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

Basic information

• Entry: Database: SASBDB / ID: SASDEW6

Sample

KRAB-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:

convergent extension involved in axis elongation / negative regulation of DNA demethylation / 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 / Generic Transcription Pathway / SUMO transferase activity / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / embryo implantation / positive regulation of DNA repair / SUMOylation of transcription cofactors / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / HCMV Early Events / 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 / transcription coactivator activity / protein kinase activity / DNA repair / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / ubiquitin protein ligase 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

Domain/homology:

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

Component:

Transcription intermediary factor 1-beta

• 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 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 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)

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)

Sample

• Sample: Name: KRAB-associated protein 1, (KAP1); TRIM28; 23-418 RBCC domain; Specimen concentration: 12 mg/ml
• 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 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 synchrotronSynchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.867 mm
• 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 /

	Min	Max
Q	0.0457	2.8547

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 598 /

	Min	Max
Q	0.0457362	2.85473
P(R) point	1	598
R	0	37

Result

Type of curve: sec /

	Experimental	Porod
MW	112 kDa	238 kDa
Volume	-	381 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	39.6	39.02	0.28
Radius of gyration, Rg	8.915 nm	8.28 nm	0.11

	Min	Max
D	-	37
Guinier point	1	18