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- PDB-5zfy: Crystal structure of human DUX4 homeodomains bound to A12C DNA mutant -

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Basic information

Entry
Database: PDB / ID: 5zfy
TitleCrystal structure of human DUX4 homeodomains bound to A12C DNA mutant
Components
  • DNA (5'-D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*AP*CP*TP*CP*AP*CP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*GP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')
  • Double homeobox protein 4-like protein 4
KeywordsTRANSCRIPTION/DNA / homeodomains / DUX4 / DNA recognition / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / Zygotic genome activation (ZGA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation ...negative regulation of G0 to G1 transition / Zygotic genome activation (ZGA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleolus / apoptotic process / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Helix-turn-helix motif / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Double homeobox protein 4-like protein 4 / Double homeobox protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, Y.Y. / Wu, B.X. / Gan, J.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural basis for multiple gene regulation by human DUX4.
Authors: Li, Y. / Wu, B. / Liu, H. / Gao, Y. / Yang, C. / Chen, X. / Zhang, J. / Chen, Y. / Gu, Y. / Li, J. / Ma, J. / Gan, J.
History
DepositionMar 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double homeobox protein 4-like protein 4
D: DNA (5'-D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*AP*CP*TP*CP*AP*CP*AP*CP*C)-3')
E: DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*GP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)29,0373
Polymers29,0373
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-21 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.256, 65.256, 150.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Double homeobox protein 4-like protein 4 / DUX4


Mass: 17386.805 Da / Num. of mol.: 1 / Fragment: double homeodomains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUX4L4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CJ87, UniProt: Q9UBX2*PLUS
#2: DNA chain DNA (5'-D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*AP*CP*TP*CP*AP*CP*AP*CP*C)-3')


Mass: 5638.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*GP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')


Mass: 6011.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M Sodium malonate pH 4.0, 12% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977776 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 17918 / % possible obs: 99.6 % / Redundancy: 12.3 % / Net I/σ(I): 22.95
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z6Z

5z6z


Resolution: 2.3→29.941 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 20.66
RfactorNum. reflection% reflection
Rfree0.216 796 4.9 %
Rwork0.1847 --
obs0.1863 16244 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 773 0 167 1972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041918
X-RAY DIFFRACTIONf_angle_d0.6632744
X-RAY DIFFRACTIONf_dihedral_angle_d28.2941030
X-RAY DIFFRACTIONf_chiral_restr0.038291
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.299-2.44290.3299820.24911967X-RAY DIFFRACTION73
2.4429-2.63150.24921310.2392533X-RAY DIFFRACTION94
2.6315-2.89610.28271370.22872676X-RAY DIFFRACTION99
2.8961-3.31470.25541400.19452694X-RAY DIFFRACTION100
3.3147-4.17440.18831110.15882743X-RAY DIFFRACTION100
4.1744-29.94390.16841950.15172835X-RAY DIFFRACTION100

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