[English] 日本語
Yorodumi- PDB-9gmo: eIF6-bound pre-60S large ribosomal subunit incorporating mutant uL16 -
+Open data
-Basic information
Entry | Database: PDB / ID: 9gmo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | eIF6-bound pre-60S large ribosomal subunit incorporating mutant uL16 | |||||||||
Components |
| |||||||||
Keywords | RIBOSOME / Complex / pre-60S / uL16 | |||||||||
Function / homology | Function and homology information preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development ...preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / embryonic brain development / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / positive regulation of kinase activity / GAIT complex / middle ear morphogenesis / regulation of glycolytic process / regulation of reactive oxygen species metabolic process / A band / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / negative regulation of ubiquitin protein ligase activity / intrinsic apoptotic signaling pathway in response to oxidative stress / response to aldosterone / retinal ganglion cell axon guidance / homeostatic process / G1 to G0 transition / maturation of 5.8S rRNA / lung morphogenesis / macrophage chemotaxis / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / blastocyst development / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / protein localization to nucleus / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / cellular response to interleukin-4 / protein targeting / ribosomal subunit export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cytosolic ribosome / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / Maturation of protein E / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Endosomal Sorting Complex Required For Transport (ESCRT) / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / embryo implantation / translation initiation factor activity / maturation of LSU-rRNA / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å | |||||||||
Authors | Bothe, A. / Ban, N. / Kostova, K. | |||||||||
Funding support | Switzerland, 2items
| |||||||||
Citation | Journal: bioRxiv / Year: 2024 Title: ZNF574 is a Quality Control Factor For Defective Ribosome Biogenesis Intermediates. Authors: Jared Akers / Adrian Bothe / Hanna Suh / Carmen Jung / Zachary Stolp / Tanushree Ghosh / Liewei Yan / Yuming Wang / Tarabryn Grismer / Andreas Reyes / Tianyi Hu / Shouling Xu / Nenad Ban / Kamena Kostova Abstract: Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. This ...Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. This complexity creates a large genetic space in which pathogenic mutations can occur. Dead-end ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway, which we term the Ribosome Assembly Surveillance Pathway (RASP). Loss of ZNF574 results in the accumulation of faulty biogenesis intermediates that interfere with global ribosome production, further emphasizing the role of RASP in protein homeostasis and cellular health. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9gmo.cif.gz | 4.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9gmo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9gmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9gmo_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9gmo_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 9gmo_validation.xml.gz | 223.5 KB | Display | |
Data in CIF | 9gmo_validation.cif.gz | 368.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/9gmo ftp://data.pdbj.org/pub/pdb/validation_reports/gm/9gmo | HTTPS FTP |
-Related structure data
Related structure data | 51452MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 3 types, 3 molecules ABC
#1: RNA chain | Mass: 1639262.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
---|---|
#2: RNA chain | Mass: 38346.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898 |
#3: RNA chain | Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853 |
+60S ribosomal protein ... , 36 types, 36 molecules DEFGIJKLMNOPQRTUVWXYZabcdefijk...
-Large ribosomal subunit protein ... , 4 types, 4 molecules HSmp
#8: Protein | Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878 |
---|---|
#19: Protein | Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254 |
#39: Protein | Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124 |
#42: Protein | Mass: 23610.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: residues 102-111 (wild type numbering) are not present in this variant Source: (natural) Homo sapiens (human) / References: UniProt: P27635 |
-Protein , 3 types, 3 molecules gh0
#33: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987 |
---|---|
#34: Protein | Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56537 |
#46: Protein | Mass: 54357.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969S3 |
-Non-polymers , 7 types, 396 molecules
#47: Chemical | ChemComp-MG / #48: Chemical | ChemComp-K / #49: Chemical | #50: Chemical | ChemComp-GTP / | #51: Chemical | ChemComp-EPE / | #52: Chemical | ChemComp-ZN / #53: Water | ChemComp-HOH / | |
---|
-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: pre-60S-eIF6 complex incorporating uL16 protein with an internal deletion Type: RIBOSOME / Entity ID: #1-#46 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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 / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6360 |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193000 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 8a3d Accession code: 8a3d / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.06 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
|