Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 9667.88 
• Atom Count: 593 
• Residue Count: 81 
• Unique protein chains: 2

4L58

Crystal structure of the MLL5 PHD finger in complex with H3K4me3

• DOI: 10.2210/pdb4L58/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-06-10 Released: 2013-06-26 
• Deposition Author(s): Tong, Q., Ali, M., Kutateladze, T.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.140 
• R-Value Work: 0.125 

Literature

Molecular basis for chromatin binding and regulation of MLL5.

Ali, M., Rincon-Arano, H., Zhao, W., Rothbart, S.B., Tong, Q., Parkhurst, S.M., Strahl, B.D., Deng, L.W., Groudine, M., Kutateladze, T.G.

(2013) Proc.Natl.Acad.Sci.USA 110: 11296-11301

• PubMed: 23798402 
• DOI: 10.1073/pnas.1310156110


• PubMed Abstract: 
  

The human mixed-lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle, and survival; however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its plant homeodomain finger with the histone mark H3K4me3. The 1.48-Å resolution crystal structure of MLL5 plant homeodomain in complex with the H3K4me3 peptide reveals a noncanonical binding mechanism, whereby K4me3 is recognized through a single aromatic residue and an aspartate. The binding induces a unique His-Asp swapping rearrangement mediated by a C-terminal α-helix. Phosphorylation of H3T3 and H3T6 abrogates the association with H3K4me3 in vitro and in vivo, releasing MLL5 from chromatin in mitosis. This regulatory switch is conserved in the Drosophila ortholog of MLL5, UpSET, and suggests the developmental control for targeting of H3K4me3. Together, our findings provide first insights into the molecular basis for the recruitment, exclusion, and regulation of MLL5 at chromatin.

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Organizational Affiliation: 

Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone-lysine N-methyltransferase MLL5	A	69	Homo sapiens	Mutation(s): 0  Gene Names: KMT2E (MLL5)
Find proteins for Q8IZD2 (Homo sapiens) Go to Gene View: KMT2E Go to UniProtKB:  Q8IZD2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H3 peptide	B	12	Homo sapiens	Mutation(s): 0  Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens) Go to Gene View: H3F3A H3F3B Go to UniProtKB:  P84243

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.140 
• R-Value Work: 0.125 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 31.286	α = 90.00
b = 43.638	β = 90.00
c = 52.856	γ = 90.00

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
HKL-2000	data reduction
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-10 
• Released Date: 2013-06-26 
• Deposition Author(s): Tong, Q., Ali, M., Kutateladze, T.G.

Revision History 

• Version 1.0: 2013-06-26
  Type: Initial release
• Version 1.1: 2013-07-17
  Type: Database references
• Version 1.2: 2013-07-24
  Type: Database references