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- PDB-8phi: Crystal structure of prefusion-stabilized RSV F Variant DS-Cav1 i... -

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Basic information

Entry
Database: PDB / ID: 8phi
TitleCrystal structure of prefusion-stabilized RSV F Variant DS-Cav1 in complex with Lonafarnib
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / RSV F Glycoprotein / inhibitor
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Chem-336 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.289 Å
AuthorsRajak, M. / Krey, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen Foundation9B811 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Drug repurposing screen identifies lonafarnib as respiratory syncytial virus fusion protein inhibitor.
Authors: Sake, S.M. / Zhang, X. / Rajak, M.K. / Urbanek-Quaing, M. / Carpentier, A. / Gunesch, A.P. / Grethe, C. / Matthaei, A. / Ruckert, J. / Galloux, M. / Larcher, T. / Le Goffic, R. / Hontonnou, ...Authors: Sake, S.M. / Zhang, X. / Rajak, M.K. / Urbanek-Quaing, M. / Carpentier, A. / Gunesch, A.P. / Grethe, C. / Matthaei, A. / Ruckert, J. / Galloux, M. / Larcher, T. / Le Goffic, R. / Hontonnou, F. / Chatterjee, A.K. / Johnson, K. / Morwood, K. / Rox, K. / Elgaher, W.A.M. / Huang, J. / Wetzke, M. / Hansen, G. / Fischer, N. / Eleouet, J.F. / Rameix-Welti, M.A. / Hirsch, A.K.H. / Herold, E. / Empting, M. / Lauber, C. / Schulz, T.F. / Krey, T. / Haid, S. / Pietschmann, T.
History
DepositionJun 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5966
Polymers61,5811
Non-polymers1,0155
Water3,189177
1
F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,78918
Polymers184,7433
Non-polymers3,04615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15670 Å2
ΔGint-175 kcal/mol
Surface area52930 Å2
Unit cell
Length a, b, c (Å)88.640, 88.640, 194.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules F

#1: Protein Fusion glycoprotein F0


Mass: 61581.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Strain: strain A2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: W8RJF9

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Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-336 / 4-{2-[4-(3,10-DIBROMO-8-CHLORO-6,11-DIHYDRO-5H-BENZO[5,6]CYCLOHEPTA[1,2-B]PYRIDIN-11-YL)PIPERIDIN-1-YL]-2-OXOETHYL}PIPERIDINE-1-CARBOXAMIDE / SCH66336 / Lonafarnib


Mass: 638.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31Br2ClN4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000-20%, CaCl2-400mM, & TrisHCl pH-8 100mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91983 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 2.289→50 Å / Num. obs: 51465 / % possible obs: 99.9 % / Redundancy: 26.1 % / CC1/2: 0.997 / Rrim(I) all: 0.243 / Net I/σ(I): 10.54
Reflection shellResolution: 2.289→2.35 Å / Mean I/σ(I) obs: 1.66 / Num. unique obs: 3770 / CC1/2: 0.882 / Rrim(I) all: 1.755 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (17-FEB-2023)refinement
XDSdata reduction
XSCALEJan 10, 2022data scaling
PHASER1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.289→26.21 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1174 4.56 %RANDOM
Rwork0.1984 ---
obs0.1998 25724 99.9 %-
Displacement parametersBiso mean: 65.03 Å2
Baniso -1Baniso -2Baniso -3
1--15.7215 Å20 Å20 Å2
2---15.7215 Å20 Å2
3---31.443 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.289→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 58 177 3687
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073584HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984867HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1261SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes604HARMONIC5
X-RAY DIFFRACTIONt_it3584HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion17.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3146SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.31 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3285 -3.69 %
Rwork0.4267 496 -
all0.4224 515 -
obs--97.29 %

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