[English] 日本語
Yorodumi- PDB-8oj5: 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oj5 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | RIBOSOME / ER / UFMylation / recycling | ||||||||||||||||||
Function / homology | Function and homology information UFM1 ligase activity / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / UFM1 transferase activity / positive regulation of metallopeptidase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum ...UFM1 ligase activity / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / UFM1 transferase activity / positive regulation of metallopeptidase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum / negative regulation of protein kinase activity by regulation of protein phosphorylation / negative regulation of IRE1-mediated unfolded protein response / regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of I-kappaB phosphorylation / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / regulation of intracellular estrogen receptor signaling pathway / eukaryotic 80S initiation complex / negative regulation of protein neddylation / positive regulation of proteasomal protein catabolic process / negative regulation of protein serine/threonine kinase activity / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / mitotic G2/M transition checkpoint / TORC2 complex binding / Transferases; Acyltransferases; Aminoacyltransferases / GAIT complex / cartilage development / middle ear morphogenesis / regulation of canonical NF-kappaB signal transduction / reticulophagy / mitogen-activated protein kinase binding / cytoplasmic side of rough endoplasmic reticulum membrane / A band / alpha-beta T cell differentiation / 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 / response to L-glutamate / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of neuron differentiation / negative regulation of ubiquitin protein ligase activity / optic nerve development / negative regulation of protein import into nucleus / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / negative regulation of NF-kappaB transcription factor activity / lung morphogenesis / male meiosis I / Protein hydroxylation / ubiquitin-like protein ligase binding / macrophage chemotaxis / Peptide chain elongation / mitotic G2 DNA damage checkpoint signaling / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / NF-kappaB binding / GTP hydrolysis and joining of the 60S ribosomal subunit / RHOA GTPase cycle / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / hematopoietic stem cell differentiation / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / protein targeting / cellular response to interleukin-4 / endomembrane system / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of autophagy / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / endoplasmic reticulum unfolded protein response / Maturation of protein E / positive regulation of glial cell proliferation / Maturation of protein E / ER Quality Control Compartment (ERQC) / MDM2/MDM4 family protein binding / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / negative regulation of protein ubiquitination / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||
Authors | Penchev, I. / DaRosa, P.A. / Peter, J.J. / Kulathu, Y. / Becker, T. / Beckmann, R. / Kopito, R. | ||||||||||||||||||
Funding support | European Union, Germany, United Kingdom, United States, 5items
| ||||||||||||||||||
Citation | Journal: Nature / Year: 2024 Title: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Authors: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / ...Authors: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / Roland Beckmann / Ron R Kopito / Abstract: Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that ...Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER). UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8oj5.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8oj5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8oj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oj5_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8oj5_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8oj5_validation.xml.gz | 219 KB | Display | |
Data in CIF | 8oj5_validation.cif.gz | 383.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/8oj5 ftp://data.pdbj.org/pub/pdb/validation_reports/oj/8oj5 | HTTPS FTP |
-Related structure data
Related structure data | 16905MC 8ohdC 8oj0C 8oj8C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 3 types, 3 molecules 578
#1: RNA chain | Mass: 1640166.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T |
---|---|
#2: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: GenBank: 23898 |
#3: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: GenBank: 555853 |
-Protein , 6 types, 6 molecules ABCDLILm
#4: Protein | Mass: 89722.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UFL1, KIAA0776, MAXER, NLBP, RCAD / Production host: Escherichia coli BL21 (bacteria) References: UniProt: O94874, Transferases; Acyltransferases; Aminoacyltransferases |
---|---|
#5: Protein | Mass: 56977.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5RAP3, IC53, LZAP, MSTP016, OK/SW-cl.114, PP1553 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q96JB5 |
#6: Protein | Mass: 35663.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDRGK1, C20orf116, UFBP1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q96HY6 |
#7: Protein | Mass: 9128.552 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UFM1, C13orf20, BM-002 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61960 |
#16: Protein | Mass: 24552.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q96L21 |
#45: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P62987 |
+60S ribosomal protein ... , 40 types, 40 molecules LALBLCLDLELFLGLHLJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLf...
-Non-polymers , 2 types, 225 molecules
#50: Chemical | ChemComp-MG / #51: Chemical | ChemComp-ZN / |
---|
-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: E3-UFM1 complex bound to the 60S ribosome / Type: RIBOSOME / Entity ID: #1-#49 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35935 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL |