Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.38 kDa 
• Atom Count: 1887 
• Modelled Residue Count: 160 
• Deposited Residue Count: 191 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

5Z6Z

Crystal structure of human DUX4 homeodomains bound to DNA

• PDB DOI: 10.2210/pdb5Z6Z/pdb
• NDB: 5Z6Z

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


• Deposited: 2018-01-26 Released: 2018-10-31 
• Deposition Author(s): Li, Y.Y., Wu, B.X., Gan, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Structural basis for multiple gene regulation by human DUX4.

Li, Y., Wu, B., Liu, H., Gao, Y., Yang, C., Chen, X., Zhang, J., Chen, Y., Gu, Y., Li, J., Ma, J., Gan, J.

(2018) Biochem Biophys Res Commun 505: 1161-1167

• PubMed: 30322619 
• DOI: 10.1016/j.bbrc.2018.10.056
• Primary Citation of Related Structures:  
  5Z6Z, 5ZFW, 5ZFY, 5ZFZ


• PubMed Abstract: 
  

DUX4 plays critical role in the molecular pathogenesis of the neuromuscular disorder facioscapulohumeral muscular dystrophy and acute lymphoblastic leukemia in humans. As a master transcription regulator, DUX4 can also bind the promoters and activate the transcription of hundreds ZGA-associated genes. Here we report on the structural and biochemical studies of DUX4 double homeodomains (DUX4-DH), representing the only structures contain both homeodomain 1 (HD1) and homeodomain 2 (HD2). HD1 and HD2 adopt classical homeobox fold; via the helix inserted into the major groove and the N-terminal extended loop inserted into the minor groove, HD1 and HD2 recognize the box1 (5'-TAA-3') and box2 (5'-TGA-3') nucleotides of the consensus sequence, respectively. Among the box1 and box2 linking nucleotides (CCTAA), the two adenine residues are reported to be highly conserved; however, they are not directly recognized by DUX4-DH in the structures. Besides different nucleotides, our ITC analysis indicated that DUX4-DH can also tolerate various changes in the linker length. Our studies not only revealed the basis for target DNA recognition by DUX4, but also advanced our understanding on multiple gene activation by DUX4.

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Organizational Affiliation: 

State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double homeobox protein 4	A	153	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*AP*AP*TP*CP*AP*CP*AP*CP*C)-3')	B [auth D]	19	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')	C [auth E]	19	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.879	α = 90
b = 64.879	β = 90
c = 152.075	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-01-26 
• Released Date: 2018-10-31 
Deposition Author(s): Li, Y.Y., Wu, B.X., Gan, J.H.

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2018-11-14
  Changes: Data collection, Database references