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- PDB-6swg: Crystal structure of the TASOR-Periphilin core complex -

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Basic information

Entry
Database: PDB / ID: 6swg
TitleCrystal structure of the TASOR-Periphilin core complex
Components
  • Periphilin-1
  • Protein TASOR
KeywordsGENE REGULATION / Nuclear protein / Transcriptional repressor / epigenetic silencing / histone H3 lysine 9 methylation (H3K9me3) / transposable element / LINE1 element / low-complexity sequence / liquid-liquid phase separation (LLPS) / membrane-less compartment / RNA-binding protein
Function / homology
Function and homology information


mesodermal to mesenchymal transition involved in gastrulation / protein localization to heterochromatin / positive regulation of DNA methylation-dependent heterochromatin formation / anterior/posterior axis specification, embryo / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression, epigenetic / keratinization / heterochromatin / chromosome / negative regulation of DNA-templated transcription ...mesodermal to mesenchymal transition involved in gastrulation / protein localization to heterochromatin / positive regulation of DNA methylation-dependent heterochromatin formation / anterior/posterior axis specification, embryo / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression, epigenetic / keratinization / heterochromatin / chromosome / negative regulation of DNA-templated transcription / chromatin binding / Golgi apparatus / RNA binding / nucleoplasm / cytosol
Similarity search - Function
Periphilin-1 / TASOR, DUF3715 / TASOR / Protein of unknown function (DUF3715)
Similarity search - Domain/homology
Periphilin-1 / Protein TASOR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsPrigozhin, D.M. / Freund, S.M.V. / Modis, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101908/Z/13/Z United Kingdom
Citation
Journal: Nucleic Acids Res. / Year: 2020
Title: Periphilin self-association underpins epigenetic silencing by the HUSH complex.
Authors: Prigozhin, D.M. / Douse, C.H. / Farleigh, L.E. / Albecka, A. / Tchasovnikarova, I.A. / Timms, R.T. / Oda, S.I. / Adolf, F. / Freund, S.M.V. / Maslen, S. / Lehner, P.J. / Modis, Y.
#1: Journal: Biorxiv / Year: 2020
Title: TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control
Authors: Prigozhin, D.M. / Albecka, A. / Douse, C.H. / Tchasovnikarova, I.A. / Timms, R.T. / Farleigh, L.E. / Freund, S.M.V. / Lehner, P.J. / Modis, Y.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 2.0Aug 12, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_target_identifier
Revision 2.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Revision 2.2Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.3Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.4May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periphilin-1
B: Periphilin-1
C: Protein TASOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6584
Polymers31,5623
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-47 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.570, 93.570, 84.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 295 or resid 297 through 298...
21(chain B and (resid 295 or resid 297 through 298...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain A and (resid 295 or resid 297 through 298...AA29522
12ARGARGSERSER(chain A and (resid 295 or resid 297 through 298...AA297 - 29824 - 25
13ALAALATYRTYR(chain A and (resid 295 or resid 297 through 298...AA300 - 31227 - 39
14GLNGLNLEULEU(chain A and (resid 295 or resid 297 through 298...AA314 - 34141 - 68
15GLNGLNLYSLYS(chain A and (resid 295 or resid 297 through 298...AA343 - 35770 - 84
16PHEPHETHRTHR(chain A and (resid 295 or resid 297 through 298...AA359 - 36586 - 92
21THRTHRTHRTHR(chain B and (resid 295 or resid 297 through 298...BB29522
22ARGARGSERSER(chain B and (resid 295 or resid 297 through 298...BB297 - 29824 - 25
23ALAALATYRTYR(chain B and (resid 295 or resid 297 through 298...BB300 - 31227 - 39
24GLNGLNLEULEU(chain B and (resid 295 or resid 297 through 298...BB314 - 34141 - 68
25GLNGLNLYSLYS(chain B and (resid 295 or resid 297 through 298...BB343 - 35770 - 84
26PHEPHETHRTHR(chain B and (resid 295 or resid 297 through 298...BB359 - 36586 - 92

