[English] 日本語
Yorodumi
- EMDB-4174: CryoEM structure of Ageratum Yellow Vein virus (AYVV) -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4174
TitleCryoEM structure of Ageratum Yellow Vein virus (AYVV)
Map dataAgeratum Yellow Vein virus cryoEM density map
SampleAgeratum yellow vein virus:
virus / Capsid proteinCapsid / (nucleic-acidNucleic acid) x 2 / (coat protein subunit ...) x 2
Function / homologyGeminivirus AR1 coat protein / Geminivirus AR1/BR1 coat protein / Viral coat protein subunit / Geminivirus coat protein/nuclear export factor BR1 family / T=1 icosahedral viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell nucleus / structural molecule activity / DNA binding ...Geminivirus AR1 coat protein / Geminivirus AR1/BR1 coat protein / Viral coat protein subunit / Geminivirus coat protein/nuclear export factor BR1 family / T=1 icosahedral viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell nucleus / structural molecule activity / DNA binding / metal ion binding / Capsid protein
Function and homology information
SourceAgeratum yellow vein virus
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsHesketh EL / Saunders K / Fisher C / Potze J / Stanley J / Lomonossoff GP / Ranson NA
CitationJournal: Nat Commun / Year: 2018
Title: The 3.3 Å structure of a plant geminivirus using cryo-EM.
Authors: Emma L Hesketh / Keith Saunders / Chloe Fisher / Joran Potze / John Stanley / George P Lomonossoff / Neil A Ranson
Validation ReportPDB-ID: 6f2s

SummaryFull reportAbout validation report
DateDeposition: Nov 27, 2017 / Header (metadata) release: Jan 17, 2018 / Map release: Jun 27, 2018 / Last update: Oct 17, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6f2s
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6f2s
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_4174.map.gz (map file in CCP4 format, 359662 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
448 pix
1.07 Å/pix.
= 477.12 Å
448 pix
1.07 Å/pix.
= 477.12 Å
448 pix
1.07 Å/pix.
= 477.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.17064932 - 0.2795285
Average (Standard dev.)0.0006186557 (0.011320367)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions448448448
Origin0.00.00.0
Limit447.0447.0447.0
Spacing448448448
CellA=B=C: 477.12003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z477.120477.120477.120
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.1710.2800.001

-
Supplemental data

-
Sample components

+
Entire Ageratum yellow vein virus

EntireName: Ageratum yellow vein virus / Number of components: 6

+
Component #1: virus, Ageratum yellow vein virus

VirusName: Ageratum yellow vein virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 251 kDa
SpeciesSpecies: Ageratum yellow vein virus
Source (natural)Host Species: Ageratum

+
Component #2: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 22.500703 kDa
SourceSpecies: Ageratum yellow vein virus
Source (engineered)Expression System: Nicotiana benthamiana (plant)

+
Component #3: nucleic-acid, ssDNA loop

Nucleic-acidName: ssDNA loop / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DA)(DA)(DC)(DC)(DA)(DC)
MassTheoretical: 2.05139 kDa
SourceSpecies: Ageratum yellow vein virus

+
Component #4: protein, coat protein subunit I

ProteinName: coat protein subunit I / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.644094 kDa
SourceSpecies: Ageratum yellow vein virus
Source (engineered)Expression System: Nicotiana benthamiana (plant)

+
Component #5: protein, coat protein subunit H

ProteinName: coat protein subunit H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.664473 kDa
SourceSpecies: Ageratum yellow vein virus
Source (engineered)Expression System: Nicotiana benthamiana (plant)

+
Component #6: nucleic-acid, ssDNA loop associated with subunit H

Nucleic-acidName: ssDNA loop associated with subunit H / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DA)(DA)(DC)(DC)(DA)
MassTheoretical: 1.762208 kDa
SourceSpecies: Ageratum yellow vein virus

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
Support filmPELCO easiglow
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 11 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2700.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 78.0 - 78.0 K)
CameraDetector: FEI FALCON III (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 12028

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D5 (2*5 fold dihedral) / Number of projections: 64932
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

+
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