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- PDB-8xo5: Crystal structure of measles virus fusion inhibitor MEK28 complex... -

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Basic information

Entry
Database: PDB / ID: 8xo5
TitleCrystal structure of measles virus fusion inhibitor MEK28 complexed with F protein HR1 (HR1-40) (H3 space group)
Components
  • Fusion glycoprotein F1
  • Measles virus fusion inhibitor MEK28
KeywordsANTIVIRAL PROTEIN / Fusion protein / fusion inhibitor / six-helix bundle
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesMeasles virus strain Edmonston
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.205 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 1.1Mar 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 MEK28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9043
Polymers7,7862
Non-polymers1181
Water84747
1
A: Fusion glycoprotein F1
B: Measles virus fusion inhibitor MEK28
hetero molecules

A: Fusion glycoprotein F1
B: Measles virus fusion inhibitor MEK28
hetero molecules

A: Fusion glycoprotein F1
B: Measles virus fusion inhibitor MEK28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7129
Polymers23,3586
Non-polymers3553
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13140 Å2
ΔGint-132 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.800, 51.800, 58.662
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide Fusion glycoprotein F1


Mass: 4426.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Measles virus strain Edmonston / References: UniProt: P69353
#2: Protein/peptide Measles virus fusion inhibitor MEK28


Mass: 3359.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Measles virus strain Edmonston
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.95 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 200 mM Ammonium Acetate, 40% (v/v) MPD, 100 mM MES buffer (pH 6.0)

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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: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.205→50 Å / Num. obs: 18126 / % possible obs: 99.8 % / Redundancy: 5.04 % / CC1/2: 0.993 / Rrim(I) all: 0.092 / Net I/σ(I): 10.98
Reflection shellResolution: 1.205→1.28 Å / Redundancy: 4.87 % / Mean I/σ(I) obs: 2.72 / Num. unique obs: 2915 / CC1/2: 0.969 / Rrim(I) all: 0.541 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.205→35.635 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.183 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.052 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.231 906 5.003 %
Rwork0.1952 17202 -
all0.197 --
obs-18108 99.719 %
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: 26.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.718 Å20.359 Å2-0 Å2
2--0.718 Å2-0 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 1.205→35.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms547 0 8 47 602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013655
X-RAY DIFFRACTIONr_bond_other_d0.0010.017672
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.666893
X-RAY DIFFRACTIONr_angle_other_deg1.441.5931601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.839592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69226.4139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5715163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.154152
X-RAY DIFFRACTIONr_chiral_restr0.0880.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0297
X-RAY DIFFRACTIONr_nbd_refined0.2170.2152
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1480.2548
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2302
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.218
X-RAY DIFFRACTIONr_nbd_other0.2010.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.211
X-RAY DIFFRACTIONr_mcbond_it2.0032.503306
X-RAY DIFFRACTIONr_mcbond_other1.9682.491304
X-RAY DIFFRACTIONr_mcangle_it2.9583.735387
X-RAY DIFFRACTIONr_mcangle_other2.9743.733387
X-RAY DIFFRACTIONr_scbond_it3.5093.068349
X-RAY DIFFRACTIONr_scbond_other3.5043.069350
X-RAY DIFFRACTIONr_scangle_it5.3664.446492
X-RAY DIFFRACTIONr_scangle_other5.3614.448493
X-RAY DIFFRACTIONr_lrange_it6.73231.478758
X-RAY DIFFRACTIONr_lrange_other6.72831.5759
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
1.205-1.2360.339670.36212770.3613730.6510.62897.88780.34
1.236-1.270.359640.33712170.33812840.7690.74599.76640.312
1.27-1.3070.404640.35312080.35612720.8280.81000.329
1.307-1.3470.3610.29311550.29412190.8220.83199.75390.274
1.347-1.3910.304590.27111320.27311910.8420.8481000.247
1.391-1.440.277590.27511100.27511690.8410.8581000.257
1.44-1.4940.393560.26510750.27111390.8070.87999.29760.263
1.494-1.5550.248530.23810070.23810660.8880.90399.43710.237
1.555-1.6240.208520.2139840.21310370.9230.92899.90360.22
1.624-1.7030.282500.2179410.229910.9070.9191000.224
1.703-1.7950.25460.2168870.2189330.9170.921000.235
1.795-1.9030.201440.1938300.1948750.9320.93799.88570.226
1.903-2.0340.207420.1997880.1998300.950.941000.229
2.034-2.1970.247390.1877430.1897820.9310.9481000.232
2.197-2.4050.181350.1766720.1767070.9580.9471000.221
2.405-2.6880.229320.1666160.1696480.9220.9491000.222
2.688-3.1010.223290.1795510.1815800.9290.941000.242
3.101-3.790.215240.1624550.1654790.9370.9551000.237
3.79-5.330.214190.1413520.1453710.9450.9651000.217
5.33-35.6350.225110.2712020.2682130.9310.9311000.508

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