[English] 日本語
Yorodumi
- EMDB-8477: CRISPR RNA-guided surveillance complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8477
TitleCRISPR RNA-guided surveillance complex
SampleCRISPR RNA-guided surveillance complex
SourceThermobifida fusca (strain yx) / bacteria / thermophilic
Map data
Methodsingle particle reconstruction, at 3.8 Å resolution
AuthorsXiao Y / Luo M
CitationCell, 2017, 170, 48-60.e11

Cell, 2017, 170, 48-60.e11 Yorodumi Papers
Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.
Yibei Xiao / Min Luo / Robert P Hayes / Jonathan Kim / Sherwin Ng / Fang Ding / Maofu Liao / Ailong Ke

Validation ReportPDB-ID: 5u07

SummaryFull reportAbout validation report
DateDeposition: Nov 23, 2016 / Header (metadata) release: Mar 22, 2017 / Map release: Aug 9, 2017 / Last update: Aug 16, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5u07
  • Surface level: 0.045
  • 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_8477.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.23 Å/pix.
= 314.88 Å
256 pix
1.23 Å/pix.
= 314.88 Å
256 pix
1.23 Å/pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.23 Å
Density
Contour Level:0.07 (by author), 0.045 (movie #1):
Minimum - Maximum-0.107699394 - 0.21361065
Average (Standard dev.)2.7352522E-5 (0.006874965)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 314.88 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1080.2140.000

-
Supplemental data

-
Sample components

+
Entire CRISPR RNA-guided surveillance complex

EntireName: CRISPR RNA-guided surveillance complex / Number of components: 9

+
Component #1: protein, CRISPR RNA-guided surveillance complex

ProteinName: CRISPR RNA-guided surveillance complex / Recombinant expression: No
SourceSpecies: Thermobifida fusca (strain yx) / bacteria / thermophilic
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
Vector: pcdf

+
Component #2: protein, CRISPR-associated protein, Cse3 family

ProteinName: CRISPR-associated protein, Cse3 family / Recombinant expression: No
MassTheoretical: 26.327938 kDa
Source (engineered)Expression System: Thermobifida fusca yx / bacteria / thermophilic
Strain: YX

+
Component #3: protein, Cse2

ProteinName: Cse2 / Recombinant expression: No
MassTheoretical: 27.446613 kDa
Source (engineered)Expression System: Thermobifida fusca yx / bacteria / thermophilic
Strain: YX

+
Component #4: protein, CRISPR-associated protein, Cse1 family

ProteinName: CRISPR-associated protein, Cse1 family / Recombinant expression: No
MassTheoretical: 61.433297 kDa
Source (engineered)Expression System: Thermobifida fusca yx / bacteria / thermophilic
Strain: YX

+
Component #5: protein, CRISPR-associated protein, Cse4 family

ProteinName: CRISPR-associated protein, Cse4 family / Recombinant expression: No
MassTheoretical: 41.043043 kDa
Source (engineered)Expression System: Thermobifida fusca yx / bacteria / thermophilic
Strain: YX

+
Component #6: nucleic-acid, crRNA

Nucleic-acidName: crRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUGGACCGCC AGUGAUAAGU GGAAUGCCAU GUGGGCUGUC GUGAGCCCCA CGCACGUGGG G
MassTheoretical: 19.790793 kDa

+
Component #7: nucleic-acid, Target Strand

Nucleic-acidName: Target Strand / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DT)(DA)(DT)(DC)(DA)(DC)(DT)(DG)(DG) (DC)(DT)(DT)(DC)(DG)(DT)(DC)(DC)(DG)(DC) (DG)
MassTheoretical: 6.381106 kDa

+
Component #8: protein, CRISPR-associated protein, Cas5e family

ProteinName: CRISPR-associated protein, Cas5e family / Recombinant expression: No
MassTheoretical: 28.27926 kDa
Source (engineered)Expression System: Thermobifida fusca yx / bacteria / thermophilic
Strain: YX

+
Component #9: nucleic-acid, Nontarget Strand

Nucleic-acidName: Nontarget Strand / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DG)(DC)(DG)(DG)(DA)(DC)(DG)(DA)(DA) (DG)(DC)(DC)
MassTheoretical: 3.9866 kDa

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.8 mg/ml / Buffer solution: 10 mM Hepes, 150 mM NaCl, 5 mM DTT, pH 7.5 / pH: 7.5
VitrificationCryogen name: ETHANE / Humidity: 85 %

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 31000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 80 - 105 K)
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1305

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 70222
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF

-
Atomic model buiding

Output model

+
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