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- PDB-6tl1: Crystal structure of the TASOR pseudo-PARP domain -

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Basic information

Entry
Database: PDB / ID: 6tl1
TitleCrystal structure of the TASOR pseudo-PARP domain
ComponentsProtein TASOR
KeywordsGENE REGULATION / Nuclear protein / Transcriptional repressor / epigenetic silencing / histone H3 lysine 9 methylation (H3K9me3) / transposable element / LINE1 element / RNA-binding protein
Function / homology
Function and homology information


mesodermal to mesenchymal transition involved in gastrulation / protein localization to heterochromatin / constitutive heterochromatin formation / anterior/posterior axis specification, embryo / transposable element silencing by heterochromatin formation / negative regulation of gene expression, epigenetic / heterochromatin / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / chromatin binding / RNA binding / nucleoplasm
Similarity search - Function
TASOR, DUF3715 / TASOR / : / : / Protein of unknown function (DUF3715) / TASOR alpha/beta domain / TASOR PIN domain / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsDouse, C.H. / Timms, R.T. / Freund, S.M.V. / Modis, Y.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust101908/Z/13/Z United Kingdom
Wellcome Trust217191/Z/19/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N011791/1 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control.
Authors: Douse, C.H. / Tchasovnikarova, I.A. / Timms, R.T. / Protasio, A.V. / Seczynska, M. / Prigozhin, D.M. / Albecka, A. / Wagstaff, J. / Williamson, J.C. / Freund, S.M.V. / Lehner, P.J. / Modis, Y.
History
DepositionNov 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Protein TASOR
B: Protein TASOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7373
Polymers49,6452
Non-polymers921
Water2,522140
1
A: Protein TASOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9152
Polymers24,8221
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein TASOR


Theoretical massNumber of molelcules
Total (without water)24,8221
Polymers24,8221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.590, 74.590, 184.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...
21(CHAIN B AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...A6 - 31
121(CHAIN A AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...A32
131(CHAIN A AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...A111 - 329
141(CHAIN A AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...A111 - 329
151(CHAIN A AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...A111 - 329
161(CHAIN A AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...A111 - 329
171(CHAIN A AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...A111 - 329
211(CHAIN B AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...B6 - 31
221(CHAIN B AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...B32
231(CHAIN B AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...B111 - 328
241(CHAIN B AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...B111 - 328
251(CHAIN B AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...B111 - 328
261(CHAIN B AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...B111 - 328
271(CHAIN B AND (RESSEQ 6:31 OR (RESID 32 AND (NAME...B111 - 328

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Components

#1: Protein Protein TASOR / CTCL tumor antigen se89-1 / Retinoblastoma-associated protein RAP140 / Transgene activation suppressor protein


