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- PDB-7od1: Crystal structure of RBR ubiquitin ligase ARIH2 -

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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 / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / Ariadne domain / Ariadne domain / IBR domain, a half RING-finger domain / E3 ubiquitin ligase RBR family / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain ...: / : / Ariadne domain / Ariadne domain / IBR domain, a half RING-finger domain / E3 ubiquitin ligase RBR family / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain 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
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
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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

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Experimental details

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Experiment

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

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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

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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

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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

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