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- PDB-8bzr: UFC1-UFM1 conjugate -

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Basic information

Entry
Database: PDB / ID: 8bzr
TitleUFC1-UFM1 conjugate
Components
  • Ubiquitin-fold modifier 1
  • Ubiquitin-fold modifier-conjugating enzyme 1
KeywordsLIGASE / ubiquitin-fold modifier conjugating enzyme 1
Function / homology
Function and homology information


UFM1 conjugating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / negative regulation of protein import into nucleus / response to endoplasmic reticulum stress / brain development / negative regulation of apoptotic process ...UFM1 conjugating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / negative regulation of protein import into nucleus / response to endoplasmic reticulum stress / brain development / negative regulation of apoptotic process / endoplasmic reticulum / extracellular exosome / nucleus / cytoplasm
Similarity search - Function
Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-fold modifier 1 / Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsMagnussen, H.M. / Kulathu, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008172/1 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 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-fold modifier-conjugating enzyme 1
B: Ubiquitin-fold modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,41610
Polymers28,9192
Non-polymers4978
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, UFC1 and UFM1 are covalently linked via an isopeptide bond (UFC1 C116K and UFM1 G83).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint18 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.005, 56.427, 86.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

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Components

#1: Protein Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1


Mass: 19923.889 Da / Num. of mol.: 1 / Mutation: C116K
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
#2: Protein Ubiquitin-fold modifier 1


Mass: 8995.383 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 (E. coli) / References: UniProt: P61960
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% v/v PEG400, 0.1M Tris, 0.2M Na citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→47.33 Å / Num. obs: 26839 / % possible obs: 99.1 % / Redundancy: 12.5 % / CC1/2: 0.998 / Net I/σ(I): 9.2
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1192 / CC1/2: 0.27 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3evx

3evx


Resolution: 1.781→47.334 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.563 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2264 1360 5.075 %
Rwork0.1822 25440 -
all0.184 --
obs-26800 98.948 %
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: 32.094 Å2
Baniso -1Baniso -2Baniso -3
1-1.417 Å20 Å2-0 Å2
2---1.57 Å20 Å2
3---0.153 Å2
Refinement stepCycle: LAST / Resolution: 1.781→47.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 32 106 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161910
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.6572688
X-RAY DIFFRACTIONr_angle_other_deg0.5761.5674393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.342511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66710315
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.51080
X-RAY DIFFRACTIONr_chiral_restr0.0820.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_nbd_refined0.2140.2362
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21691
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2994
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.286
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0840.211
X-RAY DIFFRACTIONr_nbd_other0.1630.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.216
X-RAY DIFFRACTIONr_mcbond_it2.5332.773979
X-RAY DIFFRACTIONr_mcbond_other2.5322.772978
X-RAY DIFFRACTIONr_mcangle_it3.2284.9551222
X-RAY DIFFRACTIONr_mcangle_other3.2264.9561223
X-RAY DIFFRACTIONr_scbond_it4.3683.2381007
X-RAY DIFFRACTIONr_scbond_other4.3663.2391008
X-RAY DIFFRACTIONr_scangle_it6.3355.6771466
X-RAY DIFFRACTIONr_scangle_other6.3335.6771467
X-RAY DIFFRACTIONr_lrange_it7.231.6632210
X-RAY DIFFRACTIONr_lrange_other7.08730.5162190
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
1.781-1.8270.374990.33816750.3419610.8480.88690.46410.339
1.827-1.8770.338880.31117480.31319260.8770.88895.32710.302
1.877-1.9310.267870.26317890.26318810.9370.93699.73420.249
1.931-1.990.249950.22917210.2318170.9450.95699.9450.21
1.99-2.0560.242640.19416760.19617400.9490.971000.173
2.056-2.1280.2291000.1916010.19317010.9610.9721000.169
2.128-2.2080.232940.16115610.16516560.9650.98199.93960.138
2.208-2.2980.21880.1614900.16315780.9730.9821000.133
2.298-2.40.247840.15714440.16215280.9620.9831000.132
2.4-2.5160.217770.13813890.14214660.9690.9871000.114
2.516-2.6520.187550.14113490.14214040.9810.9881000.116
2.652-2.8120.196750.15412600.15613350.9760.9871000.129
2.812-3.0060.172540.14611850.14712390.9830.9891000.121
3.006-3.2460.221710.15610990.1611700.970.9851000.136
3.246-3.5540.227540.1710330.17310870.9680.9831000.154
3.554-3.970.233440.1669400.1699840.9750.9841000.158
3.97-4.5790.215400.1768340.1788740.970.9831000.172
4.579-5.5950.258430.1957110.1997540.970.9821000.196
5.595-7.8580.275230.225910.2226140.970.9761000.217
7.858-47.3340.15250.233430.2243680.9850.9661000.249
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)
10.29-0.0664-0.01930.36830.04080.1908-0.03590.0307-0.01490.0371-0.0008-0.04870.0002-0.04590.03680.0332-0.00180.00230.0162-0.00460.043613.938317.99099.256
21.0785-0.0496-0.70490.7749-0.13340.61170.0262-0.02220.0063-0.02240.0054-0.0286-0.05210.0039-0.03160.042-0.00170.00570.0041-0.00170.024413.7866-8.447121.7069
Refinement TLS groupSelection: ALL

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