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- EMDB-18381: UFL1 E3 ligase bound 60S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-18381
TitleUFL1 E3 ligase bound 60S ribosome
Map dataDeepEMhancer map.
Sample
  • Complex: UFM1 ribosome E3 ligase complex bound to 60S ribosome
    • Protein or peptide: 60S ribosomal protein L10a
    • Protein or peptide: E3 UFM1-protein ligase 1
    • Protein or peptide: CDK5 regulatory subunit-associated protein 3
    • Protein or peptide: DDRGK domain-containing protein 1
    • Protein or peptide: Ubiquitin-fold modifier 1
KeywordsUFM1 / Ligase / Ribosome / Complex
Function / homology
Function and homology information


UFM1 ligase activity / UFM1-modified protein reader activity / positive regulation of reticulophagy / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / UFM1 transferase activity / positive regulation of metallopeptidase activity / protein ufmylation / protein K69-linked ufmylation ...UFM1 ligase activity / UFM1-modified protein reader activity / positive regulation of reticulophagy / 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 proteolysis involved in protein catabolic process / positive regulation of protein localization to endoplasmic reticulum / negative regulation of protein kinase activity by regulation of protein phosphorylation / positive regulation of plasma cell differentiation / negative regulation of IRE1-mediated unfolded protein response / regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of I-kappaB phosphorylation / negative regulation of T cell mediated immune response to tumor cell / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / negative regulation of T cell activation / regulation of intracellular estrogen receptor signaling pathway / ribosome disassembly / negative regulation of protein serine/threonine kinase activity / positive regulation of proteasomal protein catabolic process / mitotic G2/M transition checkpoint / Transferases; Acyltransferases; Aminoacyltransferases / regulation of canonical NF-kappaB signal transduction / cartilage development / mitogen-activated protein kinase binding / reticulophagy / regulation of neuron differentiation / response to L-glutamate / negative regulation of NF-kappaB transcription factor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of PERK-mediated unfolded protein response / ubiquitin-like protein ligase binding / mitotic G2 DNA damage checkpoint signaling / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / 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 / NF-kappaB binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / RHOA GTPase cycle / hematopoietic stem cell differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / ubiquitin-like ligase-substrate adaptor activity / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of autophagy / negative regulation of MAP kinase activity / endoplasmic reticulum unfolded protein response / positive regulation of glial cell proliferation / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / regulation of mitotic cell cycle / cytosolic ribosome / response to endoplasmic reticulum stress / cyclin binding / negative regulation of protein phosphorylation / rescue of stalled ribosome / liver development / erythrocyte differentiation / DNA damage checkpoint signaling / positive regulation of protein ubiquitination / brain development / regulation of protein stability / negative regulation of protein catabolic process / Regulation of expression of SLITs and ROBOs / positive regulation of protein localization to nucleus / osteoblast differentiation / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of protein localization / site of double-strand break / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / cytoplasmic translation / cytosolic large ribosomal subunit / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / cell population proliferation / postsynaptic density / protein stabilization / structural constituent of ribosome / positive regulation of cell migration / neuron projection / translation / negative regulation of gene expression / intracellular membrane-bounded organelle / focal adhesion
Similarity search - Function
Ubiquitin-fold modifier 1 / CDK5 regulatory subunit-associated protein 3 / CDK5 regulatory subunit-associated protein 3 / DDRGK domain containing protein / : / Ubiquitin fold modifier 1 protein / DDRGK domain / DDRGK / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1 ...Ubiquitin-fold modifier 1 / CDK5 regulatory subunit-associated protein 3 / CDK5 regulatory subunit-associated protein 3 / DDRGK domain containing protein / : / Ubiquitin fold modifier 1 protein / DDRGK domain / DDRGK / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1 / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMakhlouf L / Zeqiraj E / Kulathu Y
Funding support United Kingdom, European Union, 4 items
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, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18381.png

Downloads & links

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Map

FileDownload / File: emd_18381.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer map.
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 588 pix.
= 435.12 Å		0.74 Å/pix.
x 588 pix.
= 435.12 Å		0.74 Å/pix.
x 588 pix.
= 435.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
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Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0017910122 - 1.9982334
Average (Standard dev.)0.00035842624 (±0.011887603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 435.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18381_msk_1.map
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Additional map: Raw map.

