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

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5mup
TitleStructure of deformed wing virus, a honeybee pathogen
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus / viral protein / bee pathogen
Function / homologyPeptidase S1, PA clan / CRPV capsid protein like / RNA dependent RNA polymerase / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Dicistrovirus, capsid-polyprotein, C-terminal / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, catalytic domain ...Peptidase S1, PA clan / CRPV capsid protein like / RNA dependent RNA polymerase / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Dicistrovirus, capsid-polyprotein, C-terminal / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, catalytic domain / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA helicase / cysteine-type peptidase activity / host cell membrane / RNA helicase activity / viral capsid / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein / Genome polyprotein / Genome polyprotein
Function and homology information
Specimen sourceDeformed wing virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 13, 2017 / Release: Apr 5, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 5, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Refinement description / Structure summaryem_3d_fitting / em_software / struct_keywords_em_3d_fitting.target_criteria / _em_software.name / _em_software.version / _struct_keywords.text
1.2Oct 24, 2018Structure modelAdvisory / Data collection / Derived calculationspdbx_validate_close_contact / struct_conn

-
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-3570
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3570
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0624
Polyers103,7383
Non-polymers3241
Water0
1
A: VP1
B: VP2
C: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,243,716240
Polyers6,224,265180
Non-polymers19,45160
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
hetero molecules
x 5


  • icosahedral pentamer
  • 520 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)520,31020
Polyers518,68915
Non-polymers1,6215
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 624 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)624,37224
Polyers622,42718
Non-polymers1,9456
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

-
Components

#1: Protein/peptide VP1


Mass: 28679.273 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / References: UniProt: L0CTV4
#2: Protein/peptide VP2


Mass: 28360.900 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / References: UniProt: E0YTW0, UniProt: Q7TG18*PLUS
#3: Protein/peptide VP3


Mass: 46697.582 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / References: UniProt: Q7TG18
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Formula: C9H13N2O9P / Uridine monophosphate

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Deformed wing virus / Type: VIRUS / Details: Virus was purified from honeybee pupae / Entity ID: 1, 2, 3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Deformed wing virus
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRION
Natural hostOrganism: Apis mellifera
Virus shellDiameter: 390 nm / Triangulation number (T number): 3
Buffer solutionDetails: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
pH: 7.4
SpecimenConc.: 2.5 mg/ml
Details: Virus was incubated in high salt solution containing 0.8 M potassium dihydrogen phosphate, 0.8 M sodium dihydrogen phosphate, 0.1 M sodium HEPES, pH 7.5. After 12 hours incubation was virus dialysed into PBS buffer.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Calibrated magnification: 74235 / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 21 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 2-16

-
Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
2EPUimage acquisition
4GctfCTF correctionGctf
7Cootmodel fitting
9PHENIXmodel refinementReal space refinement
11RELION1.4final Euler assignmentrelion_refine_mpi
12RELION1.4classificationrelion_refine_mpi
13RELION1.43D reconstructionrelion_refine_mpi
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 3918
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 879 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL / Target criteria: R-factor

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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