6DFY | pdb_00006dfy

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 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

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 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].
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
Bristol-Myers Squibb, Redwood City, CA, 94063, USA.
Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.
Faculty of Medical Sciences, University Goce Delcev - Stip, Krste Misirkov b.b, 2000, Stip, Macedonia.

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 
• Modeled 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 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

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