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- PDB-7kqd: Prefusion RSV F Bound to RV521 -

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Basic information

Entry
Database: PDB / ID: 7kqd
TitlePrefusion RSV F Bound to RV521
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / DS-Cav1 / RSV F / inhibitor
Function / homology
Function and homology information


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-WVA / Fusion glycoprotein F0
Similarity search - Component
Biological speciesRespiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.94 Å
AuthorsMcLellan, J.S.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of Sisunatovir (RV521), an Inhibitor of Respiratory Syncytial Virus Fusion.
Authors: Cockerill, G.S. / Angell, R.M. / Bedernjak, A. / Chuckowree, I. / Fraser, I. / Gascon-Simorte, J. / Gilman, M.S.A. / Good, J.A.D. / Harland, R. / Johnson, S.M. / Ludes-Meyers, J.H. / ...Authors: Cockerill, G.S. / Angell, R.M. / Bedernjak, A. / Chuckowree, I. / Fraser, I. / Gascon-Simorte, J. / Gilman, M.S.A. / Good, J.A.D. / Harland, R. / Johnson, S.M. / Ludes-Meyers, J.H. / Littler, E. / Lumley, J. / Lunn, G. / Mathews, N. / McLellan, J.S. / Paradowski, M. / Peeples, M.E. / Scott, C. / Tait, D. / Taylor, G. / Thom, M. / Thomas, E. / Villalonga Barber, C. / Ward, S.E. / Watterson, D. / Williams, G. / Young, P. / Powell, K.
History
DepositionNov 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)64,2418
Polymers63,2181
Non-polymers1,0237
Water00
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)192,72324
Polymers189,6553
Non-polymers3,06821
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18080 Å2
ΔGint-319 kcal/mol
Surface area48810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.610, 168.610, 168.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Fusion glycoprotein F0 / Fusion glycoprotein F1 / Fusion glycoprotein F2


Mass: 63218.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus / Cell line (production host): FreeStyle 293 / Production host: Homo sapiens (human) / References: UniProt: C3UPB8
#2: Chemical ChemComp-WVA / 1'-{[5-(aminomethyl)-1-(4,4,4-trifluorobutyl)-1H-benzimidazol-2-yl]methyl}-6'-fluorospiro[cyclopropane-1,3'-indol]-2'(1'H)-one / Sisunatovir


Mass: 446.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22F4N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M CHES pH 9.0, 0.2 M lithium sulfate and 1.77 M potassium/sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→45.06 Å / Num. obs: 18058 / % possible obs: 100 % / Redundancy: 34.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.362 / Rpim(I) all: 0.063 / Rrim(I) all: 0.367 / Net I/σ(I): 13.3 / Num. measured all: 616976 / Scaling rejects: 234
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.94-3.1229.22.718334628540.5250.5062.7581.7100
8.82-45.06300.053235377850.9990.010.05444.299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ea4

5ea4


Resolution: 2.94→39.742 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 874 4.86 %
Rwork0.2055 17123 -
obs0.2077 17997 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.18 Å2 / Biso mean: 70.0373 Å2 / Biso min: 25.42 Å2
Refinement stepCycle: final / Resolution: 2.94→39.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 62 0 3468
Biso mean--117.06 --
Num. residues----441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.9405-3.12460.32071450.29682781
3.1246-3.36580.33761430.26342787
3.3658-3.70430.30941450.21682800
3.7043-4.23980.26291360.19742840
4.2398-5.33960.17841460.15912871
5.3396-39.7420.22671590.19833044
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2942-0.4216-0.16492.04731.25233.3598-0.080.3404-0.4236-0.21530.07130.12430.53680.07010.01890.356-0.16620.01380.4054-0.0030.51963.1874-9.4343.7692
22.11570.8210.61360.54810.1745.2759-0.14270.3258-0.3937-1.11620.5727-0.32770.33750.6783-0.34110.62960.0502-0.03370.43570.04060.574118.05-12.54716.3951
33.13851.50590.11842.38580.91613.8622-0.09520.3082-0.6693-0.0892-0.03280.12190.5972-0.30270.11860.7333-0.1152-0.14380.421-0.16430.74791.9524-19.89-3.0608
43.31750.4896-0.96024.49423.35768.9424-0.3281-0.3687-1.39260.75930.09140.26611.9214-0.1790.02810.7455-0.1326-0.03370.47430.080.84760.0479-18.788718.0072
51.55550.1199-0.36781.98791.49962.96270.0281-0.0964-0.1831-0.1556-0.0570.2410.0996-0.176-0.10090.26420.008-0.06260.28520.04710.29358.04561.739421.0436
61.6253-1.2545-0.88974.9835-0.50391.3604-0.0274-0.2749-0.0950.2270.0975-0.126-0.132-0.16-0.00120.2673-0.0406-0.04250.45830.06530.372910.52688.276130.1506
71.206-0.5613-0.37792.73061.00312.06160.1865-0.28310.0740.2599-0.04090.0916-0.1434-0.1743-0.03930.40850.0317-0.00250.38280.04060.30811.815219.785628.6918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 27 through 96 )F27 - 96
2X-RAY DIFFRACTION2chain 'F' and (resid 97 through 170 )F97 - 170
3X-RAY DIFFRACTION3chain 'F' and (resid 171 through 253 )F171 - 253
4X-RAY DIFFRACTION4chain 'F' and (resid 254 through 276 )F254 - 276
5X-RAY DIFFRACTION5chain 'F' and (resid 277 through 352 )F277 - 352
6X-RAY DIFFRACTION6chain 'F' and (resid 353 through 403 )F353 - 403
7X-RAY DIFFRACTION7chain 'F' and (resid 404 through 214 )F404 - 214

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