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- PDB-5yzc: Crystal structure of the prefusion form of measles virus fusion p... -

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Basic information

Entry
Database: PDB / ID: 5yzc
TitleCrystal structure of the prefusion form of measles virus fusion protein in complex with a fusion inhibitor compound (AS-48)
Components(glycoprotein ...) x 2
KeywordsVIRAL PROTEIN / glycoprotein / fusion protein / paramyxovirus / inhibitor / chemical compound
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
4-nitro-2-[(phenylacetyl)amino]benzamide / Fusion glycoprotein F0
Similarity search - Component
Biological speciesMeasles virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.334 Å
AuthorsHashiguchi, T. / Fukuda, Y. / Matsuoka, R. / Kuroda, D. / Kubota, M. / Shirogane, Y. / Watanabe, S. / Tsumoto, K. / Kohda, D. / Plemper, R.K. / Yanagi, Y.
Funding support Japan, United States, 5items
OrganizationGrant numberCountry
MEXT17K19562 Japan
MEXT24115005 Japan
AMED17fm0208022h0001 Japan
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI071002 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HD079327 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structures of the prefusion form of measles virus fusion protein in complex with inhibitors.
Authors: Hashiguchi, T. / Fukuda, Y. / Matsuoka, R. / Kuroda, D. / Kubota, M. / Shirogane, Y. / Watanabe, S. / Tsumoto, K. / Kohda, D. / Plemper, R.K. / Yanagi, Y.
History
DepositionDec 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 23, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycoprotein F2
B: glycoprotein F1,measles virus fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3955
Polymers55,4502
Non-polymers9453
Water2,846158
1
A: glycoprotein F2
B: glycoprotein F1,measles virus fusion protein
hetero molecules

A: glycoprotein F2
B: glycoprotein F1,measles virus fusion protein
hetero molecules

A: glycoprotein F2
B: glycoprotein F1,measles virus fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,18515
Polymers166,3516
Non-polymers2,8359
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area45770 Å2
ΔGint-286 kcal/mol
Surface area55110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.497, 169.497, 169.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Glycoprotein ... , 2 types, 2 molecules AB

#1: Protein glycoprotein F2


Mass: 10524.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus (strain Ichinose-B95a) / Strain: Ichinose-B95a / Gene: F / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q786F3
#2: Protein glycoprotein F1,measles virus fusion protein


Mass: 44925.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of glycoprotein F1,measles virus fusion protein and Tags
Source: (gene. exp.) Measles virus (strain Ichinose-B95a), (gene. exp.) Measles virus
Strain: Ichinose-B95a, IC-B / Gene: F / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q786F3

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 159 molecules

#5: Chemical ChemComp-95C / 4-nitro-2-[(phenylacetyl)amino]benzamide


Mass: 299.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium formate, glycerol, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.334→119.852 Å / Num. obs: 34515 / % possible obs: 100 % / Redundancy: 20.9 % / Net I/σ(I): 14.3
Reflection shellResolution: 2.334→2.342 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YXW

5yxw


Resolution: 2.334→53.6 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 1741 5.05 %
Rwork0.1837 --
obs0.1856 34508 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.334→53.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 64 159 3631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083530
X-RAY DIFFRACTIONf_angle_d0.9374800
X-RAY DIFFRACTIONf_dihedral_angle_d9.5232111
X-RAY DIFFRACTIONf_chiral_restr0.056580
X-RAY DIFFRACTIONf_plane_restr0.005609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.334-2.40260.26841400.232753X-RAY DIFFRACTION100
2.4026-2.48020.2681310.22342689X-RAY DIFFRACTION100
2.4802-2.56880.26461430.222723X-RAY DIFFRACTION100
2.5688-2.67170.2261260.21292715X-RAY DIFFRACTION100
2.6717-2.79330.26671530.19562692X-RAY DIFFRACTION100
2.7933-2.94050.2131440.19272718X-RAY DIFFRACTION100
2.9405-3.12470.23151470.19332715X-RAY DIFFRACTION100
3.1247-3.3660.221480.19042711X-RAY DIFFRACTION100
3.366-3.70460.24671650.1872717X-RAY DIFFRACTION100
3.7046-4.24050.20951290.16862764X-RAY DIFFRACTION100
4.2405-5.34180.18581500.162742X-RAY DIFFRACTION100
5.3418-53.61380.21841650.17872828X-RAY DIFFRACTION100

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