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- PDB-5ea4: Crystal Structure of Inhibitor JNJ-49153390 in Complex with Prefu... -

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Basic information

Entry
Database: PDB / ID: 5ea4
TitleCrystal Structure of Inhibitor JNJ-49153390 in Complex with Prefusion RSV F Glycoprotein
ComponentsFusion glycoprotein F0
KeywordsCELL INVASION/INHIBITOR / Class I viral fusion protein / fusion / respiratory syncytial virus / prefusion / viral protein / fusion inhibitor / CELL INVASION-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / 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 / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Chem-5NM / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBattles, M.B. / McLellan, J.S. / Arnoult, E. / Roymans, D. / Langedijk, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Charles H. Hood Foundation United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Molecular mechanism of respiratory syncytial virus fusion inhibitors.
Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / ...Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / Arnoult, E. / Peeples, M.E. / Roymans, D. / McLellan, J.S.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)64,4108
Polymers63,2181
Non-polymers1,1927
Water4,360242
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)193,23124
Polymers189,6553
Non-polymers3,57621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area17430 Å2
ΔGint-238 kcal/mol
Surface area49180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.370, 168.370, 168.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11F-905-

HOH

21F-925-

HOH

31F-939-

HOH

41F-941-

HOH

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 63218.344 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain (UNP residues 1-513) / Mutation: S190F, V207L, S155C, S290C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Plasmid: p(alpha)H / Cell line (production host): HEK293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-5NM / 3-[[5-bromanyl-1-(3-methylsulfonylpropyl)benzimidazol-2-yl]methyl]-1-cyclopropyl-imidazo[4,5-c]pyridin-2-one / JNJ-49153390


Mass: 504.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22BrN5O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.54 M potassium/sodium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.3→48.6 Å / Num. obs: 36823 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.039 / Net I/σ(I): 17.4 / Num. measured all: 731556 / Scaling rejects: 133
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3816.11.7591.85736535670.6570.449100
8.91-48.620.30.02965.81543376210.00799.5

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MMS

4mms


Resolution: 2.3→48.6 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 1848 5.03 %Random selection
Rwork0.1787 34925 --
obs0.1805 36773 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.56 Å2 / Biso mean: 50.721 Å2 / Biso min: 20.78 Å2
Refinement stepCycle: final / Resolution: 2.3→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 69 242 3735
Biso mean--84.14 47.07 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053549
X-RAY DIFFRACTIONf_angle_d0.8924809
X-RAY DIFFRACTIONf_chiral_restr0.033574
X-RAY DIFFRACTIONf_plane_restr0.004592
X-RAY DIFFRACTIONf_dihedral_angle_d13.2091290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.36240.3251440.26042638X-RAY DIFFRACTION100
2.3624-2.43190.29681430.24242630X-RAY DIFFRACTION100
2.4319-2.51040.27271350.23292646X-RAY DIFFRACTION100
2.5104-2.60010.26081400.2342623X-RAY DIFFRACTION100
2.6001-2.70420.25371380.21662648X-RAY DIFFRACTION100
2.7042-2.82730.22241650.20732612X-RAY DIFFRACTION100
2.8273-2.97630.2321520.20752659X-RAY DIFFRACTION100
2.9763-3.16270.2441380.19582656X-RAY DIFFRACTION100
3.1627-3.40690.19861360.17532685X-RAY DIFFRACTION100
3.4069-3.74960.22081360.16052711X-RAY DIFFRACTION100
3.7496-4.29190.18861260.14452730X-RAY DIFFRACTION100
4.2919-5.40620.15741450.13832755X-RAY DIFFRACTION100
5.4062-48.60.20091500.17612932X-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)
10.421.25591.02715.10634.84365.13020.1744-0.65420.12020.921-0.33010.64050.2217-0.26010.20690.25390.08450.03510.41610.13330.3543-2.91617.616836.3096
20.7107-0.2568-0.36423.53992.29963.5882-0.0506-0.0221-0.20130.12240.05720.07340.4256-0.08960.01770.22980.0054-0.02140.30560.07360.30875.9088-5.830519.7177
37.2036-2.17255.83833.6807-1.52487.38210.08640.8993-0.0569-1.0558-0.0773-0.31230.11550.5163-0.0431.2954-0.1910.08171.3476-0.27111.19970.6818-23.6391-23.422
49.39113.12536.27112.75551.75619.9747-0.39190.9257-0.0268-0.20140.16760.07360.02150.4342-0.00480.6385-0.00230.01110.4764-0.10090.51135.7933-14.2624-13.6687
52.19390.7250.55483.58881.53152.87780.02440.4603-0.9011-0.38730.1572-0.14640.69660.0165-0.31570.6666-0.0043-0.00410.3685-0.03930.60718.7539-21.9549-0.4475
60.91440.0443-0.08271.69421.84913.362-0.07570.0057-0.2738-0.1144-0.04870.23630.3366-0.2370.11860.2725-0.02-0.05210.28360.03410.36953.148-8.188310.3051
71.4016-0.39470.04713.79680.09230.9075-0.0477-0.2176-0.18430.19440.0970.00610.0333-0.0356-0.03910.2620.0161-0.01970.36810.06330.26910.4395.650430.6609
82.5803-1.0050.25942.659-0.16672.0661-0.0101-0.34610.21920.20520.01340.0145-0.1253-0.0819-0.01550.27020.04950.02890.2561-0.01590.1592.923922.572131.2008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 26 through 33 )F0
2X-RAY DIFFRACTION2chain 'F' and (resid 34 through 62 )F0
3X-RAY DIFFRACTION3chain 'F' and (resid 63 through 73 )F0
4X-RAY DIFFRACTION4chain 'F' and (resid 74 through 103 )F0
5X-RAY DIFFRACTION5chain 'F' and (resid 137 through 216 )F0
6X-RAY DIFFRACTION6chain 'F' and (resid 217 through 331 )F0
7X-RAY DIFFRACTION7chain 'F' and (resid 332 through 394 )F0
8X-RAY DIFFRACTION8chain 'F' and (resid 395 through 506 )F0

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