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- PDB-9bjm: Crystal Structure of Inhibitor 5c in Complex with Prefusion RSV F... -

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Basic information

Entry
Database: PDB / ID: 9bjm
TitleCrystal Structure of Inhibitor 5c in Complex with Prefusion RSV F Glycoprotein
ComponentsPrefusion RSV F (DS-CAV1),Envelope glycoprotein
KeywordsVIRAL PROTEIN/INHIBITOR / Inhibitor / Viral Protein / Complex / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
: / Envelope glycoprotein / Fusion glycoprotein F0
Similarity search - Component
Biological specieshuman respiratory syncytial virus
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsShaffer, P.L. / Milligan, C. / Abeywickrema, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Spiro-Azetidine Oxindoles as Long-Acting Injectables for Pre-Exposure Prophylaxis against Respiratory Syncytial Virus Infections.
Authors: Kesteleyn, B. / Herschke, F. / Darville, N. / Stoops, B. / Jacobs, T. / Jacoby, E. / Shaffer, P. / Lammens, L. / Van Rompaey, D. / Matcha, K. / Martinez Lamenca, C. / Coesemans, E. / Hache, ...Authors: Kesteleyn, B. / Herschke, F. / Darville, N. / Stoops, B. / Jacobs, T. / Jacoby, E. / Shaffer, P. / Lammens, L. / Van Rompaey, D. / Matcha, K. / Martinez Lamenca, C. / Coesemans, E. / Hache, G. / Pieters, S. / Lecomte, M. / Hu, L. / Demin, S. / Milligan, C. / Abeywickrema, P. / De Bruyn, S. / Van Den Berg, J. / Ysebaert, N. / De Zwart, L. / Najera, I. / Rigaux, P. / Roymans, D. / Jonckers, T.H.M.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prefusion RSV F (DS-CAV1),Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7452
Polymers63,2181
Non-polymers5271
Water5,963331
1
A: Prefusion RSV F (DS-CAV1),Envelope glycoprotein
hetero molecules

A: Prefusion RSV F (DS-CAV1),Envelope glycoprotein
hetero molecules

A: Prefusion RSV F (DS-CAV1),Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,2366
Polymers189,6553
Non-polymers1,5813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area13470 Å2
ΔGint-41 kcal/mol
Surface area50460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.018, 170.018, 170.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-798-

HOH

21A-1006-

HOH

31A-1024-

HOH

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Components

#1: Protein Prefusion RSV F (DS-CAV1),Envelope glycoprotein


Mass: 63218.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human respiratory syncytial virus, (gene. exp.) Human immunodeficiency virus 1
Production host: Homo sapiens (human) / References: UniProt: W8RJF9, UniProt: M1E1E4
#2: Chemical ChemComp-A1APZ / 1'-{[5-chloro-1-(4,4,4-trifluorobutyl)-1H-1,3-benzimidazol-2-yl]methyl}-1-(methanesulfonyl)spiro[azetidine-3,3'-indol]-2'(1'H)-one


Mass: 526.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C23H22ClF3N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3M NaFormate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→49.08 Å / Num. obs: 51555 / % possible obs: 99.98 % / Redundancy: 59.8 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.052 / Net I/σ(I): 22.14
Reflection shellResolution: 2.07→2.144 Å / Redundancy: 58.9 % / Mean I/σ(I) obs: 1.83 / Num. unique obs: 5080 / CC1/2: 0.733 / Rpim(I) all: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDS20210323data reduction
XDS20210323data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→49.08 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 2576 5 %
Rwork0.1846 --
obs0.1855 51551 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 35 331 3673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093393
X-RAY DIFFRACTIONf_angle_d0.9344614
X-RAY DIFFRACTIONf_dihedral_angle_d6.135452
X-RAY DIFFRACTIONf_chiral_restr0.063558
X-RAY DIFFRACTIONf_plane_restr0.007580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.110.38641420.31212679X-RAY DIFFRACTION100
2.11-2.150.23931420.26062694X-RAY DIFFRACTION100
2.15-2.20.24961400.22972664X-RAY DIFFRACTION100
2.2-2.250.24421420.20832697X-RAY DIFFRACTION100
2.25-2.30.251410.20292681X-RAY DIFFRACTION100
2.3-2.370.22141420.19552700X-RAY DIFFRACTION100
2.37-2.430.23171420.19322706X-RAY DIFFRACTION100
2.43-2.510.22781420.20692697X-RAY DIFFRACTION100
2.51-2.60.27781420.21062704X-RAY DIFFRACTION100
2.6-2.710.22951420.19032715X-RAY DIFFRACTION100
2.71-2.830.21211430.18982723X-RAY DIFFRACTION100
2.83-2.980.22511430.19462709X-RAY DIFFRACTION100
2.98-3.170.21131440.18562748X-RAY DIFFRACTION100
3.17-3.410.17511430.1682731X-RAY DIFFRACTION100
3.41-3.750.1741450.15412765X-RAY DIFFRACTION100
3.75-4.30.15681470.14812790X-RAY DIFFRACTION100
4.3-5.410.15541490.14552816X-RAY DIFFRACTION100
5.41-49.080.21361590.21773007X-RAY DIFFRACTION100
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)
10.26620.535-0.05898.31753.15411.4577-0.043-0.1160.00050.42880.05310.23170.189-0.1038-0.03460.2490.0233-0.00620.26610.05250.21710.56579.853635.6719
22.4769-0.17521.46120.8952-0.02082.6782-0.07320.354-0.5673-0.16250.07970.09421.00820.436-0.07820.5237-0.08550.03610.267-0.04070.34388.8548-17.17415.6298
33.0453.14743.46374.90592.33345.1733-0.56950.7214-0.1984-0.77080.26880.23910.35540.09340.35710.723-0.14330.04860.4764-0.15110.55085.0652-14.682-14.6143
42.42150.4430.07213.09630.76052.8568-0.15230.2719-0.6206-0.53790.2979-0.35090.49390.4306-0.14320.39940.07050.040.24010.00620.301518.3713-12.81999.66
54.1326-0.37220.3084.7193-0.61175.8864-0.530.132-1.2533-0.2898-0.481-0.31291.64710.39620.73560.8779-0.02960.14010.35490.01710.84529.1768-25.92787.7512
62.78830.48422.25491.19520.50182.1083-0.10690.3846-0.8343-0.3347-0.05750.28271.0045-0.67310.01550.8233-0.339-0.03320.5984-0.30990.7727-2.4552-19.2775-10.3193
71.17240.0326-0.25621.51020.50741.5332-0.1110.0515-0.2848-0.0015-0.02010.24450.3347-0.14540.17140.2179-0.0177-0.02660.20370.02390.24265.9877-4.45318.2662
81.65750.22950.10973.9721.12281.7003-0.0935-0.10080.00080.0680.04340.16630.0398-0.08170.04090.19640.02-0.00480.26150.05620.224211.04135.085831.7599
92.6411-0.8510.46921.8905-0.49981.53820.0001-0.17740.10590.04430.03140.092-0.0493-0.053-0.02080.2040.02880.02420.2131-0.01440.2080.108923.312330.7077
106.83096.75282.96336.6933.41962.9583-0.0708-0.03780.56740.2624-0.0716-1.0912-0.07020.5254-0.13450.3584-0.0924-0.25220.49920.02870.853829.489931.725641.6081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 170 )
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 239 )
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 345 )
8X-RAY DIFFRACTION8chain 'A' and (resid 346 through 394 )
9X-RAY DIFFRACTION9chain 'A' and (resid 395 through 491 )
10X-RAY DIFFRACTION10chain 'A' and (resid 492 through 516 )

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