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- PDB-8c0d: UFL1/DDRGK1 bound to UFC1 -

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Basic information

Entry
Database: PDB / ID: 8c0d
TitleUFL1/DDRGK1 bound to UFC1
Components
  • DDRGK domain-containing protein 1
  • E3 UFM1-protein ligase 1
  • Ubiquitin-fold modifier-conjugating enzyme 1
KeywordsLIGASE / UFM1 / E3 ligase / ubiquitin / UFBP1
Function / homology
Function and homology information


positive regulation of metallopeptidase activity / : / positive regulation of I-kappaB phosphorylation / UFM1 ligase activity / UFM1-modified protein reader activity / positive regulation of reticulophagy / UFM1 conjugating enzyme activity / UFM1 transferase activity / positive regulation of protein localization to endoplasmic reticulum / protein K69-linked ufmylation ...positive regulation of metallopeptidase activity / : / positive regulation of I-kappaB phosphorylation / UFM1 ligase activity / UFM1-modified protein reader activity / positive regulation of reticulophagy / UFM1 conjugating enzyme activity / UFM1 transferase activity / positive regulation of protein localization to endoplasmic reticulum / protein K69-linked ufmylation / positive regulation of proteolysis involved in protein catabolic process / protein ufmylation / positive regulation of plasma cell differentiation / negative regulation of IRE1-mediated unfolded protein response / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of type II interferon production / negative regulation of T cell mediated immune response to tumor cell / protein localization to endoplasmic reticulum / positive regulation of cell cycle G1/S phase transition / negative regulation of T cell activation / regulation of intracellular estrogen receptor signaling pathway / positive regulation of proteasomal protein catabolic process / ribosome disassembly / Transferases; Acyltransferases; Aminoacyltransferases / regulation of canonical NF-kappaB signal transduction / reticulophagy / cartilage development / response to L-glutamate / negative regulation of NF-kappaB transcription factor activity / negative regulation of PERK-mediated unfolded protein response / ubiquitin-like protein ligase binding / RHOA GTPase cycle / hematopoietic stem cell differentiation / positive regulation of glial cell proliferation / positive regulation of autophagy / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / rescue of stalled ribosome / negative regulation of protein ubiquitination / response to endoplasmic reticulum stress / erythrocyte differentiation / DNA damage checkpoint signaling / brain development / regulation of protein stability / positive regulation of NF-kappaB transcription factor activity / 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 / regulation of inflammatory response / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / neuron projection / protein stabilization / positive regulation of cell migration / negative regulation of gene expression / DNA repair / positive regulation of cell population proliferation / DNA damage response / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / nucleolus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
DDRGK domain containing protein / : / DDRGK domain / DDRGK / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1-like domain / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-conjugating enzyme/RWD-like ...DDRGK domain containing protein / : / DDRGK domain / DDRGK / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1-like domain / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-conjugating enzyme/RWD-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 UFM1-protein ligase 1 / DDRGK domain-containing protein 1 / Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.564 Å
AuthorsMagnussen, H.M. / Kulathu, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W007401/1 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
DepositionDec 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 UFM1-protein ligase 1
B: DDRGK domain-containing protein 1
C: Ubiquitin-fold modifier-conjugating enzyme 1
D: E3 UFM1-protein ligase 1
E: DDRGK domain-containing protein 1
F: Ubiquitin-fold modifier-conjugating enzyme 1


Theoretical massNumber of molelcules
Total (without water)108,1956
Polymers108,1956
Non-polymers00
Water1267
1
A: E3 UFM1-protein ligase 1
B: DDRGK domain-containing protein 1
C: Ubiquitin-fold modifier-conjugating enzyme 1


Theoretical massNumber of molelcules
Total (without water)54,0973
Polymers54,0973
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-30 kcal/mol
Surface area22880 Å2
MethodPISA
2
D: E3 UFM1-protein ligase 1
E: DDRGK domain-containing protein 1
F: Ubiquitin-fold modifier-conjugating enzyme 1


Theoretical massNumber of molelcules
Total (without water)54,0973
Polymers54,0973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-31 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.210, 124.565, 131.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-4 - 162
2111A-4 - 162
3221A213 - 305
4221A213 - 305
5331A5 - 166
6331A5 - 166

NCS ensembles :
IDDetails
1Global NCS restraints between domains: 1 2
2Global NCS restraints between domains: 3 4
3Global NCS restraints between domains: 5 6

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Components

#1: 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: 22350.311 Da / Num. of mol.: 2
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
#2: Protein DDRGK domain-containing protein 1 / Dashurin / UFM1-binding and PCI domain-containing protein 1


Mass: 12177.643 Da / Num. of mol.: 2
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
#3: Protein Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1


Mass: 19569.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1M HEPES, 1.03M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.564→65.732 Å / Num. obs: 25858 / % possible obs: 93.8 % / Redundancy: 12.8 % / CC1/2: 0.997 / Net I/σ(I): 8.2
Reflection shellResolution: 2.564→2.892 Å / Num. unique obs: 1293 / CC1/2: 0.674

