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- PDB-3kpe: Solution structure of the respiratory syncytial virus (RSV)six-he... -

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Basic information

Entry
Database: PDB / ID: 3kpe
TitleSolution structure of the respiratory syncytial virus (RSV)six-helix bundle complexed with TMC353121, a small-moleucule inhibitor of RSV
Components(Fusion glycoprotein F0) x 2
KeywordsVIRAL PROTEIN / FUSION PROTEIN / peptide-small-molecule complex / alpha helix / coiled-coil / Envelope protein / Glycoprotein / Host cell membrane / Host membrane / Lipoprotein / Membrane / Palmitate / Transmembrane / Virion
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / host cell Golgi membrane / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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 ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / host cell Golgi membrane / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-TM3 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsRoymans, D. / De Bondt, H. / Arnoult, E. / Cummings, M.D. / Van Vlijmen, H. / Andries, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein.
Authors: Roymans, D. / De Bondt, H.L. / Arnoult, E. / Geluykens, P. / Gevers, T. / Van Ginderen, M. / Verheyen, N. / Kim, H. / Willebrords, R. / Bonfanti, J.F. / Bruinzeel, W. / Cummings, M.D. / van ...Authors: Roymans, D. / De Bondt, H.L. / Arnoult, E. / Geluykens, P. / Gevers, T. / Van Ginderen, M. / Verheyen, N. / Kim, H. / Willebrords, R. / Bonfanti, J.F. / Bruinzeel, W. / Cummings, M.D. / van Vlijmen, H. / Andries, K.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6604
Polymers9,9072
Non-polymers7532
Water66737
1
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
hetero molecules

A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
hetero molecules

A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,98112
Polymers29,7226
Non-polymers2,2596
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area14720 Å2
ΔGint-114 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.248, 63.248, 63.248
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Fusion glycoprotein F0 / Protein F / Fusion glycoprotein F2 / Fusion glycoprotein F1


Mass: 5540.497 Da / Num. of mol.: 1 / Fragment: proteinase K-resistant core of heptad repeat 1 / Source method: isolated from a natural source / Source: (natural) Human respiratory syncytial virus / Strain: A2 / References: UniProt: P03420
#2: Protein/peptide Fusion glycoprotein F0 / Protein F / Fusion glycoprotein F2 / Fusion glycoprotein F1


Mass: 4366.819 Da / Num. of mol.: 1 / Fragment: proteinase K-resistant core of heptad repeat 2 / Source method: isolated from a natural source / Source: (natural) Human respiratory syncytial virus / Strain: A2 / References: UniProt: P03420
#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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% (v/v) PEG-400 + 100 mM HEPES, pH 7.5 + 200 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2007
RadiationMonochromator: single crystal, cilindrically bend, Si(220). / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→19.07 Å / Num. all: 14912 / Num. obs: 14596 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G2C

1g2c


Resolution: 1.47→19.07 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.995 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.065 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19638 735 5 %RANDOM
Rwork0.16329 ---
all0.1892 14612 --
obs0.16489 13877 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.481 Å2
Refinement stepCycle: LAST / Resolution: 1.47→19.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms643 0 54 37 734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022738
X-RAY DIFFRACTIONr_bond_other_d0.0020.02702
X-RAY DIFFRACTIONr_angle_refined_deg1.7362.0651002
X-RAY DIFFRACTIONr_angle_other_deg0.77331657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.953596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24227.40727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09415134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.328151
X-RAY DIFFRACTIONr_chiral_restr0.0710.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02124
X-RAY DIFFRACTIONr_nbd_refined0.240.2154
X-RAY DIFFRACTIONr_nbd_other0.1620.2650
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2370
X-RAY DIFFRACTIONr_nbtor_other0.0890.2392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3220.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7821.5597
X-RAY DIFFRACTIONr_mcbond_other0.3041.5179
X-RAY DIFFRACTIONr_mcangle_it1.7722717
X-RAY DIFFRACTIONr_scbond_it3.1533384
X-RAY DIFFRACTIONr_scangle_it4.0434.5278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.489 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.214 23 -
Rwork0.194 518 -
obs--100 %

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