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- EMDB-12040: Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 s... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12040 | |||||||||
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Title | Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 | |||||||||
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Function / homology | ![]() PKR/eIFalpha signaling / cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of protein polyubiquitination / ubiquitin-like protein transferase activity / PTK6 Regulates Cell Cycle / Lewy body / autophagic cell death ...PKR/eIFalpha signaling / cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of protein polyubiquitination / ubiquitin-like protein transferase activity / PTK6 Regulates Cell Cycle / Lewy body / autophagic cell death / Parkin-FBXW7-Cul1 ubiquitin ligase complex / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / F-box domain binding / RBR-type E3 ubiquitin transferase / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / PcG protein complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / p53-Dependent G1 DNA Damage Response / regulation of cell cycle G1/S phase transition / regulation of exit from mitosis / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / mitotic cell cycle phase transition / cullin-RING ubiquitin ligase complex / epithelial cell proliferation involved in prostate gland development / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of phosphorylation / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / cyclin-dependent protein serine/threonine kinase inhibitor activity / positive regulation of protein autoubiquitination / negative regulation of vascular associated smooth muscle cell proliferation / protein neddylation / RHO GTPases activate CIT / cyclin-dependent protein serine/threonine kinase activator activity / nuclear export / ubiquitin conjugating enzyme binding / NEDD8 ligase activity / negative regulation of mitotic cell cycle / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / AKT phosphorylates targets in the cytosol / positive regulation of intracellular estrogen receptor signaling pathway / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / SCF ubiquitin ligase complex / cellular response to antibiotic / Cul2-RING ubiquitin ligase complex / Cajal body / Cyclin E associated events during G1/S transition / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / negative regulation of kinase activity / molecular function inhibitor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to lithium ion / RSV-host interactions / positive regulation of DNA replication / protein kinase inhibitor activity / Prolactin receptor signaling / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / protein monoubiquitination / Constitutive Signaling by AKT1 E17K in Cancer / regulation of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / cullin family protein binding / inner ear development / protein K63-linked ubiquitination / cellular response to organic cyclic compound / cyclin binding / ubiquitin-like ligase-substrate adaptor activity / positive regulation of double-strand break repair via homologous recombination / response to amino acid / protein K48-linked ubiquitination / post-translational protein modification / Nuclear events stimulated by ALK signaling in cancer / response to glucose / regulation of cellular response to insulin stimulus / response to cadmium ion / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Notch signaling pathway / Myoclonic epilepsy of Lafora / positive regulation of microtubule polymerization Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.91 Å | |||||||||
![]() | Horn-Ghetko D / Prabu JR / Schulman BA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly. Authors: Daniel Horn-Ghetko / David T Krist / J Rajan Prabu / Kheewoong Baek / Monique P C Mulder / Maren Klügel / Daniel C Scott / Huib Ovaa / Gary Kleiger / Brenda A Schulman / ![]() ![]() ![]() Abstract: E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates. However, rather ...E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates. However, rather than functioning individually, many neddylated cullin-RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family-which together account for nearly half of all ubiquitin ligases in humans-form E3-E3 super-assemblies. Here, by studying CRLs in the SKP1-CUL1-F-box (SCF) family, we show how neddylated SCF ligases and ARIH1 (an RBR-type E3 ligase) co-evolved to ubiquitylate diverse substrates presented on various F-box proteins. We developed activity-based chemical probes that enabled cryo-electron microscopy visualization of steps in E3-E3 ubiquitylation, initiating with ubiquitin linked to the E2 enzyme UBE2L3, then transferred to the catalytic cysteine of ARIH1, and culminating in ubiquitin linkage to a substrate bound to the SCF E3 ligase. The E3-E3 mechanism places the ubiquitin-linked active site of ARIH1 adjacent to substrates bound to F-box proteins (for example, substrates with folded structures or limited length) that are incompatible with previously described conventional RING E3-only mechanisms. The versatile E3-E3 super-assembly may therefore underlie widespread ubiquitylation. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27 KB 27 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.1 KB | Display | ![]() |
Images | ![]() | 95.3 KB | ||
Masks | ![]() | 115.9 MB | ![]() | |
Others | ![]() ![]() | 91.1 MB 91 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b5mMC ![]() 7b5lC ![]() 7b5nC ![]() 7b5rC ![]() 7b5sC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
File | emd_12040_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_12040_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1
+Supramolecule #1: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1
+Supramolecule #2: Cullin-1, E3 ubiquitin-protein ligase RBX1
+Supramolecule #3: ARIH1, SKP2, CKS1B, SKP1, UBC
+Supramolecule #4: Cyclin-dependent kinase inhibitor 1B
+Macromolecule #1: Cullin-1
+Macromolecule #2: E3 ubiquitin-protein ligase ARIH1
+Macromolecule #3: S-phase kinase-associated protein 2
+Macromolecule #4: Cyclin-dependent kinases regulatory subunit 1
+Macromolecule #5: S-phase kinase-associated protein 1
+Macromolecule #6: Polyubiquitin-C
+Macromolecule #7: E3 ubiquitin-protein ligase RBX1
+Macromolecule #8: Cyclin-dependent kinase inhibitor 1B
+Macromolecule #9: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |