8WDK

The complex structure of Cul2-VCB-Protac-Wee1

• PDB DOI: https://doi.org/10.2210/pdb8WDK/pdb
• EM Map EMD-37464: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Insect cell expression vector pTIE1, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-15 Released: 2024-09-18 
• Deposition Author(s): Wang, P., Zhang, T.T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Cul2-VCB-Protac-Wee1 complex at 3.6 Angstrom resolution.

Wang, P., Zhang, T.T.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 170.61 kDa 
• Atom Count: 11,714 
• Modelled Residue Count: 1,436 
• Deposited Residue Count: 1,468 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-2	A	745	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1, N-terminally processed	B [auth R]	82	Homo sapiens	Mutation(s): 0  Gene Names: RBX1 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	C [auth V]	155	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	D [auth B]	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

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	E [auth C]	96	Homo sapiens	Mutation(s): 0  Gene Names: ELOC
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Wee1-like protein kinase	F [auth W]	286	Homo sapiens	Mutation(s): 0  Gene Names: WEE1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P30291 (Homo sapiens) Explore P30291  Go to UniProtKB:  P30291
PHAROS:  P30291 GTEx:  ENSG00000166483

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W6U (Subject of Investigation/LOI)	G [auth V]	(2S,4R)-1-[(2S)-3,3-dimethyl-2-[3-[4-[4-[4-[[3-oxidanylidene-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]-2-prop-2-enyl-pyrazolo[3,4-d]pyrimidin-6-yl]amino]phenyl]piperazin-1-yl]butoxy]propanoylamino]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide C55 H70 N12 O7 S QQLAKZIDPLGLSV-VZUPZQALSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Wang, P., Zhang, T.T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary