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- PDB-5z2s: Crystal structure of DUX4-HD2 domain -

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Basic information

Entry
Database: PDB / ID: 5z2s
TitleCrystal structure of DUX4-HD2 domain
ComponentsDouble homeobox protein 4
KeywordsDNA BINDING PROTEIN / acute lymphoblastic leukemia / DUX4/IGH / DUX4-Responsive-Element / transactivation / ERGalt
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
Double homeobox protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 3, 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

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Assembly

Deposited unit
A: Double homeobox protein 4


Theoretical massNumber of molelcules
Total (without water)6,2851
Polymers6,2851
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3450 Å2
Unit cell
Length a, b, c (Å)25.150, 25.390, 72.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 6285.145 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.84 Å3/Da / Density % sol: 33.27 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→36.3 Å / Num. obs: 7483 / % possible obs: 100 % / Redundancy: 6.3 % / Net I/σ(I): 19.2
Reflection shellResolution: 1.5→1.58 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: 3A02

3a02


Resolution: 1.5→23.966 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 20.82
RfactorNum. reflection% reflection
Rfree0.2154 361 4.85 %
Rwork0.1886 --
obs0.19 7442 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→23.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms407 0 0 108 515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414
X-RAY DIFFRACTIONf_angle_d1.127556
X-RAY DIFFRACTIONf_dihedral_angle_d11.058253
X-RAY DIFFRACTIONf_chiral_restr0.0559
X-RAY DIFFRACTIONf_plane_restr0.00674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.22441060.17542458X-RAY DIFFRACTION100
1.717-2.1630.17561370.1832472X-RAY DIFFRACTION100
2.163-23.96860.24341180.19912151X-RAY DIFFRACTION83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0269-0.0088-0.00910.00410.00190.00630.01350.0685-0.01110.005-0.00060.0251-0.0316-0.0577-0.00080.02720.00060.03040.036-0.00360.01974.683417.8166-12.0892
20.0334-0.01070.0350.0353-0.03680.0618-0.03010.0519-0.01650.04740.0334-0.0479-0.00390.002-0.01340.03340.0080.00670.0316-0.01370.037215.108917.2273-11.3229
30.0228-0.00840.03470.01460.00320.0781-0.0325-0.0605-0.04570.02360.05860.0085-0.012-0.06780.00170.0503-0.0035-0.00240.0324-0.00170.04159.27029.2876-8.3581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 54 )

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