[English] 日本語
Yorodumi
- PDB-8qfc: UFL1 E3 ligase bound 60S ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qfc
TitleUFL1 E3 ligase bound 60S ribosome
Components
  • 60S ribosomal protein L10a
  • CDK5 regulatory subunit-associated protein 3
  • DDRGK domain-containing protein 1
  • E3 UFM1-protein ligase 1
  • Ubiquitin-fold modifier 1
KeywordsLIGASE / UFM1 / Ribosome / Complex
Function / homology
Function and homology information


UFM1 ligase activity / apoptotic nuclear changes / regulation of phosphatase activity / definitive erythrocyte differentiation / positive regulation of metallopeptidase activity / UFM1 transferase activity / protein localization to endoplasmic reticulum / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding ...UFM1 ligase activity / apoptotic nuclear changes / regulation of phosphatase activity / definitive erythrocyte differentiation / positive regulation of metallopeptidase activity / UFM1 transferase activity / protein localization to endoplasmic reticulum / 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 cell cycle G1/S phase transition / positive regulation of I-kappaB phosphorylation / regulation of intracellular estrogen receptor signaling pathway / positive regulation of proteasomal protein catabolic process / negative regulation of protein serine/threonine kinase activity / mitotic G2/M transition checkpoint / Transferases; Acyltransferases; Aminoacyltransferases / reticulophagy / cartilage development / regulation of canonical NF-kappaB signal transduction / mitogen-activated protein kinase binding / positive regulation of signal transduction by p53 class mediator / response to L-glutamate / regulation of neuron differentiation / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Peptide chain elongation / mitotic G2 DNA damage checkpoint signaling / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / GTP hydrolysis and joining of the 60S ribosomal subunit / NF-kappaB binding / RHOA GTPase cycle / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / hematopoietic stem cell differentiation / MDM2/MDM4 family protein binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of autophagy / endoplasmic reticulum unfolded protein response / positive regulation of glial cell proliferation / maturation of LSU-rRNA / negative regulation of protein ubiquitination / regulation of mitotic cell cycle / response to endoplasmic reticulum stress / cyclin binding / cytosolic ribosome / erythrocyte differentiation / negative regulation of protein phosphorylation / liver development / negative regulation of MAP kinase activity / DNA damage checkpoint signaling / positive regulation of protein ubiquitination / brain development / regulation of protein stability / negative regulation of protein catabolic process / osteoblast differentiation / Regulation of expression of SLITs and ROBOs / positive regulation of protein localization to nucleus / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / site of double-strand break / cytoplasmic translation / positive regulation of NF-kappaB transcription factor activity / cytosolic large ribosomal subunit / regulation of inflammatory response / cell population proliferation / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / structural constituent of ribosome / neuron projection / positive regulation of cell migration / translation / negative regulation of gene expression / focal adhesion / intracellular membrane-bounded organelle / DNA repair / centrosome / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding
Similarity search - Function
CDK5 regulatory subunit-associated protein 3 / CDK5 regulatory subunit-associated protein 3 / DDRGK domain containing protein / DDRGK domain / DDRGK / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1 / Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / Ribosomal protein L1, conserved site ...CDK5 regulatory subunit-associated protein 3 / CDK5 regulatory subunit-associated protein 3 / DDRGK domain containing protein / DDRGK domain / DDRGK / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1 / Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Ubiquitin-fold modifier 1 / E3 UFM1-protein ligase 1 / Large ribosomal subunit protein uL1 / DDRGK domain-containing protein 1 / CDK5 regulatory subunit-associated protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMakhlouf, L. / Zeqiraj, E. / Kulathu, Y.
Funding support United Kingdom, European Union, 4items
OrganizationGrant numberCountry
Wellcome Trust222531/Z/21/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008172/1 United Kingdom
European Research Council (ERC)677623European Union
Medical Research Council (MRC, United Kingdom)MC_UU_00018/3 United Kingdom
CitationJournal: Nature / Year: 2024
Title: The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons.
Authors: Linda Makhlouf / Joshua J Peter / Helge M Magnussen / Rohan Thakur / David Millrine / Thomas C Minshull / Grace Harrison / Joby Varghese / Frederic Lamoliatte / Martina Foglizzo / Thomas ...Authors: Linda Makhlouf / Joshua J Peter / Helge M Magnussen / Rohan Thakur / David Millrine / Thomas C Minshull / Grace Harrison / Joby Varghese / Frederic Lamoliatte / Martina Foglizzo / Thomas Macartney / Antonio N Calabrese / Elton Zeqiraj / Yogesh Kulathu /
Abstract: Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24). This modification, ...Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24). This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. ). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a 'writer' to a 'reader' module that recognizes its product-UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER.
History
DepositionSep 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 3, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 60S ribosomal protein L10a
B: E3 UFM1-protein ligase 1
C: CDK5 regulatory subunit-associated protein 3
D: DDRGK domain-containing protein 1
E: Ubiquitin-fold modifier 1


Theoretical massNumber of molelcules
Total (without water)217,8115
Polymers217,8115
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein 60S ribosomal protein L10a / / CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down- ...CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24879.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL10A, NEDD6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62906
#2: Protein E3 UFM1-protein ligase 1 / E3 UFM1-protein transferase 1 / Multiple alpha-helix protein located at ER / Novel LZAP-binding ...E3 UFM1-protein transferase 1 / Multiple alpha-helix protein located at ER / Novel LZAP-binding protein / Regulator of C53/LZAP and DDRGK1


Mass: 91591.234 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 (E. coli)
References: UniProt: O94874, Transferases; Acyltransferases; Aminoacyltransferases
#3: Protein CDK5 regulatory subunit-associated protein 3 / CDK5 activator-binding protein C53 / LXXLL/leucine-zipper-containing ARF-binding protein / Protein HSF-27


Mass: 57458.938 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 (E. coli) / References: UniProt: Q96JB5
#4: Protein DDRGK domain-containing protein 1 / Dashurin / UFM1-binding and PCI domain-containing protein 1


Mass: 34644.445 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 (E. coli) / References: UniProt: Q96HY6
#5: Protein Ubiquitin-fold modifier 1


Mass: 9236.628 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFM1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8C2YGR4

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: UFM1 ribosome E3 ligase complex bound to 60S ribosome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Details: 25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT
SpecimenConc.: 7.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm
Image recordingAverage exposure time: 2.67 sec. / Electron dose: 33.4 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 59394
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
2EPU3.2.0image acquisition
4CTFFIND4CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 299008 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411126
ELECTRON MICROSCOPYf_angle_d0.53215139
ELECTRON MICROSCOPYf_dihedral_angle_d4.3341565
ELECTRON MICROSCOPYf_chiral_restr0.0381873
ELECTRON MICROSCOPYf_plane_restr0.0041935

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more