7ONI

Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2*


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

CUL5-ARIH2 E3-E3 ubiquitin ligase structure reveals cullin-specific NEDD8 activation.

Kostrhon, S.Prabu, J.R.Baek, K.Horn-Ghetko, D.von Gronau, S.Klugel, M.Basquin, J.Alpi, A.F.Schulman, B.A.

(2021) Nat Chem Biol 17: 1075-1083

  • DOI: 10.1038/s41589-021-00858-8
  • Primary Citation of Related Structures:  
    7OD1, 7ONI

  • PubMed 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 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) ...

    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.


    Organizational Affiliation

    Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany. schulman@biochem.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-5A [auth C]780Homo sapiensMutation(s): 0 
Gene Names: CUL5VACM1
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Find proteins for Q93034 (Homo sapiens)
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PHAROS:  Q93034
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UniProt GroupQ93034
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ARIH2B [auth H]495Homo sapiensMutation(s): 3 
Gene Names: ARIH2ARI2TRIAD1HT005
EC: 2.3.2.31
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Find proteins for O95376 (Homo sapiens)
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PHAROS:  O95376
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UniProt GroupO95376
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RING-box protein 2C [auth R]111Homo sapiensMutation(s): 0 
Gene Names: RNF7RBX2ROC2SAG
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Find proteins for Q9UBF6 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8D [auth N]83Homo sapiensMutation(s): 0 
Gene Names: NEDD8
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Find proteins for Q15843 (Homo sapiens)
Explore Q15843 
Go to UniProtKB:  Q15843
PHAROS:  Q15843
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European Research Council (ERC)GermanyH2020 789016-NEDD8Activate
German Research Foundation (DFG)GermanySCHU 3196/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2021-10-06
    Changes: Data collection, Database references