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- PDB-6eak: CRYSTAL STRUCTURE OF FUSION INHIBITOR JNJ-2408068 IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 6eak
TitleCRYSTAL STRUCTURE OF FUSION INHIBITOR JNJ-2408068 IN COMPLEX WITH HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN ESCAPE VARIANT T400A STABILIZED IN THE PREFUSION STATE
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / CLASS I VIRAL FUSION PROTEIN / FUSION / RESPIRATORY SYNCYTIAL VIRUS / PREFUSION / FUSION INHIBITOR
Function / homology
Function and homology information


Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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 ...Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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 / membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Chem-5NK / NICKEL (II) ION / Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBattles, M.B. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32AI007519-18 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: To be published
Title: Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance
Authors: Battles, M.B. / McLellan, J.S.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,42510
Polymers63,1881
Non-polymers1,2379
Water99155
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)193,27630
Polymers189,5653
Non-polymers3,71127
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area20060 Å2
ΔGint-308 kcal/mol
Surface area47610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.450, 168.450, 168.450
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-605-

SO4

21F-609-

5NK

31F-609-

5NK

41F-609-

5NK

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Components

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Protein , 1 types, 1 molecules F

#1: Protein Fusion glycoprotein F0


Mass: 63188.320 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain / Mutation: S155C, S290C, S190F, V207L, T400A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Plasmid: P(ALPHA)H / Production host: Homo sapiens (human) / Strain (production host): HEK293 FREESTYLE / References: UniProt: W8RJF9, UniProt: P03420*PLUS

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Non-polymers , 5 types, 64 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-5NK / 2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol / JNJ-2408068


Mass: 394.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N6O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.15 Å3/Da / Density % sol: 60.98 % / Mosaicity: 0.66 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.48M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→59.56 Å / Num. obs: 25761 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 55.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.035 / Rrim(I) all: 0.135 / Net I/σ(I): 15.5 / Num. measured all: 376488 / Scaling rejects: 9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 15.6 % / Rmerge(I) obs: 1.267 / Num. unique obs: 3084 / CC1/2: 0.795 / Rpim(I) all: 0.33 / Rrim(I) all: 1.31 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.28data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EA4

5ea4


Resolution: 2.6→59.556 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.01
RfactorNum. reflection% reflection
Rfree0.2211 1288 5.01 %
Rwork0.1909 --
obs0.1924 25699 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.93 Å2 / Biso mean: 62.1724 Å2 / Biso min: 23.73 Å2
Refinement stepCycle: final / Resolution: 2.6→59.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 73 55 3513
Biso mean--103.94 50.87 -
Num. residues----438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6005-2.70460.33831380.279126502788
2.7046-2.82770.29261660.241226322798
2.8277-2.97680.28531530.23226462799
2.9768-3.16330.26591380.218526642802
3.1633-3.40750.21291360.200126912827
3.4075-3.75030.23241360.177927102846
3.7503-4.29290.22861260.170727232849
4.2929-5.4080.15441450.152727622907
5.408-59.57170.21221500.200629333083

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