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- SASDEW6: KRAB-associated protein 1, (KAP1); TRIM28; 23-418 RBCC domain -

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Basic information

Entry
Database: SASBDB / ID: SASDEW6
SampleKRAB-associated protein 1, (KAP1); TRIM28; 23-418 RBCC domain
  • Transcription intermediary factor 1-beta, TIF1b, KAP1, TRIM28, Fragment 23-418, RBCC domain (protein), RBCC DOMAIN KAP1, Homo sapiens
Function / homology
Function and homology information


convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / suppression of viral release by host / chromo shadow domain binding / genomic imprinting / Generic Transcription Pathway / SUMO transferase activity / DNA methylation-dependent constitutive heterochromatin formation ...convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / suppression of viral release by host / chromo shadow domain binding / genomic imprinting / Generic Transcription Pathway / SUMO transferase activity / DNA methylation-dependent constitutive heterochromatin formation / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / embryo implantation / SUMOylation of transcription cofactors / positive regulation of DNA repair / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / HCMV Early Events / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / transcription corepressor activity / chromatin organization / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / protein kinase activity / innate immune response / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA 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 / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
CitationJournal: Life Sci Alliance / Year: 2019
Title: KAP1 is an antiparallel dimer with a functional asymmetry.
Authors: Giulia Fonti / Maria J Marcaida / Louise C Bryan / Sylvain Träger / Alexandra S Kalantzi / Pierre-Yves Jl Helleboid / Davide Demurtas / Mark D Tully / Sergei Grudinin / Didier Trono / Beat ...Authors: Giulia Fonti / Maria J Marcaida / Louise C Bryan / Sylvain Träger / Alexandra S Kalantzi / Pierre-Yves Jl Helleboid / Davide Demurtas / Mark D Tully / Sergei Grudinin / Didier Trono / Beat Fierz / Matteo Dal Peraro /
Abstract: KAP1 (KRAB domain-associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In ...KAP1 (KRAB domain-associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 small ubiquitin modifier ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering data, integrative modeling, and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with an asymmetry at the C-terminal domains. This conformation is consistent with the finding that the Really Interesting New Gene (RING) domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.
Contact author
  • Maria Josefina Marcaida (École polytechnique fédérale de Lausanne (EPFL), Switzerland)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #2559
Type: dummy / Radius of dummy atoms: 1.90 A / Symmetry: p1 / Chi-square value: 0.98 / P-value: 0.000034
Search similar-shape structures of this assembly by Omokage search (details)
Model #2560
Type: atomic / Symmetry: p1 / P-value: 0.017702
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: KRAB-associated protein 1, (KAP1); TRIM28; 23-418 RBCC domain
Specimen concentration: 12 mg/ml
BufferName: 20 mM HEPES, 500 mM NaCl, 10 % Glycerol, 2 mM TCEP / pH: 7.5
Entity #1352Name: RBCC DOMAIN KAP1 / Type: protein
Description: Transcription intermediary factor 1-beta, TIF1b, KAP1, TRIM28, Fragment 23-418, RBCC domain
Formula weight: 46.135 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q13263
Sequence: MGSSHHHHHH SQDPNSSSEN LYFQGEGSAG GEKRSTAPSA AASASASAAA SSPAGGGAEA LELLEHCGVC RERLRPEREP RLLPCLHSAC SACLGPAAPA AANSSGDGGA AGDGTVVDCP VCKQQCFSKD IVENYFMRDS GSKAATDAQD ANQCCTSCED NAPATSYCVE ...Sequence:
MGSSHHHHHH SQDPNSSSEN LYFQGEGSAG GEKRSTAPSA AASASASAAA SSPAGGGAEA LELLEHCGVC RERLRPEREP RLLPCLHSAC SACLGPAAPA AANSSGDGGA AGDGTVVDCP VCKQQCFSKD IVENYFMRDS GSKAATDAQD ANQCCTSCED NAPATSYCVE CSEPLCETCV EAHQRVKYTK DHTVRSTGPA KSRDGERTVY CNVHKHEPLV LFCESCDTLT CRDCQLNAHK DHQYQFLEDA VRNQRKLLAS LVKRLGDKHA TLQKSTKEVR SSIRQVSDVQ KRVQVDVKMA ILQIMKELNK RGRVLVNDAQ KVTEGQQERL ERQHWTMTKI QKHQEHILRF ASWALESDNN TALLLSKKLI YFQLHRALKM IVDPVEPHGE MKFQWDLNAW TKSAEAFGKI VAERPGTNS

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Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.867 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: KRAB-associated protein 1, (KAP1); TRIM28; 23-418 RBCC domain
Measurement date: Jul 6, 2017 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Unit: 1/nm /
MinMax
Q0.0457 2.8547
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 598 /
MinMax
Q0.0457362 2.85473
P(R) point1 598
R0 37
Result
Type of curve: sec /
ExperimentalPorod
MW112 kDa238 kDa
Volume-381 nm3

P(R)GuinierGuinier error
Forward scattering, I039.6 39.02 0.28
Radius of gyration, Rg8.915 nm8.28 nm0.11

MinMax
D-37
Guinier point1 18

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