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- EMDB-55686: Murine RNF213 bound to maltoheptaose -

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Basic information

Entry
Database: EMDB / ID: EMD-55686
TitleMurine RNF213 bound to maltoheptaose
Map dataComposite map
Sample
  • Complex: E3 ubiquitin-protein ligase RNF213
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
KeywordsE3 ubiquitin ligase / AAA+ ATPase / CBM20 / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / xenophagy / lipid droplet formation / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / Antigen processing: Ubiquitination & Proteasome degradation / regulation of lipid metabolic process / protein K63-linked ubiquitination / protein autoubiquitination ...lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / xenophagy / lipid droplet formation / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / Antigen processing: Ubiquitination & Proteasome degradation / regulation of lipid metabolic process / protein K63-linked ubiquitination / protein autoubiquitination / lipid droplet / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ubiquitin-protein transferase activity / angiogenesis / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / defense response to bacterium / protein ubiquitination / nucleolus / ATP hydrolysis activity / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / : / : / : / RNF213 AAA domain / RNF213 AAA domain / RNF213 AAA domain ...: / : / : / : / : / : / : / RNF213 AAA domain / RNF213 AAA domain / RNF213 AAA domain / RNF213 AAA domain / RNF213 AAA domain / RNF213 AAA domain / RNF213 stalk domain / E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF213
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsYip MCJ / Naydenova K / Randow F
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
European Molecular Biology Organization (EMBO)European Union
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: Nature / Year: 2026
Title: Quality control of glycogen through direct ubiquitylation by RNF213.
Authors: Matthew C J Yip / Katerina Naydenova / Elsje G Otten / Alexander Heatley / Agnes Moe / Leonie Anton / Lucía de Los Reyes-Ramírez / Helen E Jolin / Frederic Langevin / Michal Wiacek / ...Authors: Matthew C J Yip / Katerina Naydenova / Elsje G Otten / Alexander Heatley / Agnes Moe / Leonie Anton / Lucía de Los Reyes-Ramírez / Helen E Jolin / Frederic Langevin / Michal Wiacek / Catarina Franco / Anne Bertolotti / Wanda Kukulski / Andrew N J McKenzie / Felix Randow /
Abstract: Quality control of biomolecules is vital for organismal health. While DNA repair and protein quality control are well understood, how cells monitor other important biomolecules such as glycogen ...Quality control of biomolecules is vital for organismal health. While DNA repair and protein quality control are well understood, how cells monitor other important biomolecules such as glycogen remains ill-defined. The accumulation of aberrant, poorly branched glycogen into insoluble polyglucosan bodies causes severe disease. Here, we discover autophagy of ubiquitylated aberrant glycogen as a previously unrecognized quality control mechanism safeguarding the brain from polyglucosan buildup. This mechanism depends on the E3 ubiquitin ligase RNF213. Mice lacking ligase activity in RNF213 accumulate polyglucosan in cerebellum, pons, and hippocampus. Using cells engineered to produce polyglucosan, we show that RNF213 selectively ubiquitylates abnormal glycogen. Cryo-EM analysis of RNF213 bound to glycogen-derived maltoheptaose revealed its CBM20 domain binds linear oligosaccharides. Disrupting carbohydrate binding results in gain of E3 ligase activity towards physiological glycogen, indicating the CBM20 domain limits RNF213 activity towards physiological glycogen. Epistasis analysis places RNF213 upstream of LUBAC, suggesting a hierarchical network of multiple E3 ligases surveying glycogen quality. Ubiquitylated polyglucosan recruits the autophagy receptors SQSTM1, TAX1BP1, and optineurin, thereby triggering uptake into autophagosomes. These findings identify RNF213 as a quality control factor preventing polyglucosan accumulation in astrocytes through direct ubiquitylation of polyglucosan, revealing an essential role for non-protein ubiquitylation in glycogen quality control.
History
DepositionNov 12, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55686.png

Downloads & links

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Map

FileDownload / File: emd_55686.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 300 pix.
= 373.2 Å		1.24 Å/pix.
x 300 pix.
= 373.2 Å		1.24 Å/pix.
x 300 pix.
= 373.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.244 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0022465708 - 0.062281158
Average (Standard dev.)0.00028298429 (±0.0012112327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 373.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : E3 ubiquitin-protein ligase RNF213

EntireName: E3 ubiquitin-protein ligase RNF213
Components
  • Complex: E3 ubiquitin-protein ligase RNF213
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: E3 ubiquitin-protein ligase RNF213

SupramoleculeName: E3 ubiquitin-protein ligase RNF213 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: E3 ubiquitin-protein ligase RNF213

