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- SASDFS3: Murine transcription intermediary factor 1-beta, TRIM28 RBCC asse... -

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Basic information

Entry
Database: SASBDB / ID: SASDFS3
SampleMurine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D
  • Transcription intermediary factor 1-beta (protein), TRIM28, Mus musculus
Function / homology
Function and homology information


Generic Transcription Pathway / convergent extension involved in axis elongation / : / Krueppel-associated box domain binding / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / genomic imprinting ...Generic Transcription Pathway / convergent extension involved in axis elongation / : / Krueppel-associated box domain binding / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / genomic imprinting / chromo shadow domain binding / SUMO transferase activity / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / embryo implantation / positive regulation of DNA repair / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / chromatin organization / in utero embryonic development / transcription coactivator activity / protein kinase activity / innate immune response / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
CitationJournal: J Mol Biol / Year: 2019
Title: A Dissection of Oligomerization by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family.
Authors: Yunyuan Sun / Jeremy R Keown / Moyra M Black / Charlène Raclot / Nicholas Demarais / Didier Trono / Priscilla Turelli / David C Goldstone /
Abstract: TRIM28 (also known as KAP1 or TIF1β) is the universal co-repressor of the Krüppel-associated box-containing zinc finger proteins (Krab-ZFPs), the largest family of transcription factors in mammals. ...TRIM28 (also known as KAP1 or TIF1β) is the universal co-repressor of the Krüppel-associated box-containing zinc finger proteins (Krab-ZFPs), the largest family of transcription factors in mammals. During early embryogenesis, TRIM28 mediates the transcriptional silencing of many endogenous retroviral elements and genomic imprinted sites. Silencing is initiated by the recruitment of TRIM28 to a target locus by members of the Krab-ZFP. Subsequently, TRIM28 functions as a scaffold protein to recruit chromatin modifying effectors featuring SETDB1, HP1 and the NuRD complex. Although many protein partners involved in silencing have been identified, the molecular basis of the protein interactions that mediate silencing remains largely unclear. In the present study, we identified the first Bbox domain (T28_B1 135-203) as a molecular interface responsible for the formation of higher-order oligomers of TRIM28. The structure of this domain reveals a new interface on the surface of the Bbox domain. Mutants disrupting the interface disrupt the formation of oligomers but have no observed effect on transcriptional silencing defining a single TRIM28 dimer as the functional unit for silencing. Using assembly-deficient mutants, we employed small-angle X-ray scattering and biophysical techniques to characterize binding to member of the Krab-ZFP family. This allows us to narrow and define the binding interface to the center of the coiled-coil region (residues 294-321) of TRIM28 and define mutants that abolish binding to the Krab-ZFP proteins.
Contact author
  • Yunyuan Sun (The University of Auckland, Auckland, New Zealand)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #2839
Type: dummy / Software: (2.3i) / Radius of dummy atoms: 1.90 A / Symmetry: p2 / Chi-square value: 0.33 / P-value: 0.012949
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Murine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D
Specimen concentration: 0.15-0.20
BufferName: 10 mM Tris 300 mM NaCl 0.1 mM TCEP / pH: 8
Entity #1498Name: TRIM28 / Type: protein / Description: Transcription intermediary factor 1-beta / Formula weight: 40.928 / Num. of mol.: 2 / Source: Mus musculus / References: UniProt: Q62318
Sequence: GPGEAQELLE HCGVCRERLR PERDPRLLPC LHSACSACLG PATPAAANNS GDGGSAGDGA MVDCPVCKQQ CYSKDIVENY FMRDSGSKAS SDSQDANQCC TSCEDNAPAT SYCVECSEPL CETCVEAHQR VKYTKDHTVR STGPAKTRDG ERTVYCNVHK HEPLVLFCES ...Sequence:
GPGEAQELLE HCGVCRERLR PERDPRLLPC LHSACSACLG PATPAAANNS GDGGSAGDGA MVDCPVCKQQ CYSKDIVENY FMRDSGSKAS SDSQDANQCC TSCEDNAPAT SYCVECSEPL CETCVEAHQR VKYTKDHTVR STGPAKTRDG ERTVYCNVHK HEPLVLFCES CDTLTCRDCQ LNAHKDHQYQ FLEDAVRNQR KLLASLVKRL GDKHATLQKN TKEVRSSIRQ VSDVQKRVQV DVKMAILQIM KELNKRGRVL VNDAQKVTEG QQERLERQHW TMTKIQKHQE HILRFASWAL ESDNNTALLL SKKLIYFQLH RALKMIVDPV EPHGEMKFQW DLNAWTKSAE AFGKIVAERP GTNS

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Experimental information

BeamInstrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.113 Å / Dist. spec. to detc.: 3.3 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Murine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D
Measurement date: Aug 10, 2017 / Cell temperature: 16 °C / Exposure time: 1 sec. / Number of frames: 12 / Unit: 1/A /
MinMax
Q0.0043 0.2843
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 869 /
MinMax
Q0.00562355 0.284318
P(R) point1 869
R0 232
Result
Type of curve: sec /
ExperimentalPorod
MW70 kDa-
Volume-232 nm3

P(R)GuinierGuinier errorP(R) error
Forward scattering, I00.0351 0.03473 0.00042 -
Radius of gyration, Rg7.39 nm7.012 nm0.123 0.07

MinMax
D-23.2
Guinier point4 45

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