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

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Basic information

Entry
Database: PDB / ID: 8xne
TitleCrystal structure of measles virus fusion inhibitor M1 complexed with F protein HR1 (HR1-42) (H32 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: 1.155 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 29, 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)8,5174
Polymers8,4682
Non-polymers492
Water2,126118
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)25,55112
Polymers25,4056
Non-polymers1466
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 area13650 Å2
ΔGint-122 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.506, 28.506, 387.637
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-501-

MG

21A-249-

HOH

31B-638-

HOH

41B-652-

HOH

51B-660-

HOH

61B-665-

HOH

71B-666-

HOH

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Components

#1: Protein/peptide Fusion glycoprotein F1


Mass: 4628.080 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.79 Å3/Da / Density % sol: 31.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM MgCl2, 30% (w/v) PEG 3350, 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: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.155→50 Å / Num. obs: 22473 / % possible obs: 99.6 % / Redundancy: 8.72 % / CC1/2: 0.998 / Rrim(I) all: 0.096 / Net I/σ(I): 15.71
Reflection shellResolution: 1.155→1.22 Å / Redundancy: 7.94 % / Mean I/σ(I) obs: 5.12 / Num. unique obs: 3484 / CC1/2: 0.969 / Rrim(I) all: 0.446 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.155→24.601 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.521 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.042
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1871 1124 5.004 %
Rwork0.1597 21339 -
all0.161 --
obs-22463 99.742 %
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: 11.466 Å2
Baniso -1Baniso -2Baniso -3
1-0.119 Å20.06 Å20 Å2
2--0.119 Å20 Å2
3----0.386 Å2
Refinement stepCycle: LAST / Resolution: 1.155→24.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms595 0 2 118 715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.013668
X-RAY DIFFRACTIONr_bond_other_d0.0010.017631
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.631915
X-RAY DIFFRACTIONr_angle_other_deg1.6841.5691484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.391597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89223.95343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41215134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.462155
X-RAY DIFFRACTIONr_chiral_restr0.0880.298
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02120
X-RAY DIFFRACTIONr_nbd_refined0.2240.2159
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1540.2576
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2336
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.224
X-RAY DIFFRACTIONr_nbd_other0.2240.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1170.21
X-RAY DIFFRACTIONr_mcbond_it1.0390.929336
X-RAY DIFFRACTIONr_mcbond_other1.0010.92334
X-RAY DIFFRACTIONr_mcangle_it1.4141.399423
X-RAY DIFFRACTIONr_mcangle_other1.3961.398423
X-RAY DIFFRACTIONr_scbond_it2.151.218332
X-RAY DIFFRACTIONr_scbond_other2.151.218332
X-RAY DIFFRACTIONr_scangle_it3.0591.742480
X-RAY DIFFRACTIONr_scangle_other3.0561.745481
X-RAY DIFFRACTIONr_lrange_it4.69413.547825
X-RAY DIFFRACTIONr_lrange_other4.24712.251787
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
1.155-1.1850.273800.27615200.27616360.9270.92497.79950.229
1.185-1.2170.279780.22514720.22715500.9220.9321000.186
1.217-1.2530.194770.17514670.17615440.9460.9551000.149
1.253-1.2910.211750.15814190.1614960.9530.95999.86630.139
1.291-1.3330.209730.15113850.15414590.9540.96199.93150.134
1.333-1.380.19700.15113300.15314000.960.9671000.133
1.38-1.4320.181680.16113010.16213690.9630.9661000.144
1.432-1.490.144660.1512470.14913130.9750.9741000.14
1.49-1.5560.193630.15511920.15712570.9590.96999.84090.146
1.556-1.6320.212600.15111510.15412110.9510.9661000.144
1.632-1.7190.145580.14310950.14311540.9750.97599.91330.139
1.719-1.8230.157550.15410590.15411140.9720.9721000.148
1.823-1.9480.18520.1419840.14310370.9640.97499.90360.144
1.948-2.1030.166490.1399230.149720.9710.9771000.146
2.103-2.3020.173450.1348620.1369090.9710.97899.780.147
2.302-2.5710.204420.1397940.1428360.9590.9741000.164
2.571-2.9640.182370.1626990.1637360.9670.9691000.189
2.964-3.6170.136320.1576210.1566550.9760.97599.69470.188
3.617-5.060.201260.1554950.1575230.9740.97999.61760.196
5.06-24.6010.253180.2573230.2573440.9680.96199.12790.355

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