Fileemd_18381_additional_1.map
AnnotationRaw map.
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Half map: #2

Fileemd_18381_half_map_1.map
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Half map: #1

Fileemd_18381_half_map_2.map
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Sample components

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Entire : UFM1 ribosome E3 ligase complex bound to 60S ribosome

EntireName: UFM1 ribosome E3 ligase complex bound to 60S ribosome
Components
  • Complex: UFM1 ribosome E3 ligase complex bound to 60S ribosome
    • Protein or peptide: 60S ribosomal protein L10a
    • Protein or peptide: E3 UFM1-protein ligase 1
    • Protein or peptide: CDK5 regulatory subunit-associated protein 3
    • Protein or peptide: DDRGK domain-containing protein 1
    • Protein or peptide: Ubiquitin-fold modifier 1

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Supramolecule #1: UFM1 ribosome E3 ligase complex bound to 60S ribosome

SupramoleculeName: UFM1 ribosome E3 ligase complex bound to 60S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 60S ribosomal protein L10a

MacromoleculeName: 60S ribosomal protein L10a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.879422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSKVSRDTL YEAVREVLHG NQRKRRKFLE TVELQISLKN YDPQKDKRFS GTVRLKSTPR PKFSVCVLGD QQHCDEAKAV DIPHMDIEA LKKLNKNKKL VKKLAKKYDA FLASESLIKQ IPRILGPGLN KAGKFPSLLT HNENMVAKVD EVKSTIKFQM K KVLCLAVA ...String:
MSSKVSRDTL YEAVREVLHG NQRKRRKFLE TVELQISLKN YDPQKDKRFS GTVRLKSTPR PKFSVCVLGD QQHCDEAKAV DIPHMDIEA LKKLNKNKKL VKKLAKKYDA FLASESLIKQ IPRILGPGLN KAGKFPSLLT HNENMVAKVD EVKSTIKFQM K KVLCLAVA VGHVKMTDDE LVYNIHLAVN FLVSLLKKNW QNVRALYIKS TMGKPQRLY

UniProtKB: Large ribosomal subunit protein uL1

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Macromolecule #2: E3 UFM1-protein ligase 1

MacromoleculeName: E3 UFM1-protein ligase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.591234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHEN LYFQGMADAW EEIRRLAADF QRAQFAEATQ RLSERNCIEI VNKLIAQKQL EVVHTLDGKE YITPAQISKE MRDELHVRG GRVNIVDLQQ VINVDLIHIE NRIGDIIKSE KHVQLVLGQL IDENYLDRLA EEVNDKLQES GQVTISELCK T YDLPGNFL ...String:
MGHHHHHHEN LYFQGMADAW EEIRRLAADF QRAQFAEATQ RLSERNCIEI VNKLIAQKQL EVVHTLDGKE YITPAQISKE MRDELHVRG GRVNIVDLQQ VINVDLIHIE NRIGDIIKSE KHVQLVLGQL IDENYLDRLA EEVNDKLQES GQVTISELCK T YDLPGNFL TQALTQRLGR IISGHIDLDN RGVIFTEAFV ARHKARIRGL FSAITRPTAV NSLISKYGFQ EQLLYSVLEE LV NSGRLRG TVVGGRQDKA VFVPDIYSRT QSTWVDSFFR QNGYLEFDAL SRLGIPDAVS YIKKRYKTTQ LLFLKAACVG QGL VDQVEA SVEEAISSGT WVDIAPLLPT SLSVEDAAIL LQQVMRAFSK QASTVVFSDT VVVSEKFIND CTELFRELMH QKAE KEMKN NPVHLITEED LKQISTLESV STSKKDKKDE RRRKATEGSG SMRGGGGGNA REYKIKKVKK KGRKDDDSDD ESQSS HTGK KKPEISFMFQ DEIEDFLRKH IQDAPEEFIS ELAEYLIKPL NKTYLEVVRS VFMSSTTSAS GTGRKRTIKD LQEEVS NLY NNIRLFEKGM KFFADDTQAA LTKHLLKSVC TDITNLIFNF LASDLMMAVD DPAAITSEIR KKILSKLSEE TKVALTK LH NSLNEKSIED FISCLDSAAE ACDIMVKRGD KKRERQILFQ HRQALAEQLK VTEDPALILH LTSVLLFQFS THSMLHAP G RCVPQIIAFL NSKIPEDQHA LLVKYQGLVV KQLVSQSKKT GQGDYPLNNE LDKEQEDVAS TTRKELQELS SSIKDLVLK SRKSSVTEE

