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- PDB-6e8c: Crystal structure of the double homeodomain of DUX4 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6e8c
TitleCrystal structure of the double homeodomain of DUX4 in complex with DNA
Components
  • DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3')
  • Double homeobox protein 4
KeywordsDNA BINDING PROTEIN/DNA / Transcription Factor / Double Homeodomain / TRANSCRIPTION-DNA complex / DNA BINDING PROTEIN / 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 / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Double homeobox protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å
AuthorsLee, J.K. / Bosnakovski, D. / Toso, E.A. / Dinh, T. / Banerjee, S. / Bohl, T.E. / Shi, K. / Kurahashi, K. / Kyba, M. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR055685 United States
CitationJournal: Cell Rep / Year: 2018
Title: Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA.
Authors: Lee, J.K. / Bosnakovski, D. / Toso, E.A. / Dinh, T. / Banerjee, S. / Bohl, T.E. / Shi, K. / Orellana, K. / Kyba, M. / Aihara, H.
History
DepositionJul 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
A: Double homeobox protein 4
B: DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3')
C: DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,0333
Polymers27,0333
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-20 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.190, 73.140, 108.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 16620.936 Da / Num. of mol.: 1 / Fragment: Homeobox 1 and 2, residues 16-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUX4, DUX10 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9UBX2
#2: DNA chain DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3')


Mass: 5179.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3')


Mass: 5232.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350 0.1M Bis-TRIS pH 6.5 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9668 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9668 Å / Relative weight: 1
ReflectionResolution: 2.12→54.18 Å / Num. obs: 15112 / % possible obs: 93.9 % / Redundancy: 3 % / Biso Wilson estimate: 49.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.037 / Rrim(I) all: 0.066 / Net I/σ(I): 14
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.37 / CC1/2: 0.851 / % possible all: 83

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(dev_3126: ???)refinement
Aimless0.1.27data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LNQ

