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- PDB-8xo3: Crystal structure of measles virus fusion inhibitor M1 complexed ... -

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Basic information

Entry
Database: PDB / ID: 8xo3
TitleCrystal structure of measles virus fusion inhibitor M1 complexed with F protein HR1 (HR1-47) (P321 space group)
Components(Fusion glycoprotein F1) x 2
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: 1.104 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

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Assembly

Deposited unit
A: Fusion glycoprotein F1
B: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1063
Polymers9,0662
Non-polymers401
Water1,982110
1
A: Fusion glycoprotein F1
B: Fusion glycoprotein F1
hetero molecules

A: Fusion glycoprotein F1
B: Fusion glycoprotein F1
hetero molecules

A: Fusion glycoprotein F1
B: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3199
Polymers27,1986
Non-polymers1203
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area13680 Å2
ΔGint-121 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.899, 32.899, 124.596
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-208-

HOH

31A-242-

HOH

41B-644-

HOH

51B-657-

HOH

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Components

#1: Protein/peptide Fusion glycoprotein F1


Mass: 5225.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Measles virus strain Edmonston / References: UniProt: P69353
#2: Protein/peptide Fusion glycoprotein F1


Mass: 3840.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Measles virus strain Edmonston / References: UniProt: P69353
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM Ca Acetate, 15% (w/v) PEG 3350, 100 mM BIS-TRIS (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: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.104→50 Å / Num. obs: 32332 / % possible obs: 99.1 % / Redundancy: 8.66 % / CC1/2: 0.996 / Rrim(I) all: 0.094 / Net I/σ(I): 13.02
Reflection shellResolution: 1.104→1.17 Å / Redundancy: 5.25 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4867 / CC1/2: 0.969 / Rrim(I) all: 0.619 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.104→41.532 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.778 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.043
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2353 1615 5 %
Rwork0.2127 30686 -
all0.214 --
obs-32301 98.983 %
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: 23.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.754 Å20.377 Å20 Å2
2--0.754 Å2-0 Å2
3----2.445 Å2
Refinement stepCycle: LAST / Resolution: 1.104→41.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms636 0 1 110 747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013697
X-RAY DIFFRACTIONr_bond_other_d0.0010.017654
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.629952
X-RAY DIFFRACTIONr_angle_other_deg1.6331.5721539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.756597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.23824.0743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42615141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.491154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02119
X-RAY DIFFRACTIONr_nbd_refined0.230.2170
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1580.2561
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2346
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.267
X-RAY DIFFRACTIONr_metal_ion_refined0.2310.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1310.216
X-RAY DIFFRACTIONr_nbd_other0.1770.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2080.221
X-RAY DIFFRACTIONr_mcbond_it1.8742.21355
X-RAY DIFFRACTIONr_mcbond_other1.8532.204353
X-RAY DIFFRACTIONr_mcangle_it2.4483.301447
X-RAY DIFFRACTIONr_mcangle_other2.4323.299447
X-RAY DIFFRACTIONr_scbond_it2.8282.623340
X-RAY DIFFRACTIONr_scbond_other2.7982.622340
X-RAY DIFFRACTIONr_scangle_it4.4093.833496
X-RAY DIFFRACTIONr_scangle_other4.4153.837497
X-RAY DIFFRACTIONr_lrange_it5.828.95851
X-RAY DIFFRACTIONr_lrange_other5.39127.894816
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
1.104-1.1330.4061080.43120530.42923970.5270.52390.15440.397
1.133-1.1640.3041110.33720910.33522680.5360.597.08990.3
1.164-1.1970.3641100.31421060.31622240.6430.67599.64030.285
1.197-1.2340.321090.28120670.28321830.810.81699.67930.255
1.234-1.2750.3161060.25520080.25821170.8720.87599.85830.232
1.275-1.3190.2661040.25919690.25920730.9130.9041000.232
1.319-1.3690.23980.23318730.23319710.9240.931000.21
1.369-1.4250.249960.23718150.23719110.9260.9271000.214
1.425-1.4880.216910.22817310.22718230.9420.94299.94510.212
1.488-1.5610.209880.21316760.21317710.9410.94399.60470.202
1.561-1.6450.252840.20916020.21116860.9170.9371000.212
1.645-1.7450.236800.21115210.21216010.940.9461000.218
1.745-1.8650.245740.21414090.21514830.9360.9391000.234
1.865-2.0140.294720.21513540.21914260.9110.9371000.244
2.014-2.2060.22660.19512580.19713240.950.9581000.239
2.206-2.4650.226580.19811120.19911700.950.9541000.248
2.465-2.8450.192540.19110180.19110720.960.9571000.256
2.845-3.480.216460.2028760.2029230.960.95999.89170.274
3.48-4.9040.213370.1697050.1717420.9570.9721000.245
4.904-41.5320.255240.2594420.2594670.9240.94499.78590.482

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