+Open data
-Basic information
Entry | Database: PDB / ID: 8jr8 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | MapSPARTA dimer bound with guide-target | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | DNA BINDING PROTEIN/DNA/RNA / SPARTA / Ago / Tir / DNA BINDING PROTEIN-DNA-RNA complex | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Maribacter polysiphoniae (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å | ||||||||||||||||||
Authors | Huang, P.P. / Li, Z.X. / Guo, L.J. / Xiao, Y.B. / Chen, M.R. | ||||||||||||||||||
Funding support | China, 5items
| ||||||||||||||||||
Citation | Journal: To Be Published Title: Cryo-EM Structure of MapSPARTA Authors: Huang, P.P. / Guo, L.J. / Li, Z.X. / Yan, P.R. / Chen, M.R. / Xiao, Y.B. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jr8.cif.gz | 341 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jr8.ent.gz | 266.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jr8_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jr8_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8jr8_validation.xml.gz | 58 KB | Display | |
Data in CIF | 8jr8_validation.cif.gz | 86.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/8jr8 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/8jr8 | HTTPS FTP |
-Related structure data
Related structure data | 36592MC 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
#1: RNA chain | Mass: 6651.949 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: guide RNA / Source: (synth.) Maribacter polysiphoniae (bacteria) #2: DNA chain | Mass: 7675.000 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: target DNA / Source: (synth.) Maribacter polysiphoniae (bacteria) #3: Protein | Mass: 58091.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Gene: LX92_01809 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A316E3U6 #4: Protein | Mass: 53270.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Gene: LX92_01810 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A316E683 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Maribacter polysiphoniae short Ago complexed with TIR-APAZ Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
---|---|
Source (natural) | Organism: Maribacter polysiphoniae (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
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 / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79726 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|