UniProtKB: E3 UFM1-protein ligase 1

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Macromolecule #3: CDK5 regulatory subunit-associated protein 3

MacromoleculeName: CDK5 regulatory subunit-associated protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.458938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLVDMEDHQ HVPIDIQTSK LLDWLVDRRH CSLKWQSLVL TIREKINAAI QDMPESEEIA QLLSGSYIHY FHCLRILDLL KGTEASTKN IFGRYSSQRM KDWQEIIALY EKDNTYLVEL SSLLVRNVNY EIPSLKKQIA KCQQLQQEYS RKEEECQAGA A EMREQFYH ...String:
GPLVDMEDHQ HVPIDIQTSK LLDWLVDRRH CSLKWQSLVL TIREKINAAI QDMPESEEIA QLLSGSYIHY FHCLRILDLL KGTEASTKN IFGRYSSQRM KDWQEIIALY EKDNTYLVEL SSLLVRNVNY EIPSLKKQIA KCQQLQQEYS RKEEECQAGA A EMREQFYH SCKQYGITGE NVRGELLALV KDLPSQLAEI GAAAQQSLGE AIDVYQASVG FVCESPTEQV LPMLRFVQKR GN STVYEWR TGTEPSVVER PHLEELPEQV AEDAIDWGDF GVEAVSEGTD SGISAEAAGI DWGIFPESDS KDPGGDGIDW GDD AVALQI TVLEAGTQAP EGVARGPDAL TLLEYTETRN QFLDELMELE IFLAQRAVEL SEEADVLSVS QFQLAPAILQ GQTK EKMVT MVSVLEDLIG KLTSLQLQHL FMILASPRYV DRVTEFLQQK LKQSQLLALK KELMVQKQQE ALEEQAALEP KLDLL LEKT KELQKLIEAD ISKRYSGRPV NLMGTSL

UniProtKB: CDK5 regulatory subunit-associated protein 3

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Macromolecule #4: DDRGK domain-containing protein 1

MacromoleculeName: DDRGK domain-containing protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.644445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWSHPQFEKL EVLFQGPASA GQEPLHNEEL AGAGRVAQPG PLEPEEPRAG GRPRRRRDLG SRLQAQRRAQ RVAWAEADEN EEEAVILAQ EEEGVEKPAE THLSGKIGAK KLRKLEEKQA RKAQREAEEA EREERKRLES QREAEWKKEE ERLRLEEEQK E EEERKARE ...String:
MWSHPQFEKL EVLFQGPASA GQEPLHNEEL AGAGRVAQPG PLEPEEPRAG GRPRRRRDLG SRLQAQRRAQ RVAWAEADEN EEEAVILAQ EEEGVEKPAE THLSGKIGAK KLRKLEEKQA RKAQREAEEA EREERKRLES QREAEWKKEE ERLRLEEEQK E EEERKARE EQAQREHEEY LKLKEAFVVE EEGVGETMTE EQSQSFLTEF INYIKQSKVV LLEDLASQVG LRTQDTINRI QD LLAEGTI TGVIDDRGKF IYITPEELAA VANFIRQRGR VSIAELAQAS NSLIAWGRES PAQAPA

UniProtKB: DDRGK domain-containing protein 1

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Macromolecule #5: Ubiquitin-fold modifier 1

MacromoleculeName: Ubiquitin-fold modifier 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.236628 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGSMSKVSF KITLTSDPRL PYKVLSVPES TPFTAVLKFA AEEFKVPAAT SAIITNDGIG INPAQTAGNV FLKHGSELRI IPRDRVG

UniProtKB: Ubiquitin-fold modifier 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration7.7 mg/mL
BufferpH: 7.5
Details: 25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 59394 / Average exposure time: 2.67 sec. / Average electron dose: 33.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Model generated ab intio.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299008
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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