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

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Basic information

Entry
Database: PDB / ID: 5yzd
TitleCrystal structure of the prefusion form of measles virus fusion protein in complex with a fusion inhibitor peptide (FIP)
Components
  • (glycoprotein ...) x 2
  • peptide CBZ-DPN-PHE-GLY
KeywordsVIRAL PROTEIN/INHIBITOR / glycoprotein / viral protein / fusion protein / paramyxovirus / inhibitor / VIRAL PROTEIN-INHIBITOR complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesMeasles virus
Sendai virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.636 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 16, 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
C: glycoprotein F1,measles virus fusion protein
B: peptide CBZ-DPN-PHE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6185
Polymers55,9723
Non-polymers6462
Water70339
1
A: glycoprotein F2
C: glycoprotein F1,measles virus fusion protein
B: peptide CBZ-DPN-PHE-GLY
hetero molecules

A: glycoprotein F2
C: glycoprotein F1,measles virus fusion protein
B: peptide CBZ-DPN-PHE-GLY
hetero molecules

A: glycoprotein F2
C: glycoprotein F1,measles virus fusion protein
B: peptide CBZ-DPN-PHE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,85315
Polymers167,9179
Non-polymers1,9376
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)170.407, 170.407, 170.407
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 AC

#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 / 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 / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q786F3

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Protein/peptide / Non-polymers , 2 types, 40 molecules B

#3: Protein/peptide peptide CBZ-DPN-PHE-GLY


Mass: 521.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sendai virus
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: 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: obtained synthetically
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
#5: 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: obtained synthetically / 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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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: 3.69 Å3/Da / Density % sol: 66.63 %
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: 2.636→120.496 Å / Num. obs: 24414 / % possible obs: 100 % / Redundancy: 21.3 % / Net I/σ(I): 18.1
Reflection shellResolution: 2.636→2.645 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: 2.636→85.203 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 1244 5.1 %
Rwork0.1906 --
obs0.1927 24409 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.636→85.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 42 40 3526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113545
X-RAY DIFFRACTIONf_angle_d1.3654814
X-RAY DIFFRACTIONf_dihedral_angle_d9.6042112
X-RAY DIFFRACTIONf_chiral_restr0.081582
X-RAY DIFFRACTIONf_plane_restr0.009610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6363-2.74190.3461260.27992564X-RAY DIFFRACTION100
2.7419-2.86670.30071350.24642550X-RAY DIFFRACTION100
2.8667-3.01790.27831490.23672532X-RAY DIFFRACTION100
3.0179-3.20690.30541460.2262570X-RAY DIFFRACTION100
3.2069-3.45460.27071400.21142538X-RAY DIFFRACTION100
3.4546-3.80220.2071300.1932566X-RAY DIFFRACTION100
3.8022-4.35240.19151390.16822582X-RAY DIFFRACTION100
4.3524-5.48340.19521480.15682590X-RAY DIFFRACTION100
5.4834-85.2480.2241310.17942673X-RAY DIFFRACTION100

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