+Open data
-Basic information
Entry | Database: PDB / ID: 8k22 | ||||||
---|---|---|---|---|---|---|---|
Title | ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (half form) | ||||||
Components |
| ||||||
Keywords | RNA BINDING PROTEIN/DNA/RNA / IMMUNE SYSTEM-RNA-DNA complex / RNA BINDING PROTEIN-DNA-RNA complex | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / endonuclease activity / hydrolase activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio phage ICP1_2004_A (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||
Authors | Zhang, L.X. / Feng, Y. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Structure of csy complex with long DNA State2 Authors: Zhang, L.X. / Feng, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8k22.cif.gz | 879.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8k22.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8k22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k22_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8k22_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8k22_validation.xml.gz | 116.4 KB | Display | |
Data in CIF | 8k22_validation.cif.gz | 190.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/8k22 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/8k22 | HTTPS FTP |
-Related structure data
Related structure data | 36825MC 8k24C 8k29C 38838 M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 6 types, 15 molecules BCDEdeGIJKLMHaA
#1: Protein | Mass: 20338.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00450 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V8 | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 27401.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00445 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V7 | ||||||
#3: Protein | Mass: 33489.379 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00460 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5W0 #4: Protein | Mass: 33399.301 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00440 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V6 #5: Protein | | Mass: 18736.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00435 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V5 #9: Protein | Mass: 104703.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00455 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V9 |
-DNA chain , 3 types, 4 molecules QURV
#7: DNA chain | Mass: 13431.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli) #8: DNA chain | | Mass: 9346.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli) #10: DNA chain | | Mass: 6338.120 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli) |
---|
-RNA chain / Non-polymers , 2 types, 3 molecules P
#11: Chemical | #6: RNA chain | | Mass: 19046.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli) |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: csy complex / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES |
---|---|
Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
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: DARK FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 235177 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|