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- EMDB-55652: Composite map of LRRC58- EloB/C-CDO1 in complex with neddylated C... -

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Basic information

Entry
Database: EMDB / ID: EMD-55652
TitleComposite map of LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Map data
Sample
  • Complex: LRRC58-EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
    • Protein or peptide: LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
KeywordsCullin / E3 Ligase / Ubiquitin / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsStier L / Andree GA / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101098161European Union
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Nat Commun / Year: 2026
Title: Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1.
Authors: Gisele A Andree / Luca J Stier / Kerstin Schmiederer / Alina S Thielen / Luis Schmid / Samuel A Maiwald / Karthik V Gottemukkala / Jiale Du / Susanne von Gronau / Claudia Strasser / Judith ...Authors: Gisele A Andree / Luca J Stier / Kerstin Schmiederer / Alina S Thielen / Luis Schmid / Samuel A Maiwald / Karthik V Gottemukkala / Jiale Du / Susanne von Gronau / Claudia Strasser / Judith Müller / Lukas T Henneberg / Camille Guyot / Gary Kleiger / Matthias Mann / Peter J Murray / Brenda A Schulman /
Abstract: Cellular responses to amino acid fluctuations often hinge on ubiquitin-mediated control of metabolic enzymes, yet the underlying E3 ligase pathways remain poorly defined. Using quantitative ...Cellular responses to amino acid fluctuations often hinge on ubiquitin-mediated control of metabolic enzymes, yet the underlying E3 ligase pathways remain poorly defined. Using quantitative proteomics and active cullin-RING ligase (CRL) profiling, we identify LRRC58 as a cysteine-responsive substrate receptor whose stability increases sharply under cysteine starvation. Proteomics reveals an inverse relationship between LRRC58 and the metabolic enzyme cysteine dioxygenase 1 (CDO1), suggesting a cysteine-linked regulatory axis. Biochemical reconstitution and cryo-EM structures show that LRRC58 forms an active CUL2- or CUL5-based CRL that selectively positions CDO1 for ubiquitylation at Lys8. Disease mutant versions of CDO1 mapping to the LRRC58 interface and impaired for the endogenous ubiquitylation pathway were degraded through orthogonal targeting by a VHL-based degrader. Together, our proteomics-guided discovery pipeline, cellular stability studies, and structural analyses uncover a metabolically-tuned LRRC58-CDO1 pathway that links cysteine availability to selective proteasomal turnover, reveals principles of metabolite-regulated CRL activity, and showcases mechanisms distinguishing endogenous and targeted protein degradation.
History
DepositionNov 11, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55652.png

Downloads & links

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Map

FileDownload / File: emd_55652.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 432 pix.
= 367.718 Å		0.85 Å/pix.
x 432 pix.
= 367.718 Å		0.85 Å/pix.
x 432 pix.
= 367.718 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.364
Minimum - Maximum-0.0014611358 - 2.542193
Average (Standard dev.)0.00149139 (±0.03032701)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 367.71838 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : LRRC58-EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub

EntireName: LRRC58-EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Components
  • Complex: LRRC58-EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
    • Protein or peptide: LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub

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Supramolecule #1: LRRC58-EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub

SupramoleculeName: LRRC58-EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub