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Components

#1: Protein Periphilin-1


Mass: 11035.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TASOR binding region of Periphilin (residues 292-367)
Source: (gene. exp.) Homo sapiens (human) / Gene: PPHLN1, HSPC206, HSPC232 / Variant: Isoform 2 (identifier: Q8NEY8-2) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8NEY8
#2: Protein Protein TASOR


Mass: 9490.903 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Periphilin binding region of TASOR (residues 1014-1095)
Source: (gene. exp.) Homo sapiens (human) / Gene: TASOR, C3orf63, FAM208A, KIAA1105 / Variant: Isoform 1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9UK61
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
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: 4.4 Å3/Da / Density % sol: 72.08 % / Description: Hexagonal rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1M ammonium sulfate, 100 mM sodium citrate; protein buffer: PBS
PH range: 4.0 - 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 8, 2018 / Details: Torroidal mirror
RadiationMonochromator: single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.51→41 Å / Num. obs: 15081 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.029 / Rrim(I) all: 0.089 / Net I/σ(I): 15
Reflection shellResolution: 2.51→2.58 Å / Redundancy: 10 % / Rmerge(I) obs: 1.087 / Num. unique obs: 1113 / CC1/2: 0.735 / Rpim(I) all: 0.36 / Rrim(I) all: 1.146 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSversion 11data reduction
Aimlessversion 0.5.32data scaling
CRANK2version 2.0.148phasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→40.983 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.24
RfactorNum. reflection% reflection
Rfree0.2706 785 5.21 %
Rwork0.228 --
obs0.2303 15064 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 271.29 Å2 / Biso mean: 123 Å2 / Biso min: 70.24 Å2
Refinement stepCycle: final / Resolution: 2.51→40.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 5 0 1689
Biso mean--151.48 --
Num. residues----209
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A578X-RAY DIFFRACTION10.836TORSIONAL
12B578X-RAY DIFFRACTION10.836TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5105-2.66770.37941320.29832349
2.6677-2.87370.33531180.30482349
2.8737-3.16280.35991140.29542377
3.1628-3.62020.32681290.26012359
3.6202-4.56010.25791320.20292375
4.5601-40.980.24421600.21192470
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)
10.99430.45280.27030.83021.13681.12160.2581-0.1267-0.1105-0.1658-0.50780.84450.3448-0.0067-00.7502-0.03940.16830.8071-0.0561.0617-37.582133.401737.9641
20.1916-0.5559-0.82212.17161.8362.67730.49690.48340.5543-1.2654-0.6378-0.3733-0.34080.107-0.00490.91930.01480.00490.7267-0.00761.0905-33.77238.10329.9595
32.25550.6703-0.48980.4542-0.57530.78010.39520.51460.52130.42850.05410.2585-0.5644-0.7834-0.00030.972-0.02520.08290.9125-0.04130.9192-48.748716.041832.9149
41.72181.4705-2.65960.9042-2.66661.3402-0.4861-0.2663-0.8877-0.3479-0.3961-0.93970.30770.38880.00281.169-0.08080.1380.8953-0.06061.0356-43.01698.051534.5141
50.92571.90141.64672.95312.77410.5012-0.5934-0.70270.61810.0991.0902-0.3295-0.11250.4739-0.00361.0972-0.01510.09690.8768-0.02391.0592-29.151440.226439.1861
64.07961.03653.91544.93336.2788.16110.5434-1.3844-1.87472.07970.5016-1.07423.2094-0.60891.61361.4133-0.320.3711.2024-0.14970.9187-36.214229.057741.4804
72.7493-0.0628-0.45960.5817-0.52091.4699-0.11031.74091.2885-0.97730.92390.60120.2025-0.75720.0181.4043-0.08050.0061.1943-0.11350.8951-53.74264.298330.521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 295 through 330 )A295 - 330
2X-RAY DIFFRACTION2chain 'A' and (resid 331 through 366 )A331 - 366
3X-RAY DIFFRACTION3chain 'B' and (resid 294 through 330 )B294 - 330
4X-RAY DIFFRACTION4chain 'B' and (resid 331 through 367 )B331 - 367
5X-RAY DIFFRACTION5chain 'C' and (resid 1014 through 1043 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 1044 through 1074 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 1075 through 1093 )C0

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