[English] 日本語
Yorodumi
- PDB-8phi: Crystal structure of prefusion-stabilized RSV F Variant DS-Cav1 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8phi
TitleCrystal structure of prefusion-stabilized RSV F Variant DS-Cav1 in complex with Lonafarnib
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / RSV F Glycoprotein / inhibitor
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / 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
Chem-336 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.289 Å
AuthorsRajak, M. / Krey, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen Foundation9B811 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Drug repurposing screen identifies lonafarnib as respiratory syncytial virus fusion protein inhibitor.
Authors: Sake, S.M. / Zhang, X. / Rajak, M.K. / Urbanek-Quaing, M. / Carpentier, A. / Gunesch, A.P. / Grethe, C. / Matthaei, A. / Ruckert, J. / Galloux, M. / Larcher, T. / Le Goffic, R. / Hontonnou, ...Authors: Sake, S.M. / Zhang, X. / Rajak, M.K. / Urbanek-Quaing, M. / Carpentier, A. / Gunesch, A.P. / Grethe, C. / Matthaei, A. / Ruckert, J. / Galloux, M. / Larcher, T. / Le Goffic, R. / Hontonnou, F. / Chatterjee, A.K. / Johnson, K. / Morwood, K. / Rox, K. / Elgaher, W.A.M. / Huang, J. / Wetzke, M. / Hansen, G. / Fischer, N. / Eleouet, J.F. / Rameix-Welti, M.A. / Hirsch, A.K.H. / Herold, E. / Empting, M. / Lauber, C. / Schulz, T.F. / Krey, T. / Haid, S. / Pietschmann, T.
History
DepositionJun 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5966
Polymers61,5811
Non-polymers1,0155
Water3,189177
1
F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,78918
Polymers184,7433
Non-polymers3,04615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15670 Å2
ΔGint-175 kcal/mol
Surface area52930 Å2
Unit cell
Length a, b, c (Å)88.640, 88.640, 194.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 1 types, 1 molecules F

#1: Protein Fusion glycoprotein F0


Mass: 61581.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Strain: strain A2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: W8RJF9

-
Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-336 / 4-{2-[4-(3,10-DIBROMO-8-CHLORO-6,11-DIHYDRO-5H-BENZO[5,6]CYCLOHEPTA[1,2-B]PYRIDIN-11-YL)PIPERIDIN-1-YL]-2-OXOETHYL}PIPERIDINE-1-CARBOXAMIDE / SCH66336


Mass: 638.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31Br2ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000-20%, CaCl2-400mM, & TrisHCl pH-8 100mM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91983 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 2.289→50 Å / Num. obs: 51465 / % possible obs: 99.9 % / Redundancy: 26.1 % / CC1/2: 0.997 / Rrim(I) all: 0.243 / Net I/σ(I): 10.54
Reflection shellResolution: 2.289→2.35 Å / Mean I/σ(I) obs: 1.66 / Num. unique obs: 3770 / CC1/2: 0.882 / Rrim(I) all: 1.755 / % possible all: 99

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (17-FEB-2023)refinement
XDSdata reduction
XSCALEJan 10, 2022data scaling
PHASER1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.289→26.21 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1174 4.56 %RANDOM
Rwork0.1984 ---
obs0.1998 25724 99.9 %-
Displacement parametersBiso mean: 65.03 Å2
Baniso -1Baniso -2Baniso -3
1--15.7215 Å20 Å20 Å2
2---15.7215 Å20 Å2
3---31.443 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.289→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 58 177 3687
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073584HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984867HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1261SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes604HARMONIC5
X-RAY DIFFRACTIONt_it3584HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion17.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3146SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.31 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3285 -3.69 %
Rwork0.4267 496 -
all0.4224 515 -
obs--97.29 %

+
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://pdbjlvh1.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