6CKO | pdb_00006cko

Crystal structure of an AF10 fragment

• PDB DOI: https://doi.org/10.2210/pdb6CKO/pdb

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


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

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 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.

---

Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Life Science Research Center, Southern University of Science and Technology, Shenzhen 518055, China.
Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

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

Macromolecule Content 

• Total Structure Weight: 29.85 kDa 
• Atom Count: 1,858 
• Modeled Residue Count: 233 
• Deposited Residue Count: 254 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-79 specific	C, D	50	Danio rerio	Mutation(s): 0  Gene Names: dot1l EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
UniProt
Find proteins for F1Q4W7 (Danio rerio) Explore F1Q4W7  Go to UniProtKB:  F1Q4W7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], EA [auth D], F [auth A], G [auth A], P [auth B], Q [auth B], R [auth B], W [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	AA [auth C], BA [auth C], CA [auth C], DA [auth C], FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], S [auth B], T [auth B], U [auth B], V [auth B], X [auth C], Y [auth C], Z [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36CKO

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.701	α = 90
b = 122.558	β = 90
c = 65.404	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Zhang, H., Tempel, W., 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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary