[English] 日本語
Yorodumi
- PDB-7od1: Crystal structure of RBR ubiquitin ligase ARIH2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7od1
TitleCrystal structure of RBR ubiquitin ligase ARIH2
ComponentsE3 ubiquitin-protein ligase ARIH2
KeywordsLIGASE / TRIAD1 / ARIH2 / RBR / Ubiquitin / E3 Ligase
Function / homology
Function and homology information


developmental cell growth / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / positive regulation of protein targeting to mitochondrion / hematopoietic stem cell proliferation / protein K63-linked ubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / protein polyubiquitination / ubiquitin-protein transferase activity ...developmental cell growth / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / positive regulation of protein targeting to mitochondrion / hematopoietic stem cell proliferation / protein K63-linked ubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase ARIH2 / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, RING-type, conserved site ...E3 ubiquitin-protein ligase ARIH2 / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ARIH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsKostrhon, S.P. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)H2020 789016-NEDD8Activate Germany
German Research Foundation (DFG)SCHU 3196/1-1 Germany
CitationJournal: Nat Chem Biol / Year: 2021
Title: CUL5-ARIH2 E3-E3 ubiquitin ligase structure reveals cullin-specific NEDD8 activation.
Authors: Sebastian Kostrhon / J Rajan Prabu / Kheewoong Baek / Daniel Horn-Ghetko / Susanne von Gronau / Maren Klügel / Jérôme Basquin / Arno F Alpi / Brenda A Schulman /
Abstract: An emerging mechanism of ubiquitylation involves partnering of two distinct E3 ligases. In the best-characterized E3-E3 pathways, ARIH-family RING-between-RING (RBR) E3s ligate ubiquitin to ...An emerging mechanism of ubiquitylation involves partnering of two distinct E3 ligases. In the best-characterized E3-E3 pathways, ARIH-family RING-between-RING (RBR) E3s ligate ubiquitin to substrates of neddylated cullin-RING E3s. The E3 ARIH2 has been implicated in ubiquitylation of substrates of neddylated CUL5-RBX2-based E3s, including APOBEC3-family substrates of the host E3 hijacked by HIV-1 virion infectivity factor (Vif). However, the structural mechanisms remained elusive. Here structural and biochemical analyses reveal distinctive ARIH2 autoinhibition, and activation on assembly with neddylated CUL5-RBX2. Comparison to structures of E3-E3 assemblies comprising ARIH1 and neddylated CUL1-RBX1-based E3s shows cullin-specific regulation by NEDD8. Whereas CUL1-linked NEDD8 directly recruits ARIH1, CUL5-linked NEDD8 does not bind ARIH2. Instead, the data reveal an allosteric mechanism. NEDD8 uniquely contacts covalently linked CUL5, and elicits structural rearrangements that unveil cryptic ARIH2-binding sites. The data reveal how a ubiquitin-like protein induces protein-protein interactions indirectly, through allostery. Allosteric specificity of ubiquitin-like protein modifications may offer opportunities for therapeutic targeting.
History
DepositionApr 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 6, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase ARIH2
B: E3 ubiquitin-protein ligase ARIH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,57314
Polymers115,7882
Non-polymers78512
Water36020
1
A: E3 ubiquitin-protein ligase ARIH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2867
Polymers57,8941
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase ARIH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2867
Polymers57,8941
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.570, 80.540, 92.090
Angle α, β, γ (deg.)90.000, 105.760, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein E3 ubiquitin-protein ligase ARIH2 / ARI-2 / Protein ariadne-2 homolog / RING-type E3 ubiquitin transferase ARIH2 / Triad1 protein


Mass: 57893.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARIH2, ARI2, TRIAD1, HT005 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O95376, RBR-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium nitrate, 0.1 M Bis-Tris propane pH 8.5, 20 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.28097 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28097 Å / Relative weight: 1
ReflectionResolution: 2.45→74.65 Å / Num. obs: 75253 / % possible obs: 95.95 % / Redundancy: 18.6 % / CC1/2: 0.999 / Net I/σ(I): 19.5
Reflection shellResolution: 2.45→2.538 Å / Num. unique obs: 2974 / CC1/2: 0.565

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→74.65 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.14 / Phase error: 34.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 3651 4.85 %
Rwork0.2203 71554 -
obs0.2224 75205 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.24 Å2 / Biso mean: 76.8698 Å2 / Biso min: 33.3 Å2
Refinement stepCycle: final / Resolution: 2.45→74.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6940 0 12 20 6972
Biso mean--80.54 60.88 -
Num. residues----855
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.480.51551030.44461978208168
2.48-2.520.40561090.40872120222973
2.52-2.550.46421160.37742277239380
2.55-2.590.41351230.3682424254783
2.59-2.630.38481280.35912594272291
2.63-2.670.36511460.3572827297396
2.67-2.720.48611480.35652836298499
2.72-2.770.38551840.324728903074100
2.77-2.820.35051290.310227902919100
2.82-2.880.31691350.29972934306999
2.88-2.940.31621490.288528693018100
2.94-3.010.33171350.266628893024100
3.01-3.090.33891810.27922859304099
3.09-3.170.3091670.277228052972100
3.17-3.260.3251670.299628843051100
3.26-3.370.30931350.23682889302499
3.37-3.490.28751460.230428883034100
3.49-3.630.33831180.21722874299299
3.63-3.790.25851240.221828983022100
3.79-3.990.26171390.19662891303099
3.99-4.240.20451550.19412877303299
4.24-4.570.19971290.17652855298499
4.57-5.030.24611460.1752876302299
5.03-5.760.20871680.189228433011100
5.76-7.250.24711250.20652874299999
7.26-74.650.171460.1482813295998

+
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