+Open data
-Basic information
Entry | Database: PDB / ID: 6iqw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Csm effector complex | |||||||||
Components |
| |||||||||
Keywords | RNA BINDING PROTEIN/RNA / Cryo-EM structure / CRISPR / Csm / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information exonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Thermococcus onnurineus (archaea) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Huo, Y. / Li, T. / Wang, N. / Dong, Q. / Wang, X. / Jiang, T. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: 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 / | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6iqw.cif.gz | 377.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6iqw.ent.gz | 311.7 KB | Display | PDB format |
PDBx/mmJSON format | 6iqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/6iqw ftp://data.pdbj.org/pub/pdb/validation_reports/iq/6iqw | HTTPS FTP |
---|
-Related structure data
Related structure data | 9708MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 5 types, 6 molecules ABCDEF
#1: Protein | Mass: 88131.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea) Strain: NA1 / Gene: TON_0893 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWB8 | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 22410.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea) Strain: NA1 / Gene: TON_0894 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWB9 | ||||
#3: Protein | Mass: 32721.936 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea) Strain: NA1 / Gene: TON_0895 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC0 #4: Protein | | Mass: 32345.061 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea) Strain: NA1 / Gene: TON_0896 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC1 #5: Protein | | Mass: 45262.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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 | Mass: 7707.653 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea) Strain: NA1 / Production host: Escherichia coli (E. coli) |
---|---|
#7: Chemical | ChemComp-ATP / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ToCsm effector complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Thermococcus onnurineus NA1 (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.875 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3247: / Classification: refinement |
---|---|
CTF correction | Type: NONE |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61924 / Symmetry type: POINT |