[English] 日本語
![](img/lk-miru.gif)
- PDB-7oik: Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stab... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7oik | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized | |||||||||||||||
![]() |
| |||||||||||||||
![]() | SIGNALING PROTEIN / nucleotide / AAA / RNF213 / E3 ligase / activity based probe | |||||||||||||||
Function / homology | ![]() lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / cell cycle phase transition / ubiquitin-protein transferase activator activity / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / Transferases; Acyltransferases; Aminoacyltransferases / cellular response to glucocorticoid stimulus ...lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / cell cycle phase transition / ubiquitin-protein transferase activator activity / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / Transferases; Acyltransferases; Aminoacyltransferases / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / sprouting angiogenesis / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / immune system process / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / regulation of lipid metabolic process / protein autoubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / lipid droplet / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / protein modification process / Regulation of necroptotic cell death / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / presynapse / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / angiogenesis / cell population proliferation / transcription coactivator activity / protein ubiquitination / defense response to bacterium / ubiquitin protein ligase binding / regulation of DNA-templated transcription / nucleolus / enzyme binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
![]() | Grabarczyk, D. / Ahel, J. / Clausen, T. | |||||||||||||||
Funding support | ![]() ![]()
| |||||||||||||||
![]() | ![]() Title: E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP Authors: Ahel, J. / Fletcher, A.J. / Grabarczyk, D. / Roitinger, E. / Deszcz, L. / Lehner, A. / Virdee, S. / Clausen, T. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 824.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 675.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 113.9 KB | Display | |
Data in CIF | ![]() | 166.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12931MC ![]() 7oimC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data size: 2.1 TB Data #1: unaligned multi-frame micrographs [micrographs - multiframe]) |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 586545.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: E9Q555, RING-type E3 ubiquitin transferase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement | ||
---|---|---|---|
#2: Protein | Mass: 19197.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68036, E2 ubiquitin-conjugating enzyme | ||
#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | ChemComp-MG / | ||
#5: Chemical | 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 |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.58 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||
Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2 | ||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.92 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4591 |
-
Processing
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
|