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- PDB-6h3a: Crystal structure of the KAP1 RBCC domain in complex with the SMA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6h3a | ||||||
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Title | Crystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1 domain. | ||||||
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![]() | LIGASE / TRIM28 / transcriptional co-repressor / CUE domain / Ubuiquitin | ||||||
Function / homology | ![]() : / : / : / convergent extension involved in axis elongation / Krueppel-associated box domain binding / chromosome separation / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression ...: / : / : / convergent extension involved in axis elongation / Krueppel-associated box domain binding / chromosome separation / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / regulation of DNA recombination / genomic imprinting / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA double-strand break processing / chromo shadow domain binding / Generic Transcription Pathway / SUMO transferase activity / ATP-dependent chromatin remodeler activity / nuclear replication fork / protein sumoylation / epithelial to mesenchymal transition / ATP-dependent activity, acting on DNA / heterochromatin / positive regulation of DNA repair / embryo implantation / helicase activity / SUMOylation of transcription cofactors / ubiquitin binding / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / 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 / site of double-strand break / DNA helicase / transcription coactivator activity / protein kinase activity / chromatin remodeling / DNA repair / innate immune response / 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 / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Aitkenhead, H. / Lim, M. / Williams, H.L. / Svejstrup, J.Q. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
![]() | ![]() Title: A Ubiquitin-Binding Domain that Binds a Structural Fold Distinct from that of Ubiquitin. Authors: Lim, M. / Newman, J.A. / Williams, H.L. / Masino, L. / Aitkenhead, H. / Gravard, A.E. / Gileadi, O. / Svejstrup, J.Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.5 KB | Display | ![]() |
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PDB format | ![]() | 112.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.6 KB | Display | ![]() |
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Full document | ![]() | 474.5 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28799.678 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 42501.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13263, RING-type E3 ubiquitin transferase #3: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.2 M Sodium Malonate, 0.5 % Jeffamine ED-2003 and 0.1 M HEPES pH 7.0 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 5.5→80.1 Å / Num. obs: 14734 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 280 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.04 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 5.5→6.15 Å / Redundancy: 19.5 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3240 / CC1/2: 0.16 / Rpim(I) all: 0.29 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.505→74.978 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 5.505 Å |