- PDB-6td3: Structure of DDB1 bound to CR8-engaged CDK12-cyclinK -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 6td3
Title
Structure of DDB1 bound to CR8-engaged CDK12-cyclinK
Components
Cyclin-K
Cyclin-dependent kinase 12
DNA damage-binding protein 1
Keywords
LIGASE / ubiquitin ligase kinase cyclin CDK
Function / homology
Function and homology information
cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / host-mediated suppression of viral genome replication / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation by virus of viral protein levels in host cell / negative regulation of stem cell differentiation / spindle assembly involved in female meiosis ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / host-mediated suppression of viral genome replication / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation by virus of viral protein levels in host cell / negative regulation of stem cell differentiation / spindle assembly involved in female meiosis / regulation of cyclin-dependent protein serine/threonine kinase activity / epigenetic programming in the zygotic pronuclei / cyclin-dependent protein serine/threonine kinase activator activity / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / [RNA-polymerase]-subunit kinase / positive regulation of DNA-templated transcription, elongation / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cellular response to estrogen stimulus / regulation of signal transduction / ectopic germ cell programmed cell death / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / positive regulation of viral genome replication / Formation of HIV elongation complex in the absence of HIV Tat / proteasomal protein catabolic process / negative regulation of MAPK cascade / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of gluconeogenesis / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / cyclin binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / regulation of circadian rhythm / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Wnt signaling pathway / mRNA processing / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / chromosome, telomeric region / protein ubiquitination / protein kinase activity / nuclear speck / cell division / protein serine kinase activity / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein kinase binding / protein-containing complex binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function
Cyclin-T2-like, C-terminal domain / DNA polymerase; domain 1 - #910 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : ...Cyclin-T2-like, C-terminal domain / DNA polymerase; domain 1 - #910 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi