8R5H

Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 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

Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting.

Li, J.Purser, N.Liwocha, J.Scott, D.C.Byers, H.A.Steigenberger, B.Hill, S.Tripathi-Giesgen, I.Hinkle, T.Hansen, F.M.Prabu, J.R.Radhakrishnan, S.K.Kirkpatrick, D.S.Reichermeier, K.M.Schulman, B.A.Kleiger, G.

(2024) Mol Cell 84: 1304

  • DOI: https://doi.org/10.1016/j.molcel.2024.01.022
  • Primary Citation of Related Structures:  
    8Q7R, 8R5H

  • PubMed Abstract: 

    Cullin-RING ligases (CRLs) ubiquitylate specific substrates selected from other cellular proteins. Substrate discrimination and ubiquitin transferase activity were thought to be strictly separated. Substrates are recognized by substrate receptors, such as Fbox or BCbox proteins. Meanwhile, CRLs employ assorted ubiquitin-carrying enzymes (UCEs, which are a collection of E2 and ARIH-family E3s) specialized for either initial substrate ubiquitylation (priming) or forging poly-ubiquitin chains. We discovered specific human CRL-UCE pairings governing substrate priming. The results reveal pairing of CUL2-based CRLs and UBE2R-family UCEs in cells, essential for efficient PROTAC-induced neo-substrate degradation. Despite UBE2R2's intrinsic programming to catalyze poly-ubiquitylation, CUL2 employs this UCE for geometrically precise PROTAC-dependent ubiquitylation of a neo-substrate and for rapid priming of substrates recruited to diverse receptors. Cryo-EM structures illuminate how CUL2-based CRLs engage UBE2R2 to activate substrate ubiquitylation. Thus, pairing with a specific UCE overcomes E2 catalytic limitations to drive substrate ubiquitylation and targeted protein degradation.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-2745Homo sapiensMutation(s): 0 
Gene Names: CUL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13617 (Homo sapiens)
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PHAROS:  Q13617
GTEx:  ENSG00000108094 
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UniProt GroupQ13617
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1, N-terminally processedB [auth R]104Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
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Find proteins for P62877 (Homo sapiens)
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PHAROS:  P62877
GTEx:  ENSG00000100387 
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UniProt GroupP62877
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 R2238Homo sapiensMutation(s): 0 
Gene Names: UBE2R2CDC34BUBC3B
EC: 2.3.2.23
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GTEx:  ENSG00000107341 
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UniProt GroupQ712K3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinD [auth U]75Homo sapiensMutation(s): 0 
Gene Names: UBC
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Find proteins for P0CG48 (Homo sapiens)
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PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CE [auth D]112Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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Find proteins for Q15369 (Homo sapiens)
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GTEx:  ENSG00000154582 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4115Homo sapiensMutation(s): 5 
Gene Names: BRD4HUNK1
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GTEx:  ENSG00000141867 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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GTEx:  ENSG00000103363 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor160Homo sapiensMutation(s): 0 
Gene Names: VHL
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Find proteins for P40337 (Homo sapiens)
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GTEx:  ENSG00000134086 
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
759 (Subject of Investigation/LOI)
Query on 759

Download Ideal Coordinates CCD File 
M [auth H](2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C49 H62 Cl N9 O8 S2
HJITZUXCPZGZPX-PYNGZGNASA-N
SY8 (Subject of Investigation/LOI)
Query on SY8

Download Ideal Coordinates CCD File 
L [auth C]5-azanylpentan-2-one
C5 H11 N O
VTHKLCWOLNQWHB-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
I [auth R],
J [auth R],
K [auth R]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references
  • Version 1.2: 2024-04-17
    Changes: Database references, Derived calculations