7PS9 | pdb_00007ps9

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide (CC-220)

• PDB DOI: https://doi.org/10.2210/pdb7PS9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Magnetospirillum gryphiswaldense
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-09-22 Released: 2022-03-16 
• Deposition Author(s): Heim, C., Hartmann, M.D.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.246 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system.

Heim, C., Hartmann, M.D.

(2022) Acta Crystallogr D Struct Biol 78: 290-298

• PubMed: 35234143 
• DOI: https://doi.org/10.1107/S2059798322000092
• Primary Citation Related Structures: 
  7PS9, 7PSO


• PubMed Abstract: 
  

  Cereblon (CRBN) is the substrate receptor of the CRL4 ^CRBN E3 ubiquitin ligase and is a central player in targeted protein degradation. It is the target of the thalidomide-derived immunomodulatory drugs (IMiDs) and is one of the most widely employed receptors for proteolysis-targeting chimeras (PROTACs), both of which induce the ubiquitination and subsequent proteasomal degradation of target proteins. Structural studies of ligand binding to CRBN are crucial to elucidate the mechanisms of action and for mediation of side effects, ultimately aiding the development of next-generation IMiDs and PROTACs. With this aim, a crystal-soaking system based on the single-domain bacterial homologue MsCI4 has previously been established and used to delineate the binding modes of several classes of small molecules, including FDA-approved drugs, at the molecular level. Here, this system was used to characterize the binding of the next-generation IMiDs avadomide (CC-122) and iberdomide (CC-220) at high resolution, highlighting the advantages and limitations of the MsCI4 system and its implications for the development of future cereblon effectors.

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Organizational Affiliation: 
• Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.44 kDa 
• Atom Count: 2,603 
• Modeled Residue Count: 303 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cereblon isoform 4	A, B, C	124	Magnetospirillum gryphiswaldense	Mutation(s): 0  Gene Names: MGR_0879
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense) Explore A4TVL0  Go to UniProtKB:  A4TVL0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8W7 (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	(3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione C25 H27 N3 O5 IXZOHGPZAQLIBH-NRFANRHFSA-N
ZN	D [auth A], F [auth B], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.246 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.001	α = 90
b = 58.85	β = 90
c = 88.583	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Heim, C., Hartmann, M.D.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description