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- PDB-6a8r: Crystal structure of DUX4 HD2 domain associated with ERG DNA bind... -

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Basic information

Entry
Database: PDB / ID: 6a8r
TitleCrystal structure of DUX4 HD2 domain associated with ERG DNA binding site
Components
  • DNA (5'-D(P*AP*AP*TP*CP*TP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*AP*TP*GP*AP*GP*AP*TP*T)-3')
  • Double homeobox protein 4
KeywordsDNA BINDING PROTEIN/DNA / acute lymphoblastic leukemia / DUX4/IGH / ERG binding site / TGAT repeat / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDong, X. / Zhang, H. / Cheng, N. / Meng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81770142 China
CitationJournal: Leukemia / Year: 2019
Title: DUX4HD2-DNAERGstructure reveals new insight into DUX4-Responsive-Element.
Authors: Dong, X. / Zhang, H. / Cheng, N. / Li, K. / Meng, G.
History
DepositionJul 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 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
B: Double homeobox protein 4
A: Double homeobox protein 4
E: DNA (5'-D(P*TP*GP*AP*TP*GP*AP*GP*AP*TP*T)-3')
F: DNA (5'-D(P*AP*AP*TP*CP*TP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)20,4504
Polymers20,4504
Non-polymers00
Water2,090116
1
B: Double homeobox protein 4


Theoretical massNumber of molelcules
Total (without water)6,8731
Polymers6,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Double homeobox protein 4
E: DNA (5'-D(P*TP*GP*AP*TP*GP*AP*GP*AP*TP*T)-3')
F: DNA (5'-D(P*AP*AP*TP*CP*TP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,5773
Polymers13,5773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.550, 32.550, 126.591
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 6872.821 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 DNA (5'-D(P*TP*GP*AP*TP*GP*AP*GP*AP*TP*T)-3')


Mass: 3412.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*AP*TP*CP*TP*CP*AP*TP*CP*A)-3')


Mass: 3292.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.6→63.3 Å / Num. obs: 19696 / % possible obs: 99.2 % / Redundancy: 8.2 % / CC1/2: 0.99 / Rsym value: 0.072 / Net I/σ(I): 11.4
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 2803 / CC1/2: 0.76 / Rsym value: 0.912

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5z2s, 5z2t

5z2s

5z2t


Resolution: 1.6→28.189 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.38
RfactorNum. reflection% reflection
Rfree0.2073 999 5.09 %
Rwork0.2005 --
obs0.2008 19612 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→28.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 410 0 116 1478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131444
X-RAY DIFFRACTIONf_angle_d1.2272026
X-RAY DIFFRACTIONf_dihedral_angle_d25.656808
X-RAY DIFFRACTIONf_chiral_restr0.063216
X-RAY DIFFRACTIONf_plane_restr0.01198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6003-1.68470.34771570.28292566X-RAY DIFFRACTION96
1.6847-1.79020.30721250.27832706X-RAY DIFFRACTION100
1.7902-1.92840.35731170.28142717X-RAY DIFFRACTION100
1.9284-2.12240.28691920.23622589X-RAY DIFFRACTION100
2.1224-2.42930.25531520.22192675X-RAY DIFFRACTION99
2.4293-3.06010.21751440.22242654X-RAY DIFFRACTION99
3.0601-28.19350.1471120.16222706X-RAY DIFFRACTION99
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)
10.3461-0.08410.07670.24330.11390.2599-0.1164-0.0286-0.0452-0.167-0.07030.1221-0.0033-0.0772-00.2565-0.03110.040.2408-0.00830.264418.69454.0005-8.8314
20.1042-0.2367-0.47750.59140.58431.5715-0.16031.1128-0.0434-0.2247-0.54710.61460.3217-0.8814-0.03180.1934-0.0383-0.0330.51220.02740.36020.2577-19.6015-19.6867
30.61470.44670.43770.29840.17271.50340.18150.6845-0.11520.2880.2564-0.3280.53841.03360.05690.19620.0342-0.01010.5997-0.11690.28817.8635-22.2201-23.6671
40.69160.1769-0.07130.2059-0.20060.1940.30461.13160.6099-0.15850.29020.2455-0.39840.25920.26090.3091-0.14060.05070.62930.12540.300912.2832-15.5746-30.0597
50.0565-0.1928-0.16940.68130.67490.68770.01640.15290.21150.13210.2055-0.13730.07990.70.03810.16620.020.00720.3082-0.02230.307413.84-19.1748-17.0501
60.03130.0379-0.011-0.01050.01130.0303-0.20820.1636-0.5590.35780.0479-0.46770.53020.2903-0.00020.4940.01480.00220.3283-0.0430.447615.7872-9.58021.5384
71.36690.17311.30780.56570.32531.36720.16320.24480.21490.2980.33770.2848-0.1562-0.81990.42910.38850.15160.13410.48280.10350.29712.58571.60636.8441
80.12960.0191-0.02260.11280.23220.59740.0443-0.3340.29830.85470.1983-0.1832-0.7077-0.27780.02720.66740.0419-0.03020.2348-0.04130.334511.75245.02519.5774
90.14180.03-0.1760.316-0.01010.2257-0.0550.15520.27120.0010.2243-0.2033-0.3664-0.236-00.29210.05630.04530.2359-0.00780.25459.03612.5117-0.7914
100.0789-0.23340.22450.1662-0.28440.6609-0.0490.0372-0.0248-0.0999-0.0515-0.1540.0822-0.1626-0.00010.2462-0.02670.04640.2078-0.02330.25218.36683.5024-8.9962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 6 through 15 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 9 )
3X-RAY DIFFRACTION3chain 'B' and (resid 10 through 27 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 41 )
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 59 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2 through 9 )
7X-RAY DIFFRACTION7chain 'A' and (resid 10 through 22 )
8X-RAY DIFFRACTION8chain 'A' and (resid 23 through 41 )
9X-RAY DIFFRACTION9chain 'A' and (resid 42 through 59 )
10X-RAY DIFFRACTION10chain 'E' and (resid 6 through 15 )

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