[English] 日本語
Yorodumi
- PDB-5yzc: Crystal structure of the prefusion form of measles virus fusion p... -

+
Open data


ID or keywords:

Loading...

-
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


symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / N-Acetylglucosamine


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

-
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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more