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- PDB-5ea5: Crystal Structure of Inhibitor TMC-353121 in Complex with Prefusi... -

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Basic information

Entry
Database: PDB / ID: 5ea5
TitleCrystal Structure of Inhibitor TMC-353121 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
D(-)-TARTARIC ACID / Chem-TM3 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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 1.4Nov 20, 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)64,2305
Polymers63,2181
Non-polymers1,0124
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)192,69115
Polymers189,6553
Non-polymers3,03612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16490 Å2
ΔGint-59 kcal/mol
Surface area47140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.860, 169.860, 169.860
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 / 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-TM3 / 2-[[6-[[[2-(3-hydroxypropyl)-5-methylphenyl]amino]methyl]-2-[[3-(4-morpholinyl)propyl]amino]-1H-benzimidazol-1-yl]methyl]-6-methyl-3-pyridinol / TMC353121


Mass: 558.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N6O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
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: 3.23 Å3/Da / Density % sol: 61.92 %
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: 3.05→49.03 Å / Num. obs: 16585 / % possible obs: 100 % / Redundancy: 25.2 % / Biso Wilson estimate: 72.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.317 / Rpim(I) all: 0.064 / Net I/σ(I): 11.9 / Num. measured all: 418216 / Scaling rejects: 2404
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
3.05-3.2623.52.3791.66901529400.5440.498100
8.63-49.0324.10.03856.22048785110.00899.5

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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: 3.05→49.03 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 789 4.78 %Random selection
Rwork0.2144 15724 --
obs0.216 16513 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.02 Å2 / Biso mean: 82.6233 Å2 / Biso min: 31.38 Å2
Refinement stepCycle: final / Resolution: 3.05→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 69 0 3366
Biso mean--91.06 --
Num. residues----426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063423
X-RAY DIFFRACTIONf_angle_d0.8824630
X-RAY DIFFRACTIONf_chiral_restr0.033554
X-RAY DIFFRACTIONf_plane_restr0.003572
X-RAY DIFFRACTIONf_dihedral_angle_d14.7661248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0503-3.24140.40071230.35252534265799
3.2414-3.49160.26361310.268925622693100
3.4916-3.84280.31831270.219825792706100
3.8428-4.39860.24141190.201326112730100
4.3986-5.54050.18811500.173526262776100
5.5405-49.04070.23661390.199228122951100
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)
11.7609-0.1229-0.04480.5654-0.67820.6621-0.2957-0.3473-0.5987-0.09070.48870.34660.3010.1756-0.14350.5352-0.05-0.00480.44470.10570.55214.31-3.343220.8739
20.86260.718-1.22861.8009-1.49842.30490.43880.3768-0.624-0.6742-0.81661.3288-0.5277-0.00290.64541.2420.2064-0.03240.7218-0.34771.13533.2871-15.2352-15.4116
31.31720.68171.73870.35170.89782.27180.05410.1050.1433-0.1-0.28471.22940.10260.09160.03881.2685-0.16860.32151.41340.46811.9920.719-6.78570.7741
41.3026-0.1968-0.32981.30151.79983.5227-0.0745-0.0122-0.7427-0.2402-0.17710.39830.4893-0.38040.10470.6474-0.0059-0.04180.34050.05620.78947.0404-10.47310.3982
52.403-0.3574-0.06283.21060.15871.35440.0685-0.4845-0.03060.2104-0.0644-0.0299-0.2096-0.2616-0.02740.42140.10070.04260.56990.07980.32035.902717.117231.657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 27 through 73 )F0
2X-RAY DIFFRACTION2chain 'F' and (resid 74 through 97 )F0
3X-RAY DIFFRACTION3chain 'F' and (resid 98 through 104 )F0
4X-RAY DIFFRACTION4chain 'F' and (resid 137 through 339 )F0
5X-RAY DIFFRACTION5chain 'F' and (resid 340 through 506 )F0

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