4X8P | pdb_00004x8p

Crystal structure of Ash2L SPRY domain in complex with RbBP5

• PDB DOI: https://doi.org/10.2210/pdb4X8P/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-10 Released: 2015-01-28 
• Deposition Author(s): Zhang, P., Chaturvedi, C.P., Brunzelle, J.S., Skiniotis, G., Brand, M., Shilatifard, A., Couture, J.-F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.271 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation.

Zhang, P., Chaturvedi, C.P., Tremblay, V., Cramet, M., Brunzelle, J.S., Skiniotis, G., Brand, M., Shilatifard, A., Couture, J.F.

(2015) Genes Dev 29: 123-128

• PubMed: 25593305 
• DOI: https://doi.org/10.1101/gad.254870.114
• Primary Citation Related Structures: 
  4X8N, 4X8P


• PubMed Abstract: 
  

  The methyltransferase activity of the trithorax group (TrxG) protein MLL1 found within its COMPASS (complex associated with SET1)-like complex is allosterically regulated by a four-subunit complex composed of WDR5, RbBP5, Ash2L, and DPY30 (also referred to as WRAD). We report structural evidence showing that in WRAD, a concave surface of the Ash2L SPIa and ryanodine receptor (SPRY) domain binds to a cluster of acidic residues, referred to as the D/E box, in RbBP5. Mutational analysis shows that residues forming the Ash2L/RbBP5 interface are important for heterodimer formation, stimulation of MLL1 catalytic activity, and erythroid cell terminal differentiation. We also demonstrate that a phosphorylation switch on RbBP5 stimulates WRAD complex formation and significantly increases KMT2 (lysine [K] methyltransferase 2) enzyme methylation rates. Overall, our findings provide structural insights into the assembly of the WRAD complex and point to a novel regulatory mechanism controlling the activity of the KMT2/COMPASS family of lysine methyltransferases.

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Organizational Affiliation: 
• Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada;
The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ontario K1H 8L6, Canada;
Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA;
Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA;
Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois 60611, USA.
Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada; [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)

Macromolecule Content 

• Total Structure Weight: 22.08 kDa 
• Atom Count: 1,610 
• Modeled Residue Count: 188 
• Deposited Residue Count: 194 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Set1/Ash2 histone methyltransferase complex subunit ASH2,Set1/Ash2 histone methyltransferase complex subunit ASH2	A	182	Homo sapiens	Mutation(s): 0  Gene Names: ASH2L, ASH2L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBL3 (Homo sapiens) Explore Q9UBL3  Go to UniProtKB:  Q9UBL3
PHAROS:  Q9UBL3 GTEx:  ENSG00000129691

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoblastoma-binding protein 5	B	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15291 (Homo sapiens) Explore Q15291  Go to UniProtKB:  Q15291
PHAROS:  Q15291 GTEx:  ENSG00000117222

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.271 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.5	α = 90
b = 59.1	β = 90
c = 70.8	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Zhang, P., Chaturvedi, C.P., Brunzelle, J.S., Skiniotis, G., Brand, M., Shilatifard, A., Couture, J.-F.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy