl.
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 3.5→73.18 Å / Num. obs: 20626 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 108.65 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.04 / Rrim(I) all: 0.15 / Net I/σ(I): 13.8
Reflection shellResolution: 3.5→3.56 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2888 / CC1/2: 0.87 / Rpim(I) all: 0.29 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→55.23 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 1009 4.89 %
Rwork0.2461 --
obs0.2474 20626 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→55.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8531 0 61 0 8592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028822
X-RAY DIFFRACTIONf_angle_d0.56511995
X-RAY DIFFRACTIONf_dihedral_angle_d11.2043287
X-RAY DIFFRACTIONf_chiral_restr0.0441358
X-RAY DIFFRACTIONf_plane_restr0.0041503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.680.4071550.36342733X-RAY DIFFRACTION98
3.68-3.920.34571380.29842725X-RAY DIFFRACTION98
3.92-4.220.33141440.27542758X-RAY DIFFRACTION98
4.22-4.640.2571460.22052786X-RAY DIFFRACTION99
4.64-5.310.25631550.20932791X-RAY DIFFRACTION100
5.31-6.690.29741120.25282882X-RAY DIFFRACTION100
6.69-55.230.21851590.22682942X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 64.2573 Å / Origin y: 81.4212 Å / Origin z: 87.4874 Å
111213212223313233
T0.8317 Å2-0.0067 Å20.0164 Å2-0.8424 Å2-0.128 Å2--0.8217 Å2
L0.1806 °20.037 °20.1293 °2-0.6756 °20.0598 °2--0.3535 °2
S-0.0112 Å °0.0297 Å °0.0419 Å °-0.1247 Å °0.2278 Å °0 Å °0.0361 Å °-0.1735 Å °0.1227 Å °
Refinement TLS groupSelection details: all

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