9T32 | pdb_00009t32

The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2025-10-24 Released: 2025-12-03 
  • Deposition Author(s): Crowe, C., Ciulli, A.
  • Funding Organization(s): European Research Council (ERC), Medical Research Council (MRC, United Kingdom), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Linker-rigidified VHL homodimerizers convert degraders into stabilizers of non-ubiquitinable ternary complexes

Crowe, C., Salerno, A., Sathe, G., Marsh, G., Maple, H., Ciulli, A.

(2025) bioRxiv 


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-BA [auth D],
E [auth F]		103Homo sapiensMutation(s): 0 
Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
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Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
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UniProt GroupQ15370
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CB [auth G],
F [auth J]		95Homo sapiensMutation(s): 0 
Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
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Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-2C [auth E],
G [auth I]		655Homo sapiensMutation(s): 0 
Gene Names: CUL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13617 (Homo sapiens)
Explore Q13617 
Go to UniProtKB:  Q13617
PHAROS:  Q13617
GTEx:  ENSG00000108094 
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UniProt GroupQ13617
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1, N-terminally processedD [auth R],
H [auth S]		89Homo sapiensMutation(s): 0 
Gene Names: RBX1, RNF75, ROC1
EC: 2.3.2.32 (UniProt), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens)
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PHAROS:  P62877
GTEx:  ENSG00000100387 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressorI [auth H],
J [auth C]		141Homo sapiensMutation(s): 0 
Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens)
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PHAROS:  P40337
GTEx:  ENSG00000134086 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JTC (Subject of Investigation/LOI)
Query on A1JTC
Download Ideal Coordinates CCD File 
K [auth C](2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[2-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C58 H82 N8 O14 S2
WGJCHHJGGFCCRS-DEYDLUNASA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2012-StG-311460 DrugE3CRLs
European Research Council (ERC)European Union875510
Medical Research Council (MRC, United Kingdom)United KingdomMR/R015791/1
Wellcome TrustUnited Kingdom223816/Z/21/Z
Medical Research Council (MRC, United Kingdom)United KingdomPO 4050845509

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release