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- PDB-5z2t: Crystal structure of DNA-bound DUX4-HD2 -

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Basic information

Entry
Database: PDB / ID: 5z2t
TitleCrystal structure of DNA-bound DUX4-HD2
Components
  • 5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*TP*T)-3'
  • 5'-D(P*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3'
  • Double homeobox protein 4
KeywordsDNA BINDING PROTEIN/DNA / acute lymphoblastic leukemia / DUX4/IGH / DUX4-Responsive-Element / transactivation / ERGalt / DNA BINDING PROTEIN-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 / apoptotic process / nucleolus / regulation of transcription by RNA polymerase II / 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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Double homeobox protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.623 Å
AuthorsDong, X. / Zhang, W. / Wu, H. / Huang, J. / Zhang, M. / Wang, P. / Zhang, H. / Chen, Z. / Chen, S. / Meng, G.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81770142 China
National Natural Science Foundation of China81370620 China
National Natural Science Foundation of China81570120 China
CitationJournal: Leukemia / Year: 2018
Title: Structural basis of DUX4/IGH-driven transactivation.
Authors: Dong, X. / Zhang, W. / Wu, H. / Huang, J. / Zhang, M. / Wang, P. / Zhang, H. / Chen, Z. / Chen, S.J. / Meng, G.
History
DepositionJan 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 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
C: Double homeobox protein 4
E: 5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*TP*T)-3'
F: 5'-D(P*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3'
D: Double homeobox protein 4


Theoretical massNumber of molelcules
Total (without water)23,4244
Polymers23,4244
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-24 kcal/mol
Surface area10320 Å2
Unit cell
Length a, b, c (Å)51.610, 51.610, 166.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Double homeobox protein 4 / Double homeobox protein 10


Mass: 7286.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUX4, DUX10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBX2
#2: DNA chain 5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*TP*T)-3'


Mass: 4508.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(P*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3'


Mass: 4342.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9747 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 2.62→83.3 Å / Num. obs: 7363 / % possible obs: 99.9 % / Redundancy: 9.5 % / Net I/σ(I): 11.5
Reflection shellResolution: 2.62→2.76 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z2S

5z2s


Resolution: 2.623→49.297 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.71
RfactorNum. reflection% reflection
Rfree0.2994 341 4.69 %
Rwork0.2762 --
obs0.2779 7266 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.623→49.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 533 0 11 1412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051480
X-RAY DIFFRACTIONf_angle_d0.8262104
X-RAY DIFFRACTIONf_dihedral_angle_d26.004797
X-RAY DIFFRACTIONf_chiral_restr0.039230
X-RAY DIFFRACTIONf_plane_restr0.005185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.760.42841650.37263360X-RAY DIFFRACTION99
3.3047-49.30610.26851760.25113565X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.8174 Å / Origin y: 0.9616 Å / Origin z: 185.1903 Å
111213212223313233
T0.3118 Å2-0.1134 Å2-0.0109 Å2-0.4535 Å20.0278 Å2--0.368 Å2
L0.7603 °2-0.5851 °20.0614 °2-1.1733 °20.2112 °2--0.9139 °2
S0.0036 Å °-0.1651 Å °-0.0562 Å °-0.2114 Å °0.1141 Å °-0.0443 Å °-0.0031 Å °0.0458 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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