[English] 日本語
Yorodumi
- PDB-5l7q: Structure of deformed wing virus, a honeybee pathogen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l7q
TitleStructure of deformed wing virus, a honeybee pathogen
Components
  • VP1
  • vp2
  • vp3
KeywordsVIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus
Function / homology
Function and homology information


host cell membrane / RNA-protein covalent cross-linking / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / DNA-templated transcription / host cell cytoplasm / structural molecule activity / RNA binding ...host cell membrane / RNA-protein covalent cross-linking / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / DNA-templated transcription / host cell cytoplasm / structural molecule activity / RNA binding / membrane / ATP binding / cytoplasm
Similarity search - Function
Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / picornavirus capsid protein / Picornavirus capsid / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase ...Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / picornavirus capsid protein / Picornavirus capsid / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDeformed wing virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSkubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structure of deformed wing virus, a major honey bee pathogen.
Authors: Karel Škubník / Jiří Nováček / Tibor Füzik / Antonín Přidal / Robert J Paxton / Pavel Plevka /
Abstract: The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) ...The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) from the family , together with its vector, the mite , is likely the major threat to the world's honey bees. However, lack of knowledge of the atomic structures of iflaviruses has hindered the development of effective treatments against them. Here, we present the virion structures of DWV determined to a resolution of 3.1 Å using cryo-electron microscopy and 3.8 Å by X-ray crystallography. The C-terminal extension of capsid protein VP3 folds into a globular protruding (P) domain, exposed on the virion surface. The P domain contains an Asp-His-Ser catalytic triad that is, together with five residues that are spatially close, conserved among iflaviruses. These residues may participate in receptor binding or provide the protease, lipase, or esterase activity required for entry of the virus into a host cell. Furthermore, nucleotides of the DWV RNA genome interact with VP3 subunits. The capsid protein residues involved in the RNA binding are conserved among honey bee iflaviruses, suggesting a putative role of the genome in stabilizing the virion or facilitating capsid assembly. Identifying the RNA-binding and putative catalytic sites within the DWV virion structure enables future analyses of how DWV and other iflaviruses infect insect cells and also opens up possibilities for the development of antiviral treatments.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.name / _em_software.version
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Revision 1.3Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell / em_software
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _em_software.name
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.5Nov 6, 2019Group: Data collection / Category: em_software / Item: _em_software.name / _em_software.version
Revision 1.6Nov 13, 2019Group: Data collection / Other / Category: symmetry
Item: _symmetry.Int_Tables_number / _symmetry.space_group_name_H-M

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4009
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4009
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP1
B: vp2
C: vp3


Theoretical massNumber of molelcules
Total (without water)103,7383
Polymers103,7383
Non-polymers00
Water0
1
A: VP1
B: vp2
C: vp3
x 60


Theoretical massNumber of molelcules
Total (without water)6,224,265180
Polymers6,224,265180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1
B: vp2
C: vp3
x 5


  • icosahedral pentamer
  • 519 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)518,68915
Polymers518,68915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: vp2
C: vp3
x 6


  • icosahedral 23 hexamer
  • 622 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)622,42718
Polymers622,42718
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein VP1


Mass: 28679.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: L0CTV4
#2: Protein vp2


Mass: 28360.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: E0YTW0, UniProt: Q8B3M2*PLUS
#3: Protein vp3


Mass: 46697.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: Q7TG18, UniProt: Q8B3M2*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Deformed wing virus / Type: VIRUS / Details: Virus was purified from honeybee pupae / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Deformed wing virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Apis mellifera
Virus shellDiameter: 390 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
Details: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 74235 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 15 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 26
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 2-7

-
Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
2EPUimage acquisition
4CTFFIND4CTF correctionCTFFIND4, Grigorieff lab
7Cootmodel fitting
9JALIGNinitial Euler assignmentjalign, Jiang lab
10jalingnfinal Euler assignmentjalign, Jiang lab
11commonImagesclassificationcommonImages.py, Jiang lab
12J3DR3D reconstructionj3dr
13PHENIXmodel refinementReal space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 141860
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136828 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: R-factor
RefinementResolution: 3.44→542.25 Å / SU ML: 0.7 / σ(F): 0.01 / Phase error: 40.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3395 2001 0.29 %
Rwork0.2983 --
obs0.2984 692955 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01236454
ELECTRON MICROSCOPYf_angle_d1.15149696
ELECTRON MICROSCOPYf_dihedral_angle_d9.80913081
ELECTRON MICROSCOPYf_chiral_restr0.0585395
ELECTRON MICROSCOPYf_plane_restr0.0066445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4401-3.52610.53831420.634949244ELECTRON MICROSCOPY100
3.5261-3.62150.44871400.446749126ELECTRON MICROSCOPY100
3.6215-3.72810.41521430.398749153ELECTRON MICROSCOPY100
3.7281-3.84840.43091370.385349252ELECTRON MICROSCOPY100
3.8484-3.9860.39171450.417649202ELECTRON MICROSCOPY100
3.986-4.14560.33811410.34349165ELECTRON MICROSCOPY100
4.1456-4.33430.35971430.308249310ELECTRON MICROSCOPY100
4.3343-4.56280.33561450.27949323ELECTRON MICROSCOPY100
4.5628-4.84870.32221460.267349289ELECTRON MICROSCOPY100
4.8487-5.22310.30141410.281949342ELECTRON MICROSCOPY100
5.2231-5.74870.34541420.292149463ELECTRON MICROSCOPY100
5.7487-6.58070.341420.315649467ELECTRON MICROSCOPY100
6.5807-8.29110.26481430.285649680ELECTRON MICROSCOPY100
8.2911-549.11430.35941510.286649938ELECTRON MICROSCOPY99

+
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