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- PDB-8xo6: Crystal structure of measles virus fusion inhibitor MEK35GE compl... -

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Basic information

Entry
Database: PDB / ID: 8xo6
TitleCrystal structure of measles virus fusion inhibitor MEK35GE complexed with F protein HR1 (HR1-42) (P21212 space group)
Components
  • Fusion glycoprotein F1
  • Measles virus fusion inhibitor MEK35GE
KeywordsANTIVIRAL PROTEIN / Fusion protein / fusion inhibitor / six-helix bundle
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
ACETATE ION / Fusion glycoprotein F0
Similarity search - Component
Biological speciesMeasles virus strain Edmonston
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.457 Å
AuthorsOishi, S. / Takahara, A. / Nakatsu, T.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H05346 Japan
Japan Society for the Promotion of Science (JSPS)JP18H02555 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03701 Japan
Japan Society for the Promotion of Science (JSPS)JP21K19366 Japan
Japan Agency for Medical Research and Development (AMED)JP20ak0101140 Japan
Other private Japan
CitationJournal: J.Med.Chem. / Year: 2025
Title: Elucidation of Postfusion Structures of the Measles Virus F Protein for the Structure-Based Design of Fusion Inhibitors.
Authors: Takahara, A. / Nakatsu, T. / Hirata, K. / Hayashi, H. / Kawaji, K. / Aoki, K. / Inuki, S. / Ohno, H. / Kato, H. / Kodama, E. / Oishi, S.
History
DepositionDec 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.2Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F1
B: Measles virus fusion inhibitor MEK35GE
C: Fusion glycoprotein F1
D: Measles virus fusion inhibitor MEK35GE
E: Fusion glycoprotein F1
F: Measles virus fusion inhibitor MEK35GE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,11920
Polymers26,2296
Non-polymers89014
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.049, 59.768, 63.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-614-

HOH

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Components

#1: Protein/peptide Fusion glycoprotein F1


Mass: 4628.080 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Measles virus strain Edmonston / References: UniProt: P69353
#2: Protein/peptide Measles virus fusion inhibitor MEK35GE


Mass: 4114.887 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Measles virus strain Edmonston
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM Zn Acetate, 18% (w/v) PEG 8000, 100 mM MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.457→50 Å / Num. obs: 37542 / % possible obs: 98.6 % / Redundancy: 13.14 % / CC1/2: 0.997 / Rrim(I) all: 0.098 / Net I/σ(I): 16.92
Reflection shellResolution: 1.457→1.55 Å / Mean I/σ(I) obs: 2.83 / Num. unique obs: 5874 / CC1/2: 0.968 / Rrim(I) all: 0.875 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.457→43.604 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.377 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2081 1855 4.942 %
Rwork0.1764 35682 -
all0.178 --
obs-37537 98.584 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.054 Å2
Baniso -1Baniso -2Baniso -3
1-1.641 Å20 Å20 Å2
2---0.395 Å20 Å2
3----1.246 Å2
Refinement stepCycle: LAST / Resolution: 1.457→43.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 26 233 2051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131992
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171981
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.6522651
X-RAY DIFFRACTIONr_angle_other_deg1.5451.5924656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7565.037267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95324.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54815458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.821515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022361
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02352
X-RAY DIFFRACTIONr_nbd_refined0.2190.2472
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.21732
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2931
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2150
X-RAY DIFFRACTIONr_metal_ion_refined0.1740.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2870.231
X-RAY DIFFRACTIONr_nbd_other0.1730.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.231
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0890.25
X-RAY DIFFRACTIONr_mcbond_it1.941.949960
X-RAY DIFFRACTIONr_mcbond_other1.9211.938954
X-RAY DIFFRACTIONr_mcangle_it2.8092.8931197
X-RAY DIFFRACTIONr_mcangle_other2.8042.8921197
X-RAY DIFFRACTIONr_scbond_it3.5232.4691032
X-RAY DIFFRACTIONr_scbond_other3.5222.4691033
X-RAY DIFFRACTIONr_scangle_it5.2643.5221432
X-RAY DIFFRACTIONr_scangle_other5.2623.5221433
X-RAY DIFFRACTIONr_lrange_it6.38825.0042345
X-RAY DIFFRACTIONr_lrange_other6.38725.0142346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.457-1.4950.2861720.26924670.2727680.850.85495.33960.241
1.495-1.5360.2821250.23325030.23526910.90.89597.65890.201
1.536-1.5810.2591430.22524360.22726350.9020.90697.87480.195
1.581-1.6290.2321160.19223870.19425520.9140.92998.07990.161
1.629-1.6830.2191040.17623300.17824780.9260.9498.22440.149
1.683-1.7420.221210.17822510.1824120.9370.94198.34160.149
1.742-1.8070.2021340.17421460.17523180.9430.94598.36070.149
1.807-1.8810.2171170.1620960.16322360.940.95698.97140.142
1.881-1.9640.203780.17220400.17321350.9440.95399.20380.156
1.964-2.060.218920.1719670.17220740.950.95799.27680.158
2.06-2.1710.1851210.15318200.15519610.9640.96598.98010.148
2.171-2.3020.1991310.14817240.15118620.9590.96999.62410.147
2.302-2.4610.172880.15316470.15417450.9680.96899.42690.158
2.461-2.6570.204680.15615900.15816620.9470.95999.75930.167
2.657-2.910.228560.16414500.16615100.9550.95899.73510.179
2.91-3.2520.19470.16613240.16713720.960.96399.92710.189
3.252-3.7510.208440.15911990.1612440.9590.96799.91960.187
3.751-4.5860.198510.15910070.16110580.9560.9661000.201
4.586-6.450.221260.2488040.2478300.9620.941000.315
6.45-43.6040.208210.2524940.255150.9680.9561000.375

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