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.564→65.732 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.86 / SU B: 30.585 / SU ML: 0.293 / Cross valid method: FREE R-VALUE / ESU R Free: 0.452
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2858 1222 4.726 %
Rwork0.232 24636 -
all0.235 --
obs-25858 60.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 47.927 Å2
Baniso -1Baniso -2Baniso -3
1--1.116 Å2-0 Å20 Å2
2--1.319 Å2-0 Å2
3----0.203 Å2
Refinement stepCycle: LAST / Resolution: 2.564→65.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 0 7 6518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126627
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166189
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.6389011
X-RAY DIFFRACTIONr_angle_other_deg0.5951.56714120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.431540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53101067
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.8110306
X-RAY DIFFRACTIONr_chiral_restr0.070.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021532
X-RAY DIFFRACTIONr_nbd_refined0.2440.21450
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.25956
X-RAY DIFFRACTIONr_nbtor_refined0.1980.23360
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.214
X-RAY DIFFRACTIONr_nbd_other0.2170.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.25
X-RAY DIFFRACTIONr_mcbond_it2.6562.9113392
X-RAY DIFFRACTIONr_mcbond_other2.6562.9123391
X-RAY DIFFRACTIONr_mcangle_it4.2155.2244226
X-RAY DIFFRACTIONr_mcangle_other4.2155.2244227
X-RAY DIFFRACTIONr_scbond_it3.3533.0843235
X-RAY DIFFRACTIONr_scbond_other3.3533.0833236
X-RAY DIFFRACTIONr_scangle_it5.3485.5444785
X-RAY DIFFRACTIONr_scangle_other5.3475.5444786
X-RAY DIFFRACTIONr_lrange_it7.91835.17327219
X-RAY DIFFRACTIONr_lrange_other7.91835.17327219
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Weight Biso : 0.5 / Weight position: 0.05

Ens-IDDom-IDRms dev Biso (Å2)Rms dev position (Å)
113.665440.16772
123.665440.16772
234.109260.24891
244.109260.24891
353.056040.20318
363.056040.20318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.564-2.630.3640.251830.25530880.8940.9642.81740.244
2.63-2.7020.39340.2761790.27830110.7780.9426.07770.276
2.702-2.780.345160.2783160.28129050.8720.93911.42860.276
2.78-2.8660.293240.294920.2928620.9440.93718.02940.284
2.866-2.960.32450.2886440.2927650.9190.93524.91860.281
2.96-3.0630.418570.2839700.2926800.8870.9438.32090.278
3.063-3.1790.309470.2813480.28125820.9390.94454.02790.269
3.179-3.3080.325850.27217090.27425030.9340.94771.6740.261
3.308-3.4550.2951060.26421200.26523820.9460.95693.45090.254
3.455-3.6230.2591000.2421960.24122980.9590.96699.9130.223
3.623-3.8180.277930.22420940.22621880.9480.97299.95430.21
3.818-4.0490.261950.20419650.20720610.9540.97699.95150.196
4.049-4.3270.277860.20318680.20619540.950.9761000.193
4.327-4.6720.235760.19717720.19818480.9670.9781000.188
4.672-5.1160.238790.18916050.19116840.9670.9771000.182
5.116-5.7150.33920.24614600.25115520.9360.9621000.239
5.715-6.5910.39730.27412910.27913640.9020.9551000.273
6.591-8.0520.298750.24511010.24911760.9480.9631000.25
8.052-11.3030.218500.28900.2019400.9760.9781000.216
11.303-65.7320.364150.3085330.315650.9120.94396.99110.356
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.012-0.75511.31050.7867-0.69343.47160.07370.20330.02390.0918-0.0917-0.13070.20490.77940.0180.1538-0.0071-0.02080.2215-0.02760.137867.4738-11.848450.185
26.31140.86770.25840.9088-0.38031.61770.0940.14210.20590.0873-0.05650.2786-0.0092-0.2264-0.03750.1377-0.0267-0.05030.068-0.0210.151740.9124-25.166938.8148
32.53011.3997-1.16955.8707-1.43033.41560.0626-0.2610.02210.4761-0.11170.2646-0.0229-0.26180.04910.06070.00460.00880.0965-0.02980.030139.81816.246131.751
40.86020.87821.1971.34320.49963.16430.1375-0.24780.1432-0.0644-0.05540.29020.3729-0.836-0.08210.1678-0.0506-0.02130.25230.04890.0792-29.0245-11.597515.6444
55.40070.0752.17441.1971-0.24583.05680.48110.0138-0.22290.063-0.1864-0.41350.39920.247-0.29470.25440.0505-0.16510.05460.01550.2405-5.4255-26.131727.5664
62.3158-0.68-0.77085.72992.66863.6387-0.02040.15540.0025-0.31930.1194-0.0438-0.07880.2906-0.09890.0583-0.0239-0.0160.0571-0.00170.01031.09513.441434.3617
Refinement TLS groupSelection: ALL

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