8QU8

PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1

• PDB DOI: https://doi.org/10.2210/pdb8QU8/pdb
• EM Map EMD-18657: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-10-14 Released: 2023-12-06 
• Deposition Author(s): Fischer, G., Peter, D., Arce-Solano, S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Targeting cancer with small molecule pan-KRAS degraders

Popow, J., Farnaby, W., Gollner, A., Kofink, C., Fischer, G., Wurm, M., Zollman, D., Wijaya, A., Mischerikow, N., Hasenoehrl, C., Prokofeva, P., Arnhof, H., Arce-Solano, S., Bell, S., Boeck, G., Diers, E., Frost, A., Goodwin-Tindall, J., Karolyi-Oezguer, J., Khan, S., Klawatsch, T., Koegl, M., Kousek, R., Kratochvil, B., Kropatsch, K., Lauber, A., McLennan, R., Olt, S., Peter, D., Petermann, O., Roessler, V., Stolt-Bergner, P., Strack, P., Strauss, E., Trainor, N., Vetma, V., Whitworth, C., Zhong, S., Quant, J., Weinstabl, H., Kuster, B., Ettmayer, P., Ciulli, A.

(2023) Biorxiv 

• DOI: https://doi.org/10.1101/2023.10.24.563163

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 169.49 kDa 
• Atom Count: 10,846 
• Modelled Residue Count: 1,325 
• Deposited Residue Count: 1,461 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	A	212	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-B	B	117	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	C	111	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-2	D	744	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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1, N-terminally processed	E	107	Homo sapiens	Mutation(s): 0  Gene Names: RBX1, RNF75, ROC1
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens) Explore P62877  Go to UniProtKB:  P62877
PHAROS:  P62877 GTEx:  ENSG00000100387

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	F	170	Homo sapiens	Mutation(s): 4  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116  Go to UniProtKB:  P01116
PHAROS:  P01116 GTEx:  ENSG00000133703

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WYL (Subject of Investigation/LOI)	J [auth F]	(2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide C50 H62 N14 O6 S2 DQRZNYPHOWVXPQ-YDUPODKQSA-N
GDP	I [auth F]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN	G [auth E], H [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Fischer, G., Peter, D., Arce-Solano, S.

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Funding Organization	Location	Grant Number
Other private	Austria	Boehringer Ingelheim

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Experimental preparation, Refinement description