3lnq


Resolution: 2.12→45.024 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 757 5.02 %
Rwork0.1981 --
obs0.201 15076 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→45.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 691 0 48 1860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111922
X-RAY DIFFRACTIONf_angle_d1.1162736
X-RAY DIFFRACTIONf_dihedral_angle_d23.7081045
X-RAY DIFFRACTIONf_chiral_restr0.058284
X-RAY DIFFRACTIONf_plane_restr0.009245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1202-2.28390.40881610.32542604X-RAY DIFFRACTION90
2.2839-2.51370.2931320.25782893X-RAY DIFFRACTION99
2.5137-2.87740.30021500.26582912X-RAY DIFFRACTION99
2.8774-3.6250.26821610.2242863X-RAY DIFFRACTION98
3.625-45.03440.20341530.15323047X-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)
14.82556.1832-1.9348.6056-4.386.30590.044-0.61263.36320.837-0.22610.2826-2.81232.65050.5171.346-0.5005-0.15031.5762-0.18020.920189.400130.434521.0039
26.38865.3201-7.01119.6934-7.75088.57650.61950.04580.096-0.3563-0.34090.4314-0.19890.410.03090.8331-0.0329-0.03430.6667-0.07530.60880.26720.654625.2393
39.7576-6.9465-3.46237.28554.5153.1526-0.5794-0.40350.23170.01610.71040.1881.0858-0.5747-0.21070.52880.06710.05710.61160.03890.445173.07958.225528.3567
47.27691.8934-7.26413.98050.61059.0775-0.7168-2.1002-1.16661.35440.8798-0.38881.91211.58970.26190.93110.15930.16950.84350.1090.295875.2862.818923.977
53.7784-2.07193.6652.134-2.09683.79780.5991-0.1944-0.476-0.19660.06670.97970.3733-1.5244-1.16271.12360.01230.20330.63170.06420.645775.6871-0.630118.3286
69.1788-2.9007-0.92033.78680.89415.47410.06790.3238-0.8459-0.6562-0.31180.25050.8048-0.27380.31350.7455-0.05650.07490.5407-0.00220.501577.29883.70911.5387
79.81321.0431.78452.5862-2.07152.7319-0.34080.97060.2772-0.82650.44610.39890.7726-0.9857-0.03080.5965-0.15510.02620.69790.04890.529169.28278.869215.8195
85.0514.2591-5.60637.519-3.11926.90250.5789-1.07360.58080.22520.88490.87420.0810.3689-1.10070.49060.06680.06820.66270.00210.550271.843414.422917.9415
98.6254-4.1094-0.36249.9303-0.09146.98680.6160.23780.1219-0.2692-0.9084-0.44821.17980.49340.34220.59380.02450.05810.59580.0390.409582.51148.908418.9226
106.74051.65571.03924.72283.72272.9480.21640.4431-0.23541.1106-0.2255-0.04871.73210.99970.09380.9530.50780.12860.94430.2710.902291.94630.525822.4709
118.0717-0.10083.0093.48482.93943.72010.5717-1.39380.08740.21-0.1192-1.53042.99321.7497-0.30691.41290.51070.23261.18120.18740.998395.7107-2.501124.075
124.8006-4.26421.90414.60230.899.01130.0430.2332-0.6842-1.04940.2082-0.31130.50080.8734-0.24811.28960.14690.08740.88670.04320.69388.5104-4.380115.3808
138.5096-1.92911.891.12180.71462.37980.78650.5653-1.5673-2.7347-0.4674-1.2041.80571.3699-0.33641.67320.24980.12630.6863-0.09350.876478.88530.72746.4025
147.4862-0.9166-0.7927.9001-5.76784.7173-0.71360.6012-0.00260.27670.3776-0.09030.1771-1.63860.34450.6525-0.0783-0.11960.6495-0.06990.456376.455919.02920.5505
152.85452.48953.04862.79761.25247.0934-0.194-0.46190.28880.19450.03440.7329-1.7791-0.32860.20990.70750.0648-0.00790.58340.10970.545382.20433.02562.5962
163.09411.574-2.95134.4597-4.41985.2841-0.04641.11141.85680.9511.542-1.2371-1.81920.6687-1.48621.2245-0.2052-0.09570.7571-0.0660.875290.148834.79119.0867
175.14864.1508-5.59793.6703-3.98256.93420.2584-1.36411.20541.75620.49290.0055-2.07540.7689-0.53241.01070.1285-0.03180.6085-0.06210.682183.623129.397815.6063
185.07772.56235.17292.41943.28766.2061-1.0535-1.82822.330.9853-0.1868-0.1128-3.5637-1.54631.05321.36830.33410.09470.77290.00020.785875.013632.464711.6566
195.8291-2.49371.53015.8369-5.62415.6709-0.6744-0.9912-0.58621.69791.24660.6318-0.4739-0.681-0.54190.58710.07770.10570.49610.08230.611175.550325.40098.6863
205.77650.1773.14356.9070.39844.07130.4196-0.09350.61850.1892-0.3035-0.88850.12930.61890.03790.56290.06520.00050.51950.04190.465387.715124.08736.156
218.51627.15965.61089.1946.03444.23092.0167-1.1135-0.84081.6883-0.3968-1.04541.73020.4959-1.53520.83650.0355-0.17280.8728-0.01030.63787.921614.364532.3947
224.2903-4.5441-4.76867.07244.35695.41790.50310.2280.5259-0.0995-0.5193-1.0445-0.670.73620.01570.47490.00260.00960.65030.1130.544688.988819.512917.0492
238.0895-1.86654.59155.4056-0.59898.2450.32570.1693-0.581-1.0417-0.1355-0.56820.6961.0204-0.31470.6640.12380.16770.81770.09770.601993.702412.08373.9179
246.1435.8667-0.08016.8665-3.65379.906-0.22350.4994-0.1752-0.97180.4589-0.2251.5874-0.0882-0.32560.7083-0.00710.01520.6577-0.06020.512380.960514.0992-6.85
257.58381.99642.32447.98815.85437.596-0.06480.86560.418-0.01620.9488-0.7620.57691.525-0.8070.68930.00930.02460.80470.02560.573188.377718.4494-8.6928
264.7976-0.10341.80397.0871-2.7576.13640.0841-0.374-0.3288-0.3636-0.4498-0.4361.32210.8750.47970.61730.13510.10820.55380.03270.465584.316713.74975.2286
275.1206-1.0105-0.34526.85274.58533.06780.2246-0.5227-0.1385-0.1830.0295-1.13740.53221.1363-0.23510.61450.0442-0.02180.99030.18110.634494.225913.164718.779
286.8417-2.1636-0.50464.8130.43632.1137-0.6970.03030.42720.70130.567-0.1878-0.50360.1584-0.07140.9487-0.07940.0670.8803-0.03860.631884.803721.577231.7807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 16:19)
2X-RAY DIFFRACTION2(chain A and resid 20:25)
3X-RAY DIFFRACTION3(chain A and resid 26:32)
4X-RAY DIFFRACTION4(chain A and resid 33:36)
5X-RAY DIFFRACTION5(chain A and resid 37:40)
6X-RAY DIFFRACTION6(chain A and resid 41:48)
7X-RAY DIFFRACTION7(chain A and resid 49:56)
8X-RAY DIFFRACTION8(chain A and resid 57:60)
9X-RAY DIFFRACTION9(chain A and resid 61:74)
10X-RAY DIFFRACTION10(chain A and resid 75:78)
11X-RAY DIFFRACTION11(chain A and resid 79:82)
12X-RAY DIFFRACTION12(chain A and resid 83:88)
13X-RAY DIFFRACTION13(chain A and resid 89:95)
14X-RAY DIFFRACTION14(chain A and resid 96:102)
15X-RAY DIFFRACTION15(chain A and resid 103:113)
16X-RAY DIFFRACTION16(chain A and resid 114:117)
17X-RAY DIFFRACTION17(chain A and resid 118:124)
18X-RAY DIFFRACTION18(chain A and resid 125:130)
19X-RAY DIFFRACTION19(chain A and resid 131:136)
20X-RAY DIFFRACTION20(chain A and resid 137:150)
21X-RAY DIFFRACTION21(chain B and resid 1:5)
22X-RAY DIFFRACTION22(chain B and resid 6:9)
23X-RAY DIFFRACTION23(chain B and resid 10:13)
24X-RAY DIFFRACTION24(chain B and resid 14:17)
25X-RAY DIFFRACTION25(chain C and resid 1:4)
26X-RAY DIFFRACTION26(chain C and resid 5:8)
27X-RAY DIFFRACTION27(chain C and resid 9:13)
28X-RAY DIFFRACTION28(chain C and resid 14:17)

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