MacromoleculeName: LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MEQTEVLCPR TLADLIRILH QLFAGDEVNV EEVQAIMEAY ESDPTEWAMY AKFDQYRYTR NLVDQGNGKF NLMILAWGEG HGSSIHDHTN SHSFLKMLQG NLKETLFAWP DKKSNEMVKK SERVLRENQA AYINDSVGLH RVENISHTEP AVSLHLYSPP FDTSHAFDQR ...String:
MEQTEVLCPR TLADLIRILH QLFAGDEVNV EEVQAIMEAY ESDPTEWAMY AKFDQYRYTR NLVDQGNGKF NLMILAWGEG HGSSIHDHTN SHSFLKMLQG NLKETLFAWP DKKSNEMVKK SERVLRENQA AYINDSVGLH RVENISHTEP AVSLHLYSPP FDTSHAFDQR TGHKNKVTMT FHSKFGIRTP NATSGSLENN MDGEEKTYG GCEGPDAMYV KLISSDGHEF IVKREHALTS GTIKAMLSGP GQFAENETNE VNFREIPSHV LSKVCMYFTY KVRYTNSSTE IPEFPIAPEI ALELLMAANF LDC MDVFLM IRRHKTTIFT DAKESSTVFE LKRIVEGILK RPPDEQRLYK DDQLLDDGKT LGECGFTSQT ARPQAPATVG LAFRADDTFE ALCIEPFSSP PELPDVMKPQ DSGSSANEQA VQ MAAAMDV DTPSGTNSGA GKKRFEVKKW NAVALWAWDI VVDNCAICRN HIMDLCIECQ ANQASATSEE CTVAWGVCNH AFHFHCISRW LKTRQVCPLD NREWEFQKYG H MSLKPRVV DFDETWNKLL TTIKAVVMLE YVERATWNDR FSDIYALCVA YPEPLGERLY TETKIFLENH VRHLHKRVLE SEEQVLVMYH RYWEEYSKGA DYMDCLYRYL NTQFIKKNKL TEADLQYGYG GVDMNEPLME IGELALDMWR KLMVEPLQAI LIRMLLREIK NDRGGEDPNQ KVIHGVINSF VHVEQYKKKF PLKFYQEIFE SPFLTETGEY YKQEASNLLQ ESNCSQYMEK VLGRLKDEEI RCRKYLHPSS YTKVIHECQQ RMVADHLQFL HAECHNIIRQ EKKNDMANMY VLLRAVSTGL PHMIQELQNH IHDEGLRATS NLTQENMPTL FVESVLEVHG KFVQLINTVL NGDQHFMSAL DKALTSVVNY REPKSVCKAP ELLAKYCDNL LKKSAKGMTE NEVEDRLTSF ITVFKYIDDK DVFQKFYARM LAKRLIHGLS MSMDSEEAMI NKLKQACGYE FTSKLHRMYT DMSVSADLNN KFNNFIKNQD TVIDLGISFQ IYVLQAGAWP LTQAPSSTFA IPQELEKSVQ MFELFYSQHF SGRKLTWLHY LCTGEVKMNY LGKPYVAMVT TYQMAVLLAF NNSETVSYKE LQDSTQMNEK ELTKTIKSLL DVKMINHDSE KEDIDAESSF SLNMNFSSKR TKFKITTSMQ KDTPQEMEQT RSAVDEDRKM YLQAAIVRIM KARKVLRHNA LIQEVISQSR ARFNPSISMI KKCIEVLIDK QYIERSQASA DEYSYVA MD SDEGYNYEFD EDEECSEEDS GAEEEEDEDD DEPDDDTLDL GEVELVEPGL GVGGERDGLL CGETGGGGGS ALGPGGGGGG GGGGGGGGPG HEQEEDYRYE VLTAEQILQH MVECIREVNE VIQNPATITR ILLSHFNWDK EKLMERYFDG NLEKLFAECH VINPSKKSRT RQMNTRSSAQ DMPCQICYLN YPNSYFTGLE CGHKFCMQCW SEYLTTKIME EGMGQTISCP AHGCDILVDD NTVMRLITDS KVKLKYQHLI TNSFVECNRL LKWCPAPDCH HVVKVQYPDA KPVRCKCGRQ FCFNCGENWH DPVKCKWLKK WIKKCDDDSE TSNWIAANTK ECPKCHVTIE KDGGCNHMVC RNQNCKAEFC WVCLGPWEPH GSAWYNCNRY NEDDAKAARD AQERSRAALQ RYLFYCNRYM NHMQSLRFEH KLYAQVKQKM EEMQQHNMSW IEVQFLKKAV DVLCQCRATL MYTYVFAFYL KKNNQSIIFE NNQADLENAT EVLSGYLERD ISQDSLQDIK QKVQDKYRYC ESRRRVLLQH VHEGYEKDLW EYIED MQIF VKTLTGKTIT LEVEPSDTIE NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLSDYNIQKE STLHLVLRLR G MEEAGAAV VTAGEAELNW SRLSVSTETL ESELEARGEE RRGAREALLR LLLPHNRLVS LPRALGSGFP HLQLLDVSGN ALTALGPELL ALRGLRTLLA KNNRLGGPSA LPKGLAQSPL CRSLQVLNLS GNCFQEVPAS LLELRALQTL SLGGNQLQSI PAEIENLQSL ECLYLGGNFI KEIPPELGNL PSLNYLVLCD NKIQSIPPQL SQLHSLRSLS LHNNLLTYLP REILNLIHLE ELSLRGNPLV VRFVRDLTYD PPTLLELAAR TIKIRNISYT PYDLPGNLLR YLGSASNCPN PKCGGVYFDC CVRQIKFVDF CGKYRLPLMH YLCSPECSSP CSSASHSSTS QSESDSEDEA SVAARRMQKV LLG MLIKVK TLTGKEIEID IEPTDKVERI KERVEEKEGI PPQQQRLIYS GKQMNDEKTA ADYKILGGSV LHLVLALRGG

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 1462967
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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