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- SASDFT3: Murine transcription intermediary factor 1-beta, TRIM28 RBCC asse... -

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Basic information

Entry
Database: SASBDB / ID: SASDFT3
SampleMurine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D, complexed with the Krab domain of ZFP809 fused to an N-terminal MBP
  • Transcription intermediary factor 1-beta (protein), TRIM28, Mus musculus
  • Zinc finger protein 809 N-terminal MBP fusion (protein), MBP-ZFP809, 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 / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / positive regulation of DNA repair / embryo implantation / promoter-specific chromatin binding / RING-type E3 ubiquitin transferase / euchromatin / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / transcription corepressor activity / ubiquitin protein ligase activity / chromatin organization / in utero embryonic development / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein kinase activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / 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 / Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger C2H2 type domain signature. / Ring finger / Zinc finger PHD-type signature. / Zinc finger C2H2-type / 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
Zinc finger protein 809 / 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 #2840
Type: dummy / Radius of dummy atoms: 1.90 A / Symmetry: p1 / Chi-square value: 0.69 / P-value: 0.099471
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, complexed with the Krab domain of ZFP809 fused to an N-terminal MBP
Specimen concentration: 0.15-0.30 / Entity id: 1498 / 1504
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
Entity #1504Name: MBP-ZFP809 / Type: protein / Description: Zinc finger protein 809 N-terminal MBP fusion / Formula weight: 52.099 / Num. of mol.: 1 / Source: Mus musculus / References: UniProt: G3X9G7
Sequence: MLVIWINGDK GYNGLAQVGK KFEKDTGIKV TVEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY FTWPLIAADG GYAFKYENGK ...Sequence:
MLVIWINGDK GYNGLAQVGK KFEKDTGIKV TVEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY FTWPLIAADG GYAFKYENGK YDIKDVGVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AFNKGETAMT INGPWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYEEELAKDP RIAATMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNGSTSGGGG SNNNPPTPTP SSGSGHHHHH HSAALEVLFQ GPGMGLVSFE DVAVDFTLEE WQDLDAAQRT LYRDVMLETY SSLVFLDPCI AKPKLIFNLE RGFGPWSLAE ASSRSLP

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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, complexed with the Krab domain of ZFP809 fused to an N-terminal MBP
Measurement date: Aug 10, 2017 / Cell temperature: 16 °C / Exposure time: 1 sec. / Number of frames: 48 / 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 220
Result
Type of curve: sec /
ExperimentalPorod
MW138 kDa-
Volume-252 nm3

P(R)GuinierGuinier error
Forward scattering, I00.06258 0.062 0.00024
Radius of gyration, Rg6.58 nm6.38 nm0.046

MinMax
D-22
Guinier point3 43

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