[English] 日本語
Yorodumi
- PDB-5nd1: Viral evolution results in multiple, surface-allocated enzymatic ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5nd1
TitleViral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus
Components(Capsid proteinCapsid) x 2
KeywordsVIRUS / RnQV1 / dsRNA virus / fungal virus / virus
Function / homologyCapsid protein / Capsid protein
Function and homology information
Specimen sourceRosellinia necatrix quadrivirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsMata, C.P. / Luque, D. / Gomez Blanco, J. / Rodriguez, J.M. / Suzuki, N. / Ghabrial, S.A. / Carrascosa, J.L. / Trus, B.L. / Caston, J.R.
CitationJournal: To Be Published
Title: Viral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus
Authors: Mata, C.P. / Luque, D. / Gomez-Blanco, J. / Rodriguez, J.M. / Suzuki, N. / Ghabrial, S.A. / Carrascosa, J.L. / Trus, B.L. / Caston, J.R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2017 / Release: Nov 29, 2017
RevisionDateData content typeGroupCategoryProviderType
1.0Nov 29, 2017Structure modelrepositoryInitial release
1.1May 23, 2018Structure modelAdvisory / Data collection / Derived calculationspdbx_validate_close_contact / struct_conn

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3619
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3619
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)261,2222
Polyers261,2222
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15600
ΔGint (kcal/M)-85
Surface area (Å2)68510
MethodPISA

-
Components

#1: Protein/peptide Capsid protein / Capsid


Mass: 147782.375 Da / Num. of mol.: 1 / Source: (natural) Rosellinia necatrix quadrivirus 1 / References: UniProt: M1VMJ0
#2: Protein/peptide Capsid protein / Capsid


Mass: 113439.344 Da / Num. of mol.: 1 / Source: (natural) Rosellinia necatrix quadrivirus 1 / References: UniProt: M1VHN2

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: virus / Type: VIRUS / Entity ID: 1, 2
Molecular weightValue: 15.9 MDa / Experimental value: YES
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Rosellinia necatrix
Virus shellName: P2 and P4 capsid proteins / Diameter: 470 nm / Triangulation number (T number): 1
Buffer solutionDetails: 50 mM Tris-HCl pH 7.8, 150 mM NaCl, 5 mM EDTA / pH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

-
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 / Calibrated defocus min: 700 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 1.7 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 24 / Used frames/image: 4-21

-
Processing

EM software
IDNameVersionCategory
1Xmipp3particle selection
4CTFFIND3CTF correction
7Cootmodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13Cootmodel refinement
14REFMAC5model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNumber of particles selected: 53683
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 37531 / Symmetry type: POINT
Atomic model buildingRef protocol: BACKBONE TRACE

+
About Yorodumi

-
News

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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