+Open data
-Basic information
Entry | Database: PDB / ID: 7oim | |||||||||||||||
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Title | Mouse RNF213, with mixed nucleotides bound | |||||||||||||||
Components | E3 ubiquitin-protein ligase RNF213 | |||||||||||||||
Keywords | SIGNALING PROTEIN / nucleotide / AAA / RNF213 / E3 ligase | |||||||||||||||
Function / homology | Function and homology information lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / protein K63-linked ubiquitination / regulation of lipid metabolic process ...lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / protein K63-linked ubiquitination / regulation of lipid metabolic process / protein autoubiquitination / lipid droplet / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / angiogenesis / protein ubiquitination / defense response to bacterium / nucleolus / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||||||||
Authors | Grabarczyk, D. / Ahel, J. / Clausen, T. | |||||||||||||||
Funding support | Austria, United Kingdom, 4items
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Citation | Journal: To Be Published 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oim.cif.gz | 805.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oim.ent.gz | 651.3 KB | Display | PDB format |
PDBx/mmJSON format | 7oim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oim_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7oim_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7oim_validation.xml.gz | 110 KB | Display | |
Data in CIF | 7oim_validation.cif.gz | 161.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/7oim ftp://data.pdbj.org/pub/pdb/validation_reports/oi/7oim | HTTPS FTP |
-Related structure data
Related structure data | 12932MC 7oikC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-10712 (Title: Transmission electron micrographs of mouse RNF213 incubated with ATPγS Data size: 2.3 TB Data #1: unaligned multi-frame micrographs from a dataset collected without grid tilting [micrographs - multiframe] Data #2: unaligned multi-frame micrographs from a dataset collected with a 30 deg grid tilt [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 552623.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnf213, Mystr / Production host: Trichoplusia ni (cabbage looper) References: UniProt: E9Q555, RING-type E3 ubiquitin transferase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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-Non-polymers , 5 types, 6 molecules
#2: Chemical | ChemComp-ATP / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-AGS / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RNF213 incubated with ATPgS / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES | ||||||||||||||||
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Molecular weight | Value: 0.58 MDa / Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | ||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | ||||||||||||||||
Buffer solution | pH: 7.2 | ||||||||||||||||
Buffer component |
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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 | |||||||||||||||||||||
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Microscopy | Model: TFS KRIOS | |||||||||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN | |||||||||||||||||||||
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -1500 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 | Imaging-ID: 1 / Num. of grids imaged: 1
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Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6TAX Pdb chain-ID: A |