6DFY

Remodeled crystal structure of DNA-bound DUX4-HD2

• PDB DOI: https://doi.org/10.2210/pdb6DFY/pdb
• NAKB: 6DFY

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 


• Deposited: 2018-05-15 Released: 2018-09-05 
• Deposition Author(s): Aihara, H., Shi, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.279 
• R-Value Work: 0.246 
• R-Value Observed: 0.247 

Starting Model: experimental

Literature

Comment on structural basis of DUX4/IGH-driven transactivation.

Aihara, H., Shi, K., Lee, J.K., Bosnakovski, D., Kyba, M.

(2018) Leukemia 32: 2090-2092

• PubMed: 30054554 
• DOI: https://doi.org/10.1038/s41375-018-0217-7
• Primary Citation of Related Structures:  
  6DFY

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA. [e-mail].

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 23.13 kDa 
• Atom Count: 1,420 
• Modelled Residue Count: 134 
• Deposited Residue Count: 156 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double homeobox protein 4	A [auth C], D	64	Homo sapiens	Mutation(s): 0  Gene Names: DUX4, DUX10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBX2 (Homo sapiens) Explore Q9UBX2  Go to UniProtKB:  Q9UBX2
PHAROS:  Q9UBX2 GTEx:  ENSG00000260596

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3')	B [auth E]	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*A)-3')	C [auth F]	14	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.279 
• R-Value Work: 0.246 
• R-Value Observed: 0.247 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.61	α = 90
b = 51.61	β = 90
c = 166.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Aihara, H., Shi, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103403

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description