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- PDB-7oik: Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stab... -

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Basic information

Entry
Database: PDB / ID: 7oik
TitleMouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized
Components
  • E3 ubiquitin-protein ligase RNF213
  • Ubiquitin-conjugating enzyme E2 L3
KeywordsSIGNALING PROTEIN / nucleotide / AAA / RNF213 / E3 ligase / activity based probe
Function / homology
Function and homology information


lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / cell cycle phase transition / ubiquitin-protein transferase activator activity / xenophagy / protein K11-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases ...lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / cell cycle phase transition / ubiquitin-protein transferase activator activity / xenophagy / protein K11-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / positive regulation of protein targeting to mitochondrion / cellular response to glucocorticoid stimulus / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / regulation of lipid metabolic process / protein K63-linked ubiquitination / immune system process / ubiquitin ligase complex / protein autoubiquitination / lipid droplet / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein modification process / Regulation of necroptotic cell death / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / angiogenesis / transcription coactivator activity / cell population proliferation / defense response to bacterium / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 ...E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / E3 ubiquitin-protein ligase RNF213 / Ubiquitin-conjugating enzyme E2 L3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGrabarczyk, D. / Ahel, J. / Clausen, T.
Funding support Austria, United Kingdom, 4items
OrganizationGrant numberCountry
European Research Council (ERC)694978 Austria
Austrian Research Promotion Agency852936 Austria
Medical Research Council (MRC, United Kingdom)MC_UU_12016/8 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/ P003982/1 United Kingdom
CitationJournal: 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
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF213
B: Ubiquitin-conjugating enzyme E2 L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)606,4066
Polymers605,7432
Non-polymers6624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2410 Å2
ΔGint-17 kcal/mol
Surface area199900 Å2

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Components

#1: Protein E3 ubiquitin-protein ligase RNF213 / Mysterin / RING finger protein 213 / RING-type E3 ubiquitin transferase RNF213


Mass: 586545.500 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
#2: Protein Ubiquitin-conjugating enzyme E2 L3 / E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin- ...E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


Mass: 19197.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68036, E2 ubiquitin-conjugating enzyme
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1RNF213-ABP(UBE2L3-Ub)COMPLEXchemically stabilized complex between mouse RNF213 and a modified human UBE2L3 ABP (activity based probe), coupled to modified human ubiquitin#1-#20RECOMBINANT
2RNF213-ABP(UBE2L3-Ub)COMPLEXE3 ubiquitin-protein ligase RNF213#11RECOMBINANT
3RNF213-ABP(UBE2L3-Ub)COMPLEXUbiquitin-conjugating enzyme E2 L3#21RECOMBINANT
Molecular weightValue: 0.58 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Mus musculus (house mouse)10090
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trichoplusia ni (cabbage looper)7111
23Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.2
Buffer component
IDConc.FormulaBuffer-ID
1200 mMKCl1
225 mMHEPES1
30.25 mMTCEP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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

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Processing

EM software
IDNameVersionCategoryDetails
1SPHIRE1.5.1particle selectioncryolo
2RELION3.1particle selection3d template picking
3EPUimage acquisitionDiamond 2020-12-16
5CTFFIND4.1CTF correction
8UCSF Chimeramodel fitting
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 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

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
16TAX

6tax

A6TAX1
24Q5E

4q5e

C4Q5E2

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