[English] 日本語
Yorodumi- PDB-7b5r: Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b5r | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27 | |||||||||
Components |
| |||||||||
Keywords | LIGASE / ubiquitin / ubiquitin ligase / E3 ligase / F-box protein / RBR ligase / Cullin-RING-Ligase / CRL / SCF / NEDD8 / Post-translational modification / ubiquitylation | |||||||||
Function / homology | Function and homology information 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 / 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 ...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 / 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 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / cell cycle G1/S phase transition / regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / cellular response to luteinizing hormone stimulus / regulation of exit from mitosis / mitotic cell cycle phase transition / epithelial cell proliferation involved in prostate gland development / cullin-RING ubiquitin ligase complex / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / Cul7-RING ubiquitin ligase complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / maintenance of protein location in nucleus / cellular response to leptin stimulus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cyclin-dependent protein serine/threonine kinase inhibitor activity / RHO GTPases activate CIT / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / nuclear export / cellular response to cocaine / response to glucagon / AKT phosphorylates targets in the cytosol / positive regulation of intracellular estrogen receptor signaling pathway / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / epithelial cell apoptotic process / SCF ubiquitin ligase complex / cellular response to antibiotic / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / molecular function inhibitor activity / positive regulation of DNA biosynthetic process / negative regulation of kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to lithium ion / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cochlea development / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / protein kinase inhibitor activity / Prolactin receptor signaling / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / protein monoubiquitination / Constitutive Signaling by AKT1 E17K in Cancer / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / negative regulation of vascular associated smooth muscle cell proliferation / Regulation of APC/C activators between G1/S and early anaphase / cullin family protein binding / centrosome duplication / telomere maintenance in response to DNA damage / inner ear development / protein K63-linked ubiquitination / cellular response to organic cyclic compound / G0 and Early G1 / Telomere Extension By Telomerase / negative regulation of mitotic cell cycle / positive regulation of double-strand break repair via homologous recombination / cellular response to nitric oxide / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ubiquitin-like ligase-substrate adaptor activity / Activation of the pre-replicative complex / response to amino acid / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / protein K48-linked ubiquitination / animal organ regeneration Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Horn-Ghetko, D. / Prabu, J.R. / Schulman, B.A. | |||||||||
Funding support | Germany, 2items
| |||||||||
Citation | Journal: Nature / Year: 2021 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7b5r.cif.gz | 280.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7b5r.ent.gz | 221 KB | Display | PDB format |
PDBx/mmJSON format | 7b5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b5r_validation.pdf.gz | 953.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7b5r_full_validation.pdf.gz | 982.4 KB | Display | |
Data in XML | 7b5r_validation.xml.gz | 58.7 KB | Display | |
Data in CIF | 7b5r_validation.cif.gz | 86.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b5r ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b5r | HTTPS FTP |
-Related structure data
Related structure data | 12048MC 7b5lC 7b5mC 7b5nC 7b5sC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 3 types, 3 molecules CKY
#1: Protein | Mass: 89800.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616 |
---|---|
#3: Protein | Mass: 9679.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CKS1B, CKS1, PNAS-143, PNAS-16 / Production host: Escherichia coli (E. coli) / References: UniProt: P61024 |
#6: Protein | Mass: 48609.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P20248 |
-S-phase kinase-associated protein ... , 2 types, 2 molecules TS
#2: Protein | Mass: 47817.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKP2, FBXL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13309 |
---|---|
#4: Protein | Mass: 18679.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli (E. coli) / References: UniProt: P63208 |
-Cyclin-dependent kinase ... , 2 types, 2 molecules LP
#5: Protein | Mass: 34056.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase |
---|---|
#7: Protein | Mass: 22188.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDKN1B, KIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P46527 |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 composite map. Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.30 MDa |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213213 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|