6CKN

Crystal structure of an AF10 fragment

• PDB DOI: https://doi.org/10.2210/pdb6CKN/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-02-28 Released: 2018-03-21 
• Deposition Author(s): Qin, S., Tempel, W., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.262 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 

Literature

Structural and functional analysis of the DOT1L-AF10 complex reveals mechanistic insights into MLL-AF10-associated leukemogenesis.

Zhang, H., Zhou, B., Qin, S., Xu, J., Harding, R., Tempel, W., Nayak, V., Li, Y., Loppnau, P., Dou, Y., Min, J.

(2018) Genes Dev 32: 341-346

• PubMed: 29563185 
• DOI: https://doi.org/10.1101/gad.311639.118
• Primary Citation of Related Structures:  
  6CKN, 6CKO


• PubMed Abstract: 
  

  The mixed-lineage leukemia (MLL)-AF10 fusion oncoprotein recruits DOT1L to the homeobox A ( HOXA ) gene cluster through its octapeptide motif leucine zipper (OM-LZ), thereby inducing and maintaining the MLL-AF10-associated leukemogenesis. However, the recognition mechanism between DOT1L and MLL-AF10 is unclear. Here, we present the crystal structures of both apo AF10 ^OM-LZ and its complex with the coiled-coil domain of DOT1L. Disruption of the DOT1L-AF10 interface abrogates MLL-AF10-associated leukemic transformation. We further show that zinc stabilizes the DOT1L-AF10 complex and may be involved in the regulation of the HOXA gene expression. Our studies may also pave the way for the rational design of therapeutic drugs against MLL -rearranged leukemia.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 17.58 kDa 
• Atom Count: 975 
• Modelled Residue Count: 132 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein AF-10	A, B	77	Homo sapiens	Mutation(s): 0  Gene Names: MLLT10, AF10
UniProt & NIH Common Fund Data Resources
Find proteins for P55197 (Homo sapiens) Explore P55197  Go to UniProtKB:  P55197
PHAROS:  P55197 GTEx:  ENSG00000078403

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	C [auth A], D [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.262 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M36CKN

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.058	α = 90
b = 40.058	β = 90
c = 205.57	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing
SHELXD	phasing
PARROT	phasing
BUCCANEER	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Qin, S., Tempel, W., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary