4J2X | pdb_00004j2x

CSL (RBP-Jk) with corepressor KyoT2 bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb4J2X/pdb
• NAKB: 4J2X

• Classification: TRANSCRIPTION/DNA BINDING PROTEIN/DNA
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-02-05 Released: 2013-11-06 
• Deposition Author(s): Collins, K.J., Kovall, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.231 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure and Function of the CSL-KyoT2 Corepressor Complex: A Negative Regulator of Notch Signaling.

Collins, K.J., Yuan, Z., Kovall, R.A.

(2014) Structure 22: 70-81

• PubMed: 24290140 
• DOI: https://doi.org/10.1016/j.str.2013.10.010
• Primary Citation Related Structures: 
  4J2X


• PubMed Abstract: 
  

  Notch refers to a highly conserved cell-to-cell signaling pathway with essential roles in embryonic development and tissue maintenance. Dysfunctional signaling causes human disease, highlighting the importance of pathway regulation. Notch signaling ultimately results in the activation of target genes, which is regulated by the nuclear effector CSL (CBF-1/RBP-J, Su(H), Lag-1). CSL dually functions as an activator and a repressor of transcription through differential interactions with coactivator or corepressor proteins, respectively. Although the structures of CSL-coactivator complexes have been determined, the structures of CSL-corepressor complexes are unknown. Here, using a combination of structural, biophysical, and cellular approaches, we characterize the structure and function of CSL in complex with the corepressor KyoT2. Collectively, our studies provide molecular insights into how KyoT2 binds CSL with high affinity and competes with coactivators, such as Notch, for binding CSL. These studies are important for understanding how CSL functions as both an activator and a repressor of transcription of Notch target genes.

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Organizational Affiliation: 
• Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH 45267 USA.
Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH 45267 USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 120.72 kDa 
• Atom Count: 8,160 
• Modeled Residue Count: 931 
• Deposited Residue Count: 970 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombining binding protein suppressor of hairless	A, C	427	Mus musculus	Mutation(s): 1  Gene Names: Igkjrb1, Igkrsbp, RBP-Jk, Rbpj, Rbpsuh
UniProt & NIH Common Fund Data Resources
Find proteins for P31266 (Mus musculus) Explore P31266  Go to UniProtKB:  P31266
IMPC:  MGI:96522

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Four and a half LIM domains protein 1	B, D	28	Mus musculus	Mutation(s): 0  Gene Names: Fhl1
UniProt & NIH Common Fund Data Resources
Find proteins for P97447 (Mus musculus) Explore P97447  Go to UniProtKB:  P97447
IMPC:  MGI:1298387

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'	E, G	15	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'	F, H	15	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.231 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.157	α = 90
b = 97.293	β = 93.17
c = 144.102	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Collins, K.J., Kovall, R.A.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references
• Version 1.2: 2014-01-29
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description