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- PDB-5kww: Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefu... -

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Basic information

Entry
Database: PDB / ID: 5kww
TitleCrystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein
ComponentsFusion glycoprotein F0, Envelope glycoprotein chimera
KeywordsVIRAL PROTEIN/INHIBITOR / Class I viral fusion protein / respiratory syncytial virus / viral protein / fusion inhibitor / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Chem-6YA / Envelope glycoprotein / Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMcLellan, J.S. / Battles, M.B. / Arnoult, E. / Roymans, D. / Langedijk, J.P.
CitationJournal: Nat Commun / Year: 2017
Title: Therapeutic efficacy of a respiratory syncytial virus fusion inhibitor.
Authors: Roymans, D. / Alnajjar, S.S. / Battles, M.B. / Sitthicharoenchai, P. / Furmanova-Hollenstein, P. / Rigaux, P. / Berg, J.V.D. / Kwanten, L. / Ginderen, M.V. / Verheyen, N. / Vranckx, L. / ...Authors: Roymans, D. / Alnajjar, S.S. / Battles, M.B. / Sitthicharoenchai, P. / Furmanova-Hollenstein, P. / Rigaux, P. / Berg, J.V.D. / Kwanten, L. / Ginderen, M.V. / Verheyen, N. / Vranckx, L. / Jaensch, S. / Arnoult, E. / Voorzaat, R. / Gallup, J.M. / Larios-Mora, A. / Crabbe, M. / Huntjens, D. / Raboisson, P. / Langedijk, J.P. / Ackermann, M.R. / McLellan, J.S. / Vendeville, S. / Koul, A.
History
DepositionJul 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 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, Envelope glycoprotein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,10814
Polymers63,2181
Non-polymers1,89013
Water2,414134
1
F: Fusion glycoprotein F0, Envelope glycoprotein chimera
hetero molecules

F: Fusion glycoprotein F0, Envelope glycoprotein chimera
hetero molecules

F: Fusion glycoprotein F0, Envelope glycoprotein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,32542
Polymers189,6553
Non-polymers5,67039
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area20560 Å2
ΔGint-459 kcal/mol
Surface area50200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.990, 169.990, 169.990
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-731-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules F

#1: Protein Fusion glycoprotein F0, Envelope glycoprotein chimera


Mass: 63218.344 Da / Num. of mol.: 1
Fragment: F0 (UNP residues 1-513) + Envelope glycoprotein (UNP residues 1-28)
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, UniProt: P03420*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 146 molecules

#3: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-6YA / 3-[[5-chloranyl-1-(3-methylsulfonylpropyl)indol-2-yl]methyl]-1-[2,2,2-tris(fluoranyl)ethyl]imidazo[4,5-c]pyridin-2-one


Mass: 500.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20ClF3N4O3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 62.01 %
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: 5.0.2 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2014
RadiationMonochromator: liquid nitrogen-cooled dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→56.66 Å / Num. obs: 29656 / % possible obs: 100 % / Redundancy: 22.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.042 / Rrim(I) all: 0.201 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.6220.82.1260.621100
8.29-56.6620.60.0321199.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EA4

5ea4


Resolution: 2.5→53.756 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1478 4.99 %
Rwork0.2102 28127 -
obs0.2116 29605 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.39 Å2 / Biso mean: 58.9745 Å2 / Biso min: 23.34 Å2
Refinement stepCycle: final / Resolution: 2.5→53.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 110 134 3562
Biso mean--113.87 47.98 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053476
X-RAY DIFFRACTIONf_angle_d0.8334711
X-RAY DIFFRACTIONf_chiral_restr0.032559
X-RAY DIFFRACTIONf_plane_restr0.003572
X-RAY DIFFRACTIONf_dihedral_angle_d14.3551255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5004-2.58110.33171340.286424992633
2.5811-2.67330.30591250.263425072632
2.6733-2.78040.3111340.253124862620
2.7804-2.90690.29091590.244724922651
2.9069-3.06020.24421430.226525162659
3.0602-3.25190.26791180.209825382656
3.2519-3.50290.23351350.208425282663
3.5029-3.85530.21861280.188125712699
3.8553-4.4130.21351170.186725872704
4.413-5.5590.19421460.187726102756
5.559-53.7680.24871390.221427932932
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)
11.0277-0.7639-0.82234.66081.39941.5352-0.1011-0.3154-0.17740.46060.18470.40010.1226-0.2345-0.08650.27710.0322-0.03420.49750.11040.23962.95296.015232.5448
25.42261.98154.8254.17344.72598.8118-0.10710.8392-0.4312-0.50490.2290.15830.23770.0096-0.22670.62940.0401-0.04440.5835-0.04360.63545.115-17.7743-10.0864
31.9518-0.08050.63041.81191.31784.08530.13480.1521-0.8272-0.1208-0.22630.2041.0842-0.4122-0.00370.6431-0.0728-0.02910.3328-0.01020.67856.3867-16.95096.0972
42.26321.3587-0.02166.48392.31682.74610.0605-0.1345-0.0583-0.2613-0.05350.3627-0.1893-0.1464-0.0250.23680.0616-0.01830.35190.07790.19338.6210.665728.8986
53.7-0.86990.01133.05780.15931.50880.0401-0.43270.23040.1911-0.0421-0.0372-0.0874-0.11180.00630.31560.04950.04120.3461-0.02380.16355.217622.043133.1602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 27 through 52 )F27 - 52
2X-RAY DIFFRACTION2chain 'F' and (resid 53 through 98 )F53 - 98
3X-RAY DIFFRACTION3chain 'F' and (resid 137 through 312 )F137 - 312
4X-RAY DIFFRACTION4chain 'F' and (resid 313 through 376 )F313 - 376
5X-RAY DIFFRACTION5chain 'F' and (resid 377 through 506 )F377 - 506

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