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- PDB-5zfw: Crystal structure of human DUX4 homeodomains bound to A11G DNA mutant -

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Basic information

Entry
Database: PDB / ID: 5zfw
TitleCrystal structure of human DUX4 homeodomains bound to A11G DNA mutant
Components
  • DNA (5'-D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*GP*AP*TP*CP*AP*CP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*TP*CP*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 / cytosol / cytoplasm
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: 2.103 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*GP*AP*TP*CP*AP*CP*AP*CP*C)-3')
E: DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*TP*CP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)29,0373
Polymers29,0373
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-23 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.748, 64.748, 153.484
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-310-

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


Mass: 5678.703 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*TP*CP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')


Mass: 5971.854 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.: 214 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
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 PILATUS3 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: 2.1→30 Å / Num. obs: 22217 / % possible obs: 98.9 % / Redundancy: 11.8 % / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.18 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: 2.103→29.828 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 22.52
RfactorNum. reflection% reflection
Rfree0.2272 1052 5.34 %
Rwork0.1922 --
obs0.1941 19697 87.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.103→29.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 773 0 214 2008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041907
X-RAY DIFFRACTIONf_angle_d0.7062730
X-RAY DIFFRACTIONf_dihedral_angle_d27.7171022
X-RAY DIFFRACTIONf_chiral_restr0.037290
X-RAY DIFFRACTIONf_plane_restr0.005227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1031-2.19880.3377460.2952988X-RAY DIFFRACTION38
2.1988-2.31470.32371090.27751872X-RAY DIFFRACTION72
2.3147-2.45970.30911010.24042427X-RAY DIFFRACTION93
2.4597-2.64950.26811460.22562604X-RAY DIFFRACTION99
2.6495-2.91590.24461740.22422617X-RAY DIFFRACTION100
2.9159-3.33730.21671560.17972642X-RAY DIFFRACTION100
3.3373-4.20280.17291540.15722669X-RAY DIFFRACTION100
4.2028-29.83140.21211660.16052826X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 33.4762 Å / Origin y: -25.3014 Å / Origin z: -12.6557 Å
111213212223313233
T0.1505 Å20.0296 Å20.0897 Å2-0.2148 Å2-0.0174 Å2--0.1825 Å2
L0.5792 °2-0.2747 °2-0.055 °2-0.4359 °20.0333 °2--0.6199 °2
S-0.1382 Å °-0.1927 Å °-0.0809 Å °-0.0143 Å °0.1207 Å °-0.0824 Å °0.0127 Å °0.0866 Å °-0.013 Å °
Refinement TLS groupSelection details: all

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