5NLB | pdb_00005nlb

Crystal structure of human CUL3 N-terminal domain bound to KEAP1 BTB and 3-box

• PDB DOI: https://doi.org/10.2210/pdb5NLB/pdb

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


• Deposited: 2017-04-04 Released: 2017-04-19 
• Deposition Author(s): Adamson, R., Krojer, T., Pinkas, D.M., Bartual, S.G., Burgess-Brown, N.A., Borkowska, O., Chalk, R., Newman, J.A., Kopec, J., Dixon-Clarke, S.E., Mathea, S., Sethi, R., Velupillai, S., Mackinnon, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 
  0.288 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Structural and biochemical characterization establishes a detailed understanding of KEAP1-CUL3 complex assembly.

Adamson, R.J., Payne, N.C., Bartual, S.G., Mazitschek, R., Bullock, A.N.

(2023) Free Radic Biol Med 204: 215-225

• PubMed: 37156295 
• DOI: https://doi.org/10.1016/j.freeradbiomed.2023.04.021
• Primary Citation Related Structures: 
  5NLB


• PubMed Abstract: 
  

  KEAP1 promotes the ubiquitin-dependent degradation of NRF2 by assembling into a CUL3-dependent ubiquitin ligase complex. Oxidative and electrophilic stress inhibit KEAP1 allowing NRF2 to accumulate for the transactivation of stress response genes. To date there are no structures of the KEAP1-CUL3 interaction nor binding data to show the contributions of different domains to their binding affinity. We determined a crystal structure of the BTB and 3-box domains of human KEAP1 in complex with the CUL3 N-terminal domain that showed a heterotetrameric assembly with 2:2 stoichiometry. To support the structural data, we developed a versatile TR-FRET-based assay system to profile the binding of BTB-domain-containing proteins to CUL3 and determine the contribution of distinct protein features, revealing the importance of the CUL3 N-terminal extension for high affinity binding. We further provide direct evidence that the investigational drug CDDO does not disrupt the KEAP1-CUL3 interaction, even at high concentrations, but reduces the affinity of KEAP1-CUL3 binding. The TR-FRET-based assay system offers a generalizable platform for profiling this protein class and may form a suitable screening platform for ligands that disrupt these interactions by targeting the BTB or 3-box domains to block E3 ligase function.

---

Organizational Affiliation: 
• Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. Electronic address: [e-mail].
Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.9 kDa 
• Atom Count: 3,882 
• Modeled Residue Count: 502 
• Deposited Residue Count: 510 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A	154	Homo sapiens	Mutation(s): 0  Gene Names: KEAP1, INRF2, KIAA0132, KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens) Explore Q14145  Go to UniProtKB:  Q14145
PHAROS:  Q14145 GTEx:  ENSG00000079999

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-3	B	356	Homo sapiens	Mutation(s): 2  Gene Names: CUL3, KIAA0617
UniProt & NIH Common Fund Data Resources
Find proteins for Q13618 (Homo sapiens) Explore Q13618  Go to UniProtKB:  Q13618
PHAROS:  Q13618 GTEx:  ENSG00000036257

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free:  0.288 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41	α = 90
b = 233.38	β = 90
c = 164.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Adamson, R., Krojer, T., Pinkas, D.M., Bartual, S.G., Burgess-Brown, N.A., Borkowska, O., Chalk, R., Newman, J.A., Kopec, J., Dixon-Clarke, S.E., Mathea, S., Sethi, R., Velupillai, S., Mackinnon, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-08-02
  Changes: Database references, Structure summary
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references
• Version 1.4: 2024-01-17
  Changes: Refinement description