[English] 日本語
Yorodumi
- PDB-6iqw: Cryo-EM structure of Csm effector complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6iqw
TitleCryo-EM structure of Csm effector complex
Components
  • Csm1
  • Csm2
  • Csm3
  • Csm4Sainte-Julienne Aerodrome
  • Csm5
  • RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / Cryo-EM structure / CRISPR / Csm / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homologyCsm1 subunit domain B / CRISPR-associated RAMP Csm3 / HD domain profile. / GGDEF domain profile. / RAMP superfamily / Csm2 Type III-A / GGDEF domain / HD domain / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / CRISPR-associated protein Csm5 ...Csm1 subunit domain B / CRISPR-associated RAMP Csm3 / HD domain profile. / GGDEF domain profile. / RAMP superfamily / Csm2 Type III-A / GGDEF domain / HD domain / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / CRISPR-associated protein Csm5 / CRISPR-associated protein, Csm2 Type III-A / HD domain / CRISPR type III-associated protein / CRISPR type III-associated RAMP protein Csm4 / HD/PDEase domain / identical protein binding / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Specimen sourceThermococcus onnurineus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.35 Å resolution
AuthorsHuo, Y. / Li, T. / Wang, N. / Dong, Q. / Wang, X. / Jiang, T.
CitationJournal: Cell Res. / Year: 2018
Title: Cryo-EM structure of Type III-A CRISPR effector complex.
Authors: Yangao Huo / Tao Li / Nan Wang / Qinghua Dong / Xiangxi Wang / Tao Jiang
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 9, 2018 / Release: Jan 16, 2019

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9708
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Csm1
B: Csm2
C: Csm3
D: Csm3
E: Csm4
F: Csm5
I: RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,8098
Polyers261,3017
Non-polymers5071
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26750
ΔGint (kcal/M)-126
Surface area (Å2)83520

-
Components

-
Protein/peptide , 5 types, 6 molecules ABCDEF

#1: Protein/peptide Csm1 /


Mass: 88131.898 Da / Num. of mol.: 1
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0893 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWB8
#2: Protein/peptide Csm2


Mass: 22410.691 Da / Num. of mol.: 1
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0894 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWB9
#3: Protein/peptide Csm3


Mass: 32721.936 Da / Num. of mol.: 2
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0895 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC0
#4: Protein/peptide Csm4 / Sainte-Julienne Aerodrome


Mass: 32345.061 Da / Num. of mol.: 1
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0896 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC1
#5: Protein/peptide Csm5


Mass: 45262.145 Da / Num. of mol.: 1
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0897 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC2

-
RNA chain / Non-polymers , 2 types, 2 molecules I

#6: RNA chain RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')


Mass: 7707.653 Da / Num. of mol.: 1
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Production host: Escherichia coli (E. coli)
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: ToCsm effector complex / Type: COMPLEX / Entity ID: 1,2,3,4,5,6 / Source: RECOMBINANT
Source (natural)Organism: Thermococcus onnurineus NA1 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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
Image recordingElectron dose: 1.875 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.14_3247: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 61924 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. 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

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