6DKS | pdb_00006dks

Structure of the Rbpj-SHARP-DNA Repressor Complex

• PDB DOI: https://doi.org/10.2210/pdb6DKS/pdb
• NAKB: 6DKS

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus, Escherichia coli O157:H7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-30 Released: 2019-01-02 
• Deposition Author(s): Kovall, R.A., VanderWielen, B.D., Yuan, Z.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.228 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Models: experimental

Literature

Structural and Functional Studies of the RBPJ-SHARP Complex Reveal a Conserved Corepressor Binding Site.

Yuan, Z., VanderWielen, B.D., Giaimo, B.D., Pan, L., Collins, C.E., Turkiewicz, A., Hein, K., Oswald, F., Borggrefe, T., Kovall, R.A.

(2019) Cell Rep 26: 845-854.e6

• PubMed: 30673607 
• DOI: https://doi.org/10.1016/j.celrep.2018.12.097
• Primary Citation Related Structures: 
  6DKS


• PubMed Abstract: 
  

  Notch is a conserved signaling pathway that is essential for metazoan development and homeostasis; dysregulated signaling underlies the pathophysiology of numerous human diseases. Receptor-ligand interactions result in gene expression changes, which are regulated by the transcription factor RBPJ. RBPJ forms a complex with the intracellular domain of the Notch receptor and the coactivator Mastermind to activate transcription, but it can also function as a repressor by interacting with corepressor proteins. Here, we determine the structure of RBPJ bound to the corepressor SHARP and DNA, revealing its mode of binding to RBPJ. We tested structure-based mutants in biophysical and biochemical-cellular assays to characterize the role of RBPJ as a repressor, clearly demonstrating that RBPJ mutants deficient for SHARP binding are incapable of repressing transcription of genes responsive to Notch signaling in cells. Altogether, our structure-function studies provide significant insights into the repressor function of RBPJ.

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Organizational Affiliation: 
• Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
Institute of Biochemistry, University of Giessen, Giessen, Germany.
Department of Internal Medicine I, Center for Internal Medicine, University Medical Center Ulm, 89081 Ulm, Germany.
Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 203.47 kDa 
• Atom Count: 13,438 
• Modeled Residue Count: 1,711 
• Deposited Residue Count: 1,718 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombining binding protein suppressor of hairless	C, G	422	Mus musculus	Mutation(s): 0  Gene Names: Rbpj, Igkjrb1, Igkrsbp, Rbpsuh
UniProt & NIH Common Fund Data Resources
Find proteins for P31266 (Mus musculus) Explore P31266  Go to UniProtKB:  P31266
IMPC:  MGI:96522

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein	D, H	407	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3')	A, E	15	Mus musculus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3')	B, F	15	Mus musculus

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	I, J	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	I, J	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.228 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.45	α = 90
b = 231.57	β = 99.88
c = 90.26	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-02 
Deposition Author(s): Kovall, R.A., VanderWielen, B.D., Yuan, Z.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	NCI CA178974

Revision History  

• Version 1.0: 2019-01-02
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-07-17
  Changes: Data collection, Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary