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- PDB-9qd1: Structure of J paramyxovirus virus receptor binding protein -

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Basic information

Entry
Database: PDB / ID: 9qd1
TitleStructure of J paramyxovirus virus 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
Attachment glycoprotein
Similarity search - Component
Biological speciesJ virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

Downloads & links

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Assembly

Deposited unit
A: Attachment glycoprotein
B: Attachment glycoprotein


Theoretical massNumber of molelcules
Total (without water)96,1982
Polymers96,1982
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-16 kcal/mol
Surface area30900 Å2
Unit cell
Length a, b, c (Å)164.240, 164.240, 112.470
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 Attachment glycoprotein


Mass: 48099.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) J virus / Production host: Homo sapiens (human) / References: UniProt: Q49HN3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystals grew in 0.1 M carboxylic acid, 0.1 M tris/bicine pH 8.5, 6% sucrose, 0.2 M ammonium sulphate, 37.5% Morpheus (Molecular dimensions) precipitant mix 4, consisting of 25% v/v 2-methyl- ...Details: Crystals grew in 0.1 M carboxylic acid, 0.1 M tris/bicine pH 8.5, 6% sucrose, 0.2 M ammonium sulphate, 37.5% Morpheus (Molecular dimensions) precipitant mix 4, consisting of 25% v/v 2-methyl-2,4-pentanediol (MPD), 25% w/v PEG 1000 (P1k) and 25% w/v polyethylene glycol 3350 (PEG 3350).
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: Feb 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.2→60.11 Å / Num. obs: 87311 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.06 / Rrim(I) all: 0.19 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 2.34 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2889 / CC1/2: 0.48 / Rpim(I) all: 0.76 / Rrim(I) all: 2.46

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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: 2.2→46.4 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 4448 5.09 %
Rwork0.1893 --
obs0.1903 87311 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6764 0 0 286 7050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.632
X-RAY DIFFRACTIONf_dihedral_angle_d13.6072453
X-RAY DIFFRACTIONf_chiral_restr0.0471056
X-RAY DIFFRACTIONf_plane_restr0.0051219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.33471190.34212770X-RAY DIFFRACTION100
2.23-2.250.36971630.33772722X-RAY DIFFRACTION100
2.25-2.280.36251390.33162765X-RAY DIFFRACTION100
2.28-2.310.34071460.32412742X-RAY DIFFRACTION100
2.31-2.340.36721600.32392756X-RAY DIFFRACTION100
2.34-2.370.30941570.3042738X-RAY DIFFRACTION100
2.37-2.40.29871210.29332734X-RAY DIFFRACTION100
2.4-2.440.29981560.27062769X-RAY DIFFRACTION100
2.44-2.480.29441540.26682736X-RAY DIFFRACTION100
2.48-2.520.31161650.26352746X-RAY DIFFRACTION100
2.52-2.560.36711540.24492740X-RAY DIFFRACTION100
2.56-2.610.27721290.24052787X-RAY DIFFRACTION100
2.61-2.660.23251530.23692761X-RAY DIFFRACTION100
2.66-2.710.2531610.23362713X-RAY DIFFRACTION100
2.71-2.770.24821270.22562772X-RAY DIFFRACTION100
2.77-2.840.26331530.22312778X-RAY DIFFRACTION100
2.84-2.910.2341460.21782734X-RAY DIFFRACTION100
2.91-2.990.24361400.20722778X-RAY DIFFRACTION100
2.99-3.070.26271530.20472754X-RAY DIFFRACTION100
3.07-3.170.21021400.19682778X-RAY DIFFRACTION100
3.17-3.290.20391410.18122772X-RAY DIFFRACTION100
3.29-3.420.19531260.18082793X-RAY DIFFRACTION100
3.42-3.570.19811640.17662766X-RAY DIFFRACTION100
3.57-3.760.18041400.17592750X-RAY DIFFRACTION100
3.76-40.16591470.15952782X-RAY DIFFRACTION100
4-4.30.17371430.14322774X-RAY DIFFRACTION100
4.31-4.740.13811950.13232748X-RAY DIFFRACTION100
4.74-5.420.14141410.13772782X-RAY DIFFRACTION100
5.42-6.820.19161630.17262785X-RAY DIFFRACTION100
6.83-46.40.17021520.1522838X-RAY DIFFRACTION100

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