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

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Basic information

Entry
Database: PDB / ID: 8ejo
TitleCrystal structure of the homeodomain of Platypus sDUX 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')
  • 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: 2.67 Å
AuthorsYin, L. / Shi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR055685 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
Revision 1.2Sep 18, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.name

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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)27,0775
Polymers27,0154
Non-polymers621
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-19 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.022, 74.022, 97.309
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: 5232.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M CaCl2, 0.05M HEPES sodium 7.5, 28 % v/v PEG 400, 0.002M Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.67→74.02 Å / Num. obs: 8096 / % possible obs: 99.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 79.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Net I/σ(I): 14.3 / Num. measured all: 50642
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.67-2.86.41.253651610210.5610.5311.366198
8.84-74.025.20.03313632610.9990.0140.03635.996.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.67→58.91 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 628 4.9 %
Rwork0.2244 12192 -
obs0.225 7146 86.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.4 Å2 / Biso mean: 87.5704 Å2 / Biso min: 63.01 Å2
Refinement stepCycle: final / Resolution: 2.67→58.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 691 4 4 1645
Biso mean--73.9 88.01 -
Num. residues----146
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A559X-RAY DIFFRACTION9.654TORSIONAL
12B559X-RAY DIFFRACTION9.654TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.710.4014120.622531732945
2.71-2.760.3681160.513638840455
2.76-2.810.5713290.47541144060
2.81-2.870.3376230.420346448766
2.87-2.930.3469230.356151253575
2.93-30.4381230.338359161483
3-3.080.516310.366363266389
3.08-3.160.2301340.287265068494
3.16-3.250.2201420.268367171395
3.25-3.360.4074290.265369572498
3.36-3.480.2447350.263468972499
3.48-3.620.2274290.2604700729100
3.62-3.780.256340.243470273699
3.78-3.980.3089330.225169172499
3.98-4.230.2504450.231569173699
4.23-4.560.1518340.205969072498
4.56-5.020.2875340.194866369795
5.02-5.740.2845450.181767972498
5.74-7.230.1926440.187367471898
7.24-58.910.1117330.145468271596
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)
13.5266-1.59031.9163.3998-0.33755.932-0.60860.67160.31570.00840.464-0.6867-0.30861.02180.1640.4096-0.21470.07280.67280.02330.7807-6.911122.11583.6608
25.6684-0.77284.79226.57582.96877.4314-0.39620.6971-1.0087-0.69780.25610.1940.33510.24770.15310.3404-0.18150.10840.5686-0.05240.8258-10.503815.42481.583
38.7009-7.7118-0.86449.1722.87861.9657-0.64280.0736-2.9689-0.12950.27261.42420.6822-0.56160.4350.6683-0.10730.17460.4920.0141.0275-26.89417.34994.4464
43.37392.3723-3.47753.5946-1.52154.6179-0.62770.54240.2222-0.8591-0.1650.65120.0085-1.25490.57240.3891-0.1309-0.09170.82940.04810.8376-38.04920.82251.7759
54.9553-0.7511-4.32584.7821-2.33627.1741-0.31850.508-0.011-0.41030.14330.03530.0294-0.49730.04160.3569-0.12620.1160.50650.07231.0669-30.307319.63822.3065
62.4353-1.5672-2.90971.94170.7574.9506-0.78220.67180.4725-1.04750.0619-0.355-0.52290.23120.41440.8382-0.4409-0.15580.84570.23280.9614-14.835726.9178-7.1811
77.2612-1.67070.92481.90780.23895.7542-0.409-0.6018-0.7288-1.1548-0.13590.97782.19310.92690.11131.1377-0.45280.19930.9672-0.16191.4183-26.48372.8327-5.3589
80.35671.18491.31953.94034.41144.9302-0.56250.3981-2.2655-0.8421-1.46140.76660.8809-1.6884-0.1151.0638-0.47820.35060.9646-0.32971.7189-33.75812.6724-4.8749
96.1282-0.6520.36365.53122.44333.7451-0.44120.76720.2554-1.61280.739-0.16810.14071.57170.64750.8657-0.42820.22891.0383-0.0751.0732-18.674812.7578-7.819
102.6351-0.70030.50038.96946.02434.5923-0.56241.73710.4848-2.0818-0.19840.3376-1.0541-2.23960.44311.1006-0.3396-0.05511.23080.13211.1153-16.522830.2191-10.409
119.5695.2816-2.71424.52170.09843.45820.61670.4372-0.08280.43521.52382.20321.4756-1.031-1.92021.237-0.343-0.21321.04850.06341.2891-8.760735.76911.9871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 42 )A21 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 76 )A43 - 76
3X-RAY DIFFRACTION3chain 'B' and (resid 21 through 29 )B21 - 29
4X-RAY DIFFRACTION4chain 'B' and (resid 30 through 47 )B30 - 47
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 76 )B48 - 76
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 10 )C1 - 10
7X-RAY DIFFRACTION7chain 'C' and (resid 11 through 17 )C11 - 17
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 5 )D1 - 5
9X-RAY DIFFRACTION9chain 'D' and (resid 6 through 10 )D6 - 10
10X-RAY DIFFRACTION10chain 'D' and (resid 11 through 15 )D11 - 15
11X-RAY DIFFRACTION11chain 'D' and (resid 16 through 17 )D16 - 17

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