7B5L

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly.

Horn-Ghetko, D.Krist, D.T.Prabu, J.R.Baek, K.Mulder, M.P.C.Klugel, M.Scott, D.C.Ovaa, H.Kleiger, G.Schulman, B.A.

(2021) Nature 590: 671-676

  • DOI: 10.1038/s41586-021-03197-9
  • Primary Citation of Related Structures:  
    7B5L, 7B5M, 7B5N, 7B5R, 7B5S

  • PubMed Abstract: 
  • E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates 1,2 . However, rather than functioning individually, many neddylated cullin-RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family-which together account for nearly half of all ubiquitin ligases in humans-form E3-E3 super-assemblies 3-7 ...

    E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates 1,2 . However, rather than functioning individually, many neddylated cullin-RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family-which together account for nearly half of all ubiquitin ligases in humans-form E3-E3 super-assemblies 3-7 . Here, by studying CRLs in the SKP1-CUL1-F-box (SCF) family, we show how neddylated SCF ligases and ARIH1 (an RBR-type E3 ligase) co-evolved to ubiquitylate diverse substrates presented on various F-box proteins. We developed activity-based chemical probes that enabled cryo-electron microscopy visualization of steps in E3-E3 ubiquitylation, initiating with ubiquitin linked to the E2 enzyme UBE2L3, then transferred to the catalytic cysteine of ARIH1, and culminating in ubiquitin linkage to a substrate bound to the SCF E3 ligase. The E3-E3 mechanism places the ubiquitin-linked active site of ARIH1 adjacent to substrates bound to F-box proteins (for example, substrates with folded structures or limited length) that are incompatible with previously described conventional RING E3-only mechanisms. The versatile E3-E3 super-assembly may therefore underlie widespread ubiquitylation.


    Organizational Affiliation

    Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA. schulman@biochem.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-1A [auth C]776Homo sapiensMutation(s): 0 
Gene Names: CUL1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ARIH1B [auth H]557Homo sapiensMutation(s): 0 
Gene Names: ARIH1ARIMOP6UBCH7BPHUSSY-27
EC: 2.3.2.31
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 2C [auth T]424Homo sapiensMutation(s): 0 
Gene Names: SKP2FBXL1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinases regulatory subunit 1D [auth K]73Homo sapiensMutation(s): 0 
Gene Names: CKS1BCKS1PNAS-143PNAS-16
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1E [auth S]163Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CF [auth U]75Homo sapiensMutation(s): 0 
Gene Names: UBC
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8G [auth N]76Homo sapiensMutation(s): 0 
Gene Names: NEDD8
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1H [auth R]108Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 L3I [auth D]154Homo sapiensMutation(s): 2 
Gene Names: UBE2L3UBCE7UBCH7
EC: 2.3.2.23
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2J [auth L]298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
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Entity ID: 11
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Cyclin-A2K [auth Y]432Homo sapiensMutation(s): 0 
Gene Names: CCNA2CCN1CCNA
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase inhibitor 1BL [auth P]198Homo sapiensMutation(s): 0 
Gene Names: CDKN1BKIP1
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Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
J [auth L]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
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: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2021-03-10
    Changes: Database references