[English] 日本語
Yorodumi
- EMDB-3454: RNA activation-independent DNA targeting by a Csm complex of the ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3454
TitleRNA activation-independent DNA targeting by a Csm complex of the Type III CRISPR-Cas system
SampleCsm complex with crRNA from T.onnurineus
SourceThermococcus onnurineus na1 / archaea / thermophilic
Map dataCsm complex with crRNA from T.onnurineus
Methodsingle particle reconstruction, at 25 Å resolution
AuthorsJung TY / Song JJ / Hebert H / Woo EJ / Oh BH / Park KH / An Y
CitationEMBO Rep., 2017, 18, 826-840

EMBO Rep., 2017, 18, 826-840 Yorodumi Papers
RNA activation-independent DNA targeting of the Type III CRISPR-Cas system by a Csm complex.
Kwang-Hyun Park / Yan An / Tae-Yang Jung / In-Young Baek / Haemin Noh / Woo-Chan Ahn / Hans Hebert / Ji-Joon Song / Jeong-Hoon Kim / Byung-Ha Oh / Eui-Jeon Woo

DateDeposition: Nov 2, 2016 / Header (metadata) release: Dec 7, 2016 / Map release: Apr 5, 2017 / Last update: Aug 2, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_3454.map.gz (map file in CCP4 format, 19653 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
170 pix
2.07 Å/pix.
= 351.9 Å
170 pix
2.07 Å/pix.
= 351.9 Å
170 pix
2.07 Å/pix.
= 351.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.07 Å
Density
Contour Level:0.5 (by author), 0.5 (movie #1):
Minimum - Maximum-0.8233378 - 2.4102547
Average (Standard dev.)0.007941852 (0.1374122)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions170170170
Origin-85-85-85
Limit848484
Spacing170170170
CellA=B=C: 351.9 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.072.072.07
M x/y/z170170170
origin x/y/z0.0000.0000.000
length x/y/z351.900351.900351.900
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-85-85-85
NC/NR/NS170170170
D min/max/mean-0.8232.4100.008

-
Supplemental data

-
Sample components

-
Entire Csm complex with crRNA from T.onnurineus

EntireName: Csm complex with crRNA from T.onnurineus / Number of components: 1
MassExperimental: 280 kDa

-
Component #1: protein, Csm complex with crRNA from T.onnurineus

ProteinName: Csm complex with crRNA from T.onnurineus / Recombinant expression: No
MassExperimental: 280 kDa
SourceSpecies: Thermococcus onnurineus na1 / archaea / thermophilic
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pRSFDuet-1, pETDuel-1, pACYCDuet-1

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.025 mg/ml / pH: 8
VitrificationCryogen name: NONE

-
Electron microscopy imaging

ImagingMicroscope: JEOL 2100F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: JEOL
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7644
3D reconstructionSoftware: EMAN / Resolution: 25 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot (resolution assessment)

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more