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- PDB-5zfz: Crystal structure of human DUX4 homeodomains bound to A12T DNA mutant -

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Basic information

Entry
Database: PDB / ID: 5zfz
TitleCrystal structure of human DUX4 homeodomains bound to A12T DNA mutant
Components
  • DNA (5'-D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*AP*TP*TP*CP*AP*CP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*AP*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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / apoptotic process / regulation of transcription by RNA polymerase II / chromatin / nucleolus / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / 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: 1.9 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

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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*TP*TP*CP*AP*CP*AP*CP*C)-3')
E: DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*AP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)29,0363
Polymers29,0363
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-20 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.013, 65.013, 151.661
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

21A-330-

HOH

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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*TP*TP*CP*AP*CP*AP*CP*C)-3')


Mass: 5653.690 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*AP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')


Mass: 5995.879 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.: 265 / 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: 61.4 %
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: 1.9→30 Å / Num. obs: 29905 / % possible obs: 98.7 % / Redundancy: 12.6 % / Net I/σ(I): 39.64
Reflection shellResolution: 1.9→1.97 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: 1.9→29.877 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 21.03
RfactorNum. reflection% reflection
Rfree0.2211 1370 5.14 %
Rwork0.1858 --
obs0.1876 26645 88.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 773 0 265 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091907
X-RAY DIFFRACTIONf_angle_d0.9922730
X-RAY DIFFRACTIONf_dihedral_angle_d26.8371022
X-RAY DIFFRACTIONf_chiral_restr0.051290
X-RAY DIFFRACTIONf_plane_restr0.007227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8959-1.96360.2853320.2751932X-RAY DIFFRACTION32
1.9636-2.04220.30051100.25961736X-RAY DIFFRACTION62
2.0422-2.13510.30381250.24822403X-RAY DIFFRACTION85
2.1351-2.24770.2751490.23222830X-RAY DIFFRACTION98
2.2477-2.38840.24121510.20162834X-RAY DIFFRACTION100
2.3884-2.57270.25721660.19522818X-RAY DIFFRACTION100
2.5727-2.83150.26861570.20632868X-RAY DIFFRACTION100
2.8315-3.24080.23181580.17832876X-RAY DIFFRACTION100
3.2408-4.08140.16421510.14482919X-RAY DIFFRACTION100
4.0814-29.88080.17161710.15623059X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -37.7334 Å / Origin y: 14.5991 Å / Origin z: 164.5078 Å
111213212223313233
T0.1329 Å20.0141 Å20.0057 Å2-0.0836 Å2-0.0465 Å2--0.1048 Å2
L0.1979 °2-0.0217 °20.0376 °2-0.5198 °20.0531 °2--0.3684 °2
S0.0089 Å °0.0328 Å °-0.0838 Å °0.0987 Å °0.0175 Å °0.0078 Å °0.0558 Å °0.0018 Å °0.0525 Å °
Refinement TLS groupSelection details: all

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