Mass: 24822.430 Da / Num. of mol.: 2 / Mutation: residues 261-269 deleted
Source method: isolated from a genetically manipulated source
Details: TASOR pseudo PARP domain, residues 110-332 with internal deletion of residues 261-269
Source: (gene. exp.) Homo sapiens (human) / Gene: TASOR, C3orf63, FAM208A, KIAA1105 / Variant: Isoform 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UK61
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.58 Å3/Da / Density % sol: 52.4 % / Description: Cuboid
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.1 M NaPi,, 0.1 M KPi, 2 M NaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0210.97949
SYNCHROTRONDiamond I0320.9798
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELMar 5, 2016Perpendicular focussing mirrors
DECTRIS EIGER2 XE 16M2PIXELApr 16, 2014Perpendicular focussing mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.97981
ReflectionResolution: 2.03→57.945 Å / Num. obs: 34589 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 43.21 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Net I/σ(I): 16.1
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.46 / Num. unique obs: 2513 / Rpim(I) all: 0.427 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSOct 15, 2015data reduction
Aimless0.5.17data scaling
AutoSolphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.03→57.94 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.229 1670 4.84 %
Rwork0.195 32836 -
obs0.197 34506 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.53 Å2 / Biso mean: 56.56 Å2 / Biso min: 28.01 Å2
Refinement stepCycle: final / Resolution: 2.03→57.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 6 140 3505
Biso mean--82.9 49.22 -
Num. residues----412
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1649X-RAY DIFFRACTIONPOSITIONAL0
12B1649X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.03-2.08980.32331330.316426792812
2.0898-2.15720.30231480.278326712819
2.1572-2.23430.27561390.241726842823
2.2343-2.32380.24721330.220926802813
2.3238-2.42960.26661470.229626862833
2.4296-2.55770.25611490.233227072856
2.5577-2.71790.26281350.229427032838
2.7179-2.92780.31331260.221427442870
2.9278-3.22240.22751330.214127372870
3.2224-3.68860.21721360.183127612897
3.6886-4.64690.20281550.155727972952
4.6469-57.940.19751360.176529873123
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)
12.9280.80690.42653.35981.57961.62150.0719-0.15190.6458-0.3574-0.08770.2802-0.1746-0.2152-0.09930.349-0.0475-0.03950.39660.11370.32398.570992.2761198.1167
24.12522.4629-1.05684.1562-0.76982.07280.0480.58030.0568-0.03560.1847-0.0148-0.20270.0204-0.16130.4074-0.0419-0.0330.41650.05890.316316.581689.2606195.6098
34.9811-0.3748-1.19937.2449-2.6681.91190.1414-0.3447-0.24980.07320.53751.42310.0518-0.4804-0.59170.3096-0.02290.02240.43830.1010.4838-1.195172.88207.9477
46.2380.4226-2.23685.0047-2.44725.68890.038-0.85250.39550.36210.35920.2938-0.45720.1942-0.06610.30370.0152-0.00810.4241-0.02840.279810.331376.1462208.974
53.6149-2.30870.92715.4944-1.46221.4558-0.08870.82050.0999-0.88040.17390.8588-0.0023-0.2309-0.22060.5335-0.1586-0.15190.6031-0.00430.34049.79772.8368189.5532
62.0282-0.49410.25266.9951-1.24062.36770.03560.22630.0961-0.4411-0.0692-0.0982-0.00650.0916-0.03570.3312-0.0437-0.02010.36620.01210.233218.937476.7479195.4018
74.4978-1.75820.20084.9673-1.25281.9943-0.13410.2109-0.4184-0.23260.0694-0.26840.0908-0.01410.05810.39610.0204-0.03540.3931-0.0050.399821.594663.4868207.2198
82.89281.4197-0.87675.18-2.3082.31840.0046-0.2048-0.26180.403-0.0109-0.3723-0.23710.18470.00610.3121-0.0165-0.07080.3777-0.01050.277123.095870.9803204.1941
98.0101-0.6219-0.21516.8283-0.05886.7728-0.14730.1048-0.5878-0.17660.2121.2461.2817-0.8016-0.0720.527-0.1256-0.01680.50620.08110.47315.139262.5322202.3397
103.45310.7547-1.76029.5906-1.84824.17360.03690.0470.6315-0.95330.4471-0.20470.1390.128-0.41990.3524-0.0481-0.02360.3996-0.01520.281315.012685.8572193.2504
113.28430.96581.21075.5656-0.65452.93920.3014-0.88010.03771.0554-0.5104-0.19360.11210.01590.13790.5280.01420.06270.64860.0790.3577-1.199199.0526226.9472
122.07842.62420.9033.35840.62663.220.0084-1.06150.72220.69530.10630.6102-0.3888-0.6384-0.38360.55250.16060.18660.6830.07190.9302-22.6086109.3153219.4914
134.32740.99111.49313.0984-0.24152.58150.0414-0.33990.1470.3785-0.17090.4999-0.0679-0.28760.09780.43390.04290.09470.463-0.0130.5273-11.6563102.1236217.2948
141.3969-0.14930.76045.2384-0.46732.90090.03180.434-0.0014-0.301-0.13950.5720.18720.1140.03850.3610.07670.04850.52260.01910.5639-12.159397.1169205.5366
153.57450.32570.48634.77890.29652.89330.08340.1443-0.31610.0283-0.08860.50730.1504-0.19050.00250.37190.05620.11980.36940.08880.5145-11.391793.1726213.984
161.6438-0.2550.33822.2712-0.12810.70440.2834-0.1734-0.2393-0.2751-0.24830.77820.3772-0.3233-0.02380.50730.0050.03060.52420.0230.7929-12.791785.2969212.4655
175.5396-1.1692-0.42782.84441.04661.49840.10330.00930.0968-0.0001-0.12770.6585-0.329-0.2091-0.01550.37550.03310.14280.47370.10430.5694-13.2278102.2968212.5121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 28 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 29 THROUGH 48 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 49 THROUGH 64 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 65 THROUGH 81 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 82 THROUGH 102 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 103 THROUGH 138 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 139 THROUGH 156 )A0
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 157 THROUGH 188 )A0
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 189 THROUGH 202 )A0
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 203 THROUGH 215 )A0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 6 THROUGH 48 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 49 THROUGH 64 )B0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 65 THROUGH 92 )B0
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 93 THROUGH 114 )B0
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 115 THROUGH 162 )B0
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 163 THROUGH 188 )B0
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 189 THROUGH 214 )B0

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