9H30 | pdb_00009h30

VHL:ElonginC:ElonginB-PROTAC4 complex

• PDB DOI: https://doi.org/10.2210/pdb9H30/pdb

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


• Deposited: 2024-10-15 Released: 2025-10-29 
• Deposition Author(s): Maiocchi, A., Abel, A.-C., Steinmetz, M.O., Passarella, D., Prota, A.E.
• Funding Organization(s): European Union (EU), Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Effective Tubulin Degradation by Rationally Designed Proteolysis Targeting Chimeras

Maiocchi, A., Abel, A.C., Basellini, M., Perez-Pena, H., Boiarska, Z., Ferrandi, E.E., Kozicka, Z., Fasano, V., Pieraccini, S., Cappelletti, G., Steinmetz, M.O., Passarella, D., Prota, A.E.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.05.22.655572

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.5 kDa 
• Atom Count: 2,829 
• Modeled Residue Count: 334 
• Deposited Residue Count: 398 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	A [auth B]	197	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B [auth C]	97	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	C [auth D]	104	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ISE	D [auth B]	N-[5-(1-{2-[4-({[(1S,2R,3S,5S,6S,16E,18E,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl]oxy}carbonyl)phenyl]ethyl}-1H-1,2,3-triazol-4-yl)pentanoyl]-3-methyl-D-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide C66 H82 Cl N9 O13 S DVEWGFCZXIGIAS-CIXJPGMKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.461	α = 90
b = 67.043	β = 94.058
c = 101.845	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Maiocchi, A., Abel, A.-C., Steinmetz, M.O., Passarella, D., Prota, A.E.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	860070 TubInTrain
Swiss National Science Foundation	Switzerland	31003A_166608

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release
  
• Version 1.1: 2026-05-13
  Changes: Database references