[English] 日本語
Yorodumi
- PDB-7oik: Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stab... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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, catalytic domain homologues / 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, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / Adenosine 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

-
Experimental details

-
Experiment

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

-
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

-
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 FIELDBright-field microscopy / 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

-
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
IDPDB-IDPdb chain-ID 3D fitting-ID
16TAX

6tax

A1
24Q5E

4q5e

C1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more