+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDEW6 |
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Sample | KRAB-associated protein 1, (KAP1); TRIM28; 23-418 RBCC domain
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Function / homology | Function and homology information convergent extension involved in axis elongation / Krueppel-associated box domain binding / suppression of viral release by host / embryonic placenta morphogenesis / : / genomic imprinting / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromo shadow domain binding / Generic Transcription Pathway / SUMO transferase activity ...convergent extension involved in axis elongation / Krueppel-associated box domain binding / suppression of viral release by host / embryonic placenta morphogenesis / : / genomic imprinting / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromo shadow domain binding / Generic Transcription Pathway / SUMO transferase activity / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / embryo implantation / positive regulation of DNA repair / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of transcription cofactors / promoter-specific chromatin binding / RING-type E3 ubiquitin transferase / euchromatin / positive regulation of protein import into nucleus / HCMV Early Events / RNA polymerase II transcription regulator complex / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase 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 |
Biological species | Homo sapiens (human) |
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDEW6 |
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-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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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) |
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Model #2560 | Type: atomic / Symmetry: p1 / P-value: 0.017702 Search similar-shape structures of this assembly by Omokage search (details) |
-Sample
Sample | Name: KRAB-associated protein 1, (KAP1); TRIM28; 23-418 RBCC domain Specimen concentration: 12 mg/ml |
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Buffer | Name: 20 mM HEPES, 500 mM NaCl, 10 % Glycerol, 2 mM TCEP / pH: 7.5 |
Entity #1352 | Name: 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 |
-Experimental information
Beam | Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.867 mm | ||||||||||||||||||||||||||||||
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Detector | Name: 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 /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 598 /
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Result | Type of curve: sec /
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