8EI1 | pdb_00008ei1

Crystal structure of the N-terminal domain of CUL4B in complex with H316, a Helicon Polypeptide

• PDB DOI: https://doi.org/10.2210/pdb8EI1/pdb

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


• Deposited: 2022-09-14 Released: 2023-10-25 
• Deposition Author(s): Li, K., Tokareva, O.S., Thomson, T.M., Verdine, G.L., McGee, J.H.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.254 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides.

Tokareva, O.S., Li, K., Travaline, T.L., Thomson, T.M., Swiecicki, J.M., Moussa, M., Ramirez, J.D., Litchman, S., Verdine, G.L., McGee, J.H.

(2023) Nat Commun 14: 6992-6992

• PubMed: 37914719 
• DOI: https://doi.org/10.1038/s41467-023-42395-z
• Primary Citation Related Structures: 
  8EHZ, 8EI0, 8EI1, 8EI2, 8EI3, 8EI4, 8EI5, 8EI6, 8EI7, 8EI8, 8EI9, 8EIA, 8EIB, 8EIC


• PubMed Abstract: 
  

  Molecules that induce novel interactions between proteins hold great promise for the study of biological systems and the development of therapeutics, but their discovery has been limited by the complexities of rationally designing interactions between three components, and because known binders to each protein are typically required to inform initial designs. Here, we report a general and rapid method for discovering α-helically constrained (Helicon) polypeptides that cooperatively induce the interaction between two target proteins without relying on previously known binders or an intrinsic affinity between the proteins. We show that Helicons are capable of binding every major class of E3 ubiquitin ligases, which are of great biological and therapeutic interest but remain largely intractable to targeting by small molecules. We then describe a phage-based screening method for discovering "trimerizer" Helicons, and apply it to reprogram E3s to cooperatively bind an enzyme (PPIA), a transcription factor (TEAD4), and a transcriptional coactivator (β-catenin).

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Organizational Affiliation: 
• FOG Pharmaceuticals Inc., Cambridge, MA, USA.
Kymera Therapeutics, Inc., Watertown, MA, USA.
Relay Therapeutics, Inc., Cambridge, MA, USA.
FOG Pharmaceuticals Inc., Cambridge, MA, USA. [e-mail].
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. [e-mail].
Department of Chemistry and Chemical Biology, Harvard, University, Cambridge, MA, USA. [e-mail].
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. [e-mail].
FOG Pharmaceuticals Inc., Cambridge, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B2C1D1 

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

Macromolecule Content 

• Total Structure Weight: 176.68 kDa 
• Atom Count: 11,809 
• Modeled Residue Count: 1,429 
• Deposited Residue Count: 1,492 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-4B	A, B, C, D	354	Homo sapiens	Mutation(s): 0  Gene Names: CUL4B, KIAA0695
UniProt & NIH Common Fund Data Resources
Find proteins for Q13620 (Homo sapiens) Explore Q13620  Go to UniProtKB:  Q13620
PHAROS:  Q13620 GTEx:  ENSG00000158290

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H316	E, F, G, H	19	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WHL	I [auth E], J [auth F], K [auth G], L [auth H]	N,N'-(1,4-phenylene)diacetamide C10 H12 N2 O2 KVEDKKLZCJBVNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.254 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.65	α = 90
b = 99.65	β = 90
c = 366.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Li, K., Tokareva, O.S., Thomson, T.M., Verdine, G.L., McGee, J.H.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary
• Version 1.3: 2026-03-04
  Changes: Refinement description