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- PDB-8ejp: Crystal structure of the homeodomain of Platypus sDUX in complex ... -

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Basic information

Entry
Database: PDB / ID: 8ejp
TitleCrystal structure of the homeodomain of Platypus sDUX in complex with DNA containing 5-Bromouracil
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')
  • Homeobox domain-containing protein
KeywordsDNA BINDING PROTEIN/DNA / DUX4 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox domain-containing protein
Similarity search - Component
Biological speciesOrnithorhynchus anatinus (platypus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.174 Å
AuthorsYin, L.L. / Shi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR055685 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165 United States
CitationJournal: Iscience / Year: 2023
Title: Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein.
Authors: Bosnakovski, D. / Toso, E.A. / Ener, E.T. / Gearhart, M.D. / Yin, L. / Luttmann, F.F. / Magli, A. / Shi, K. / Kim, J. / Aihara, H. / Kyba, M.
History
DepositionSep 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox domain-containing protein
B: Homeobox domain-containing protein
C: DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3')
D: DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2046
Polymers27,0804
Non-polymers1242
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-10 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.499, 74.499, 99.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 21 through 74 or resid 76))
21(chain B and (resid 21 through 74 or resid 76))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 21 through 74 or resid 76))A0
211(chain B and (resid 21 through 74 or resid 76))B0

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Components

#1: Protein Homeobox domain-containing protein


Mass: 8301.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ornithorhynchus anatinus (platypus) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6I8NF41
#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: 5297.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.174→59.676 Å / Num. obs: 10466 / % possible obs: 94.4 % / Redundancy: 13.4 % / Biso Wilson estimate: 63.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Net I/σ(I): 10.7 / Num. measured all: 139973
Reflection shell

Num. unique obs: 523 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.174-2.32912.91.44467390.6490.4161.5041.564.5
7.091-59.67611.50.09160260.9970.0260.0952199.6

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.174→59.676 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 42.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 1006 5.27 %
Rwork0.2384 18070 -
obs0.2397 10450 67.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.52 Å2 / Biso mean: 89.4784 Å2 / Biso min: 52.62 Å2
Refinement stepCycle: final / Resolution: 2.174→59.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 691 8 3 1648
Biso mean--75.24 66.57 -
Num. residues----146
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A561X-RAY DIFFRACTION11.4TORSIONAL
12B561X-RAY DIFFRACTION11.4TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.174-2.210.14740.4652705
2.21-2.250.3221160.361121016
2.25-2.30.3768220.355330924
2.3-2.340.4167240.415946235
2.34-2.390.4348300.389653240
2.39-2.450.2651390.380660546
2.45-2.510.4639330.381566851
2.51-2.580.3648460.377275657
2.58-2.650.5035440.362785663
2.65-2.740.2756410.3792970
2.74-2.840.476430.3685105877
2.84-2.950.4924510.3656114985
2.95-3.080.2116680.3392123492
3.09-3.250.341740.2949128096
3.25-3.450.3318700.2665132099
3.45-3.720.2608780.25491326100
3.72-4.090.2654850.22921307100
4.09-4.680.2214800.19211335100
4.68-5.90.2065930.19521318100
5.9-59.6760.1795650.15771346100
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)
19.9086-2.48625.09962.8108-2.458.2013-0.43960.64841.21080.00340.07220.5799-1.32130.22850.35450.6346-0.1101-0.05050.59870.03481.3118-14.791828.74163.4275
22.11731.04872.44566.11183.70599.8843-0.54130.7797-0.3772-0.41390.4143-0.48910.60291.11080.10520.4302-0.06020.08850.7028-0.04081.0922-3.643714.95422.5267
31.24920.69882.05859.79432.52463.5964-0.1416-0.6694-1.20680.8278-0.0073-0.31560.0895-0.02630.13760.382-0.02330.07930.49080.1360.9872-11.588914.06679.7906
42.78142.61313.01469.51221.41286.1071-0.91020.9566-0.7199-1.34220.21960.4327-0.09630.40950.71580.4764-0.18770.010.66310.05851.0527-10.850918.025-2.7718
55.676-5.8354-6.39776.02636.58257.2011-1.40260.0734-1.65670.39860.46330.61210.64510.37610.91740.6461-0.08260.16640.57670.00791.4431-27.27277.25254.8821
61.97593.8171-3.30288.4818-4.1639.8241-0.71570.94820.1627-0.41090.67751.2146-0.2977-1.63310.07480.4294-0.0896-0.04620.74030.13571.0321-38.519320.74022.0785
72.75920.9104-0.08465.3987-4.67868.6891-0.1944-0.24430.90160.69890.48550.3083-1.20360.8535-0.31250.3796-0.02690.0370.4879-0.08031.3466-30.641522.62839.099
83.2018-0.14550.45282.3138-1.41042.1787-0.31440.5083-0.5934-0.53650.2587-0.11720.6166-0.3718-0.29520.2991-0.66220.34670.5222-0.06671.4464-30.749217.0882-2.3408
91.5081-1.5596-1.88494.54750.77632.8347-1.35690.37930.5577-1.49630.2967-0.396-0.49740.25730.3940.7737-0.5143-0.23190.81090.2281.1696-15.332826.7714-7.1027
104.8128-0.59830.93673.2353.66028.9251-0.4996-0.39-0.5744-0.92280.76550.52321.92610.4717-0.35820.8844-0.45580.03971.0209-0.07751.7118-26.87262.5795-4.8912
110.8704-1.02170.13421.1984-0.14640.0207-0.19940.5363-0.8612-0.6380.37720.63010.7845-0.794-0.66710.7353-0.72420.31010.789-0.36831.9593-32.48813.4136-4.0372
121.97251.9056-0.68187.7672-0.78583.1234-0.98991.0040.453-0.8810.33140.5204-0.5147-0.2510.39380.7354-0.4322-0.04871.09540.05261.3424-15.808624.9198-7.6179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 29 )A21 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 47 )A30 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 61 )A48 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 76 )A62 - 76
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 29 )B21 - 29
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 47 )B30 - 47
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 61 )B48 - 61
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 76 )B62 - 76
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 10 )C1 - 10
10X-RAY DIFFRACTION10chain 'C' and (resid 11 through 17 )C11 - 17
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 6 )D1 - 6
12X-RAY DIFFRACTION12chain 'D' and (resid 7 through 17 )D7 - 17

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