9T32 | pdb_00009t32

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

PDB DOI: https://doi.org/10.2210/pdb9T32/pdb
EM Map EMD-55480: EMDB EMDataResource

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

DOI: https://doi.org/10.1101/2025.11.18.689129

Macromolecule Content

Total Structure Weight: 252.9 kDa
Atom Count: 17,498
Modeled Residue Count: 2,136
Deposited Residue Count: 2,166
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A [auth D], E [auth F]	103	Homo sapiens	Mutation(s): 0 Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370 Go to UniProtKB: Q15370
PHAROS: Q15370 GTEx: ENSG00000103363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15370
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B [auth G], F [auth J]	95	Homo sapiens	Mutation(s): 0 Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369 Go to UniProtKB: Q15369
PHAROS: Q15369 GTEx: ENSG00000154582
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15369
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-2	C [auth E], G [auth I]	655	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13617
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1, N-terminally processed	D [auth R], H [auth S]	89	Homo sapiens	Mutation(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) Explore P62877 Go to UniProtKB: P62877
PHAROS: P62877 GTEx: ENSG00000100387
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62877
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	I [auth H], J [auth C]	141	Homo sapiens	Mutation(s): 0 Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337 Go to UniProtKB: P40337
PHAROS: P40337 GTEx: ENSG00000134086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40337
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JTC (Subject of Investigation/LOI) Query on A1JTC Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	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		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Crowe, C.

Ciulli, A.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	ERC-2012-StG-311460 DrugE3CRLs
European Research Council (ERC)	European Union	875510
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/R015791/1
Wellcome Trust	United Kingdom	223816/Z/21/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	PO 4050845509