[English] 日本語
Yorodumi
- PDB-3j3i: Penicillium chrysogenum virus (PcV) capsid structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j3i
TitlePenicillium chrysogenum virus (PcV) capsid structure
ComponentsCapsid protein
KeywordsVIRUS / double-stranded RNA / fungal virus / viral structure / T=1 virus / duplicated helical fold
Function / homology: / : / Fungal virus Capsid protein, N-terminal domain / Fungal virus Capsid protein, C-terminal domain / T=1 icosahedral viral capsid / Capsid protein
Function and homology information
Biological speciesPenicillium chrysogenum virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLuque, D. / Gomez-Blanco, J. / Garriga, D. / Brilot, A. / Gonzalez, J.M. / Havens, W.H. / Carrascosa, J.L. / Trus, B.L. / Verdaguer, N. / Grigorieff, N. ...Luque, D. / Gomez-Blanco, J. / Garriga, D. / Brilot, A. / Gonzalez, J.M. / Havens, W.H. / Carrascosa, J.L. / Trus, B.L. / Verdaguer, N. / Grigorieff, N. / Ghabrial, S.A. / Caston, J.R.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Cryo-EM near-atomic structure of a dsRNA fungal virus shows ancient structural motifs preserved in the dsRNA viral lineage.
Authors: Daniel Luque / Josué Gómez-Blanco / Damiá Garriga / Axel F Brilot / José M González / Wendy M Havens / José L Carrascosa / Benes L Trus / Nuria Verdaguer / Said A Ghabrial / José R Castón /
Abstract: Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of ...Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of viral classes or lineages that can be grouped by capsid protein (CP) folds. Here, we report that the CP structure of the fungal dsRNA Penicillium chrysogenum virus (PcV) shows the progenitor fold of the dsRNA virus lineage and suggests a relationship between lineages. Cryo-EM structure at near-atomic resolution showed that the 982-aa PcV CP is formed by a repeated α-helical core, indicative of gene duplication despite lack of sequence similarity between the two halves. Superimposition of secondary structure elements identified a single "hotspot" at which variation is introduced by insertion of peptide segments. Structural comparison of PcV and other distantly related dsRNA viruses detected preferential insertion sites at which the complexity of the conserved α-helical core, made up of ancestral structural motifs that have acted as a skeleton, might have increased, leading to evolution of the highly varied current structures. Analyses of structural motifs only apparent after systematic structural comparisons indicated that the hallmark fold preserved in the dsRNA virus lineage shares a long (spinal) α-helix tangential to the capsid surface with the head-tailed phage and herpesvirus viral lineage.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
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-5600
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5600
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)108,9521
Polymers108,9521
Non-polymers00
Water00
1
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)6,537,13360
Polymers6,537,13360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
x 5


  • icosahedral pentamer
  • 545 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)544,7615
Polymers544,7615
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 654 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)653,7136
Polymers653,7136
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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 Capsid protein / CP / Coat protein


Mass: 108952.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Penicillium chrysogenum virus (isolate Caston)
References: UniProt: Q8JVC1

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Penicillium chrysogenum virus / Type: VIRUS / Details: icosahedral
Molecular weightValue: 6.5 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: FUNGI / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Penicillium chrysogenum / Strain: ATCC 9480
Buffer solutionName: 50 mM Tris-HCl, pH 7.8, 150 mM NaCl, 5 mM EDTA / pH: 7.8 / Details: 50 mM Tris-HCl, pH 7.8, 150 mM NaCl, 5 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 50 mM Tris-HCl , 150 mM NaCl, 5 mM EDTA
Specimen supportDetails: C flat CF 1/2 4C grids
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 80 %
Details: Samples were applied to grids, blotted 7 seconds, and plunged into liquid ethane (FEI VITROBOT MARK II).
Method: Blot for 7 seconds before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Feb 23, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 58333 X / Calibrated magnification: 56910 X / Nominal defocus max: 3800 nm / Nominal defocus min: 1100 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 650
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: Xmipp / Category: 3D reconstruction
CTF correctionDetails: Phase flipping & amplitude
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Projection Matching / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27566 / Nominal pixel size: 1.2 Å / Actual pixel size: 1.23 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms7515 0 0 0 7515

+
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