MacromoleculeName: E3 ubiquitin-protein ligase RNF213 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 589.281562 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAMS MECPQCGHVS SEKAPKFCSE CGQKLPSAAT VQGDLKNDNT LVVSSTPEG KTEQGAVLRE EEVLLSSTDP GKELEKPEES DSNASWTTQM SKKEKRRRKR QGTISSSEAP SSGLWSLDMP P SPGSHNSA ...String:
MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAMS MECPQCGHVS SEKAPKFCSE CGQKLPSAAT VQGDLKNDNT LVVSSTPEG KTEQGAVLRE EEVLLSSTDP GKELEKPEES DSNASWTTQM SKKEKRRRKR QGTISSSEAP SSGLWSLDMP P SPGSHNSA LPQNQAQQGG AASQPGHPLD TENMPMEDGF VHTEGSGSPL QGQAAERTDA QSNLAPSDLA EVKDLNTSKP SV DKGLPLD GGPALSAFKG HPKMTDASQK APLPESKGET SGQEKKVPPI DAAASPVKTA GKETGEDVRK PKPSPVSPVA SKH GDQEAE LKGKLATPVR KSNEGGNTQP EDQRKPGEGR NFAAAVKTQQ AAAPQQAAAP EPTSAFNPRD TVTVYFHAIV SRHF GFNPE EHKVYVRGGE GLGQKGWTDA CEMYCTQDLH DLGSLVEGKM DIPRQSLDKP IPYKYVIHRG GSSKDTVEYE FIYEQ AQKK GEHVNRCLRV VSTSLGNGDW HQYDDIICMR STGFFQQAKN RILDSTRKEL LKGKKQAAVV MLDRIFSVLQ PWSDIN LQS FMTQFLQFYS VVREPMIHDG RARKWTSLQY EEKEVWTNLW EHVKKQMAPF LEGKSGESLP ADCPVRSKLT LGLSILF MV EAAEFTVPKK DLDSLCYLLI PSAGSPEALH SDLSPVLRIR QRWRIYLTNL CLRCIDERCD RWLGILPLLH TCMQKSPP K KNSKSQPEDT WAGLEGISFS EFRDKAPTRS QPLQFMQSKM ALLRVDEYLF RSWLSVVPLE SLSSYLENSI DYLSDVPVR VLDCLQGISY RLPGLRKISN QNMKKDVENV FKMLMHLVDI YQHRIFGENL LQIYLTECLT LHETVCNITA NHQFFEIPAL SAELICKLL ELSPPGHTDE GLPEKSYEDL VTSTLQEALA TTRNWLRSLF KSRMLSISSA YVRLTYSEEM AVWRRLVEIG F PEKHGWKG SLLGDMEGRL KQEPPRLQIS FFCSSQCRDG GLHDSVSRSF EKCVIEAVSS ACQSQTSVLE GLSCQDLQKF GT LLSAVIT KSWPVHNGEP VFDVDEIFKY LLKWPDVRQL FELCGTNEKI IDNITEEGRQ LMATAESVFQ KVAGELENGT IVV GQLELI LEHQSQFLDI WNLNRRRLPS QEKACDVRSL LKRRRDDLLF LKQEKRYVES LLRQLGRVKH LVQVDFGNIE IIHS QDLSN KKLNEAVIKL PNSSSYKRET HYCLSPDIRE MASKLDSLKD SHIFQDFWQE TAESLNTLDK DPRELKVSLP EVLEY LYNP CYDNFYTLYE NLKSGKITFA EVDAIFKDFV DKYDELKNDL KFMCTMNPQD QKGWISERVG QIKEYHTLHQ AVSSAK VIL QVRRALGVTG DFSVLNPLLN FADSFEDFGN EKLDQISPQF IKAKQLLQDI SEPRQRCLEE LARQTELVAW LHKALED IN ELKVFVDLAS ISAGENDIDV DRVACFHDAV QGYASLLYKM DERTNFSDFM NHLQELWRAL DNDQHLPDKL KDSARNLE W LKTVKESHGS VELSSLSLAT AINSRGVYVI EAPKDGQKIS PDTVLRLLLP DGHGYPEALR TYSTEELKEL LNKLMLMSG KKDHNSNTEV EKFSEVFSNM QRLVHVFIKL HCAGNMLFRT WTAKVYCCPD GGIFMNFGLE LLSQLTEKGD VIQLLGALCR QMEDFLDNW KTVVAQKRAE HFYLNFYTAE QLVYLSSELR KPRPSEAALM MLSFIKGKCT VQDLVQATSA CESKADRYCL R EVMKKLPQ QLLSEPSLMG KLQVIMMQSL VYMSAFLPHC LDLDALGRCL AHLATMGGTP VERPLPKGLQ AGQPNLILCG HS EVLPAAL AIYMQAPRQP LPTFDEVLLC TPATTIEEVE LLLRRCLTSG SQGHKVYSLL FADQLSYEVG CQAEEFFQSL CTR AHREDY QLVILCDAAR EHCYIPSTFS QYKVPLVPQA PLPNIQAYLQ SHYQVPKRLL SAATVFRDGL CVGIVTSERA GVGK SLYVN TLHTKLKAKL RDETVPLKII RLTEPHLDEN QVLSALLPFL KEKYQKMPVI FHIDISTSVQ TGIPIFLFKL LILQY LMDI NGKIWRRSPG HLYLVEIPQG LSVQPKRSSK LNARAPLFKF LDLFPKVTCR PPKEVIDMEL TPERSHTDPA MDPVEF CSE AFQRPYQYLK RFHQQQNLDT FQYEKGSVEG SPEECLQHFL IYCGLINPSW SELRNFAWFL NCQLKDCEAS IFCKSAF TG DTLRGFKNFV VTFMILMARD FATPTLHTSD QSPGRQSVTI GEVVEEDLAP FSLRKRWESE PHPYVFFNGD HMTMTFIG F HLETNNNGYV DAINPSNGKV IKKDVMTKEL FDGLRLQRVP FNIDFDNLPR YEKLERLCLA LGIEWPIDPD ETYELTTDN MLKILAIEMR FRCGIPVIIM GETGCGKTRL IKFLSDLKRG SVEAETMKLV KVHGGTTPSM IYSKVKEAER TAFSNKAQHK LDTILFFDE ANTTEAVSCI KEILCDRTVD GEHLHEDSGL HIIAACNPYR KHSQEMILRL ESAGLGYRVS AEETADRLGS I PLRQLