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- PDB-7oim: Mouse RNF213, with mixed nucleotides bound -

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Basic information

Entry
Database: PDB / ID: 7oim
TitleMouse RNF213, with mixed nucleotides bound
ComponentsE3 ubiquitin-protein ligase RNF213
KeywordsSIGNALING 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
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) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. ...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) / 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'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ADENOSINE-5'-TRIPHOSPHATE / E3 ubiquitin-protein ligase RNF213
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF213
hetero molecules


Theoretical massNumber of molelcules
Total (without water)554,2367
Polymers552,6231
Non-polymers1,6136
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2740 Å2
ΔGint-19 kcal/mol
Surface area197380 Å2
MethodPISA

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Components

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Protein , 1 types, 1 molecules A

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


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 / ADENOSINE-5'-TRIPHOSPHATE


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


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Details

Has ligand of interestY

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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

ComponentName: RNF213 incubated with ATPgS / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.58 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
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: -1500 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 recording

Imaging-ID: 1 / Num. of grids imaged: 1

IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector modelNum. of real imagesDetailsDetector mode
1245GATAN K3 BIOQUANTUM (6k x 4k)3055grid tilted 30 degrees 1 image per "hole"
21040.5GATAN K2 QUANTUM (4k x 4k)5950non-tilted dataset 10 images per "hole"COUNTING
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategoryDetails
1SPHIRE1.5.1particle selectioncryolo
2RELION3.1particle selection3d template picking
3SerialEMimage acquisitionHeidelberg 2019-09
4SerialEMimage acquisitionHeidelberg 2020-07
6CTFFIND4.1CTF correction
9UCSF Chimeramodel fitting
14RELION3.13D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 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 buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6TAX

6tax


Pdb chain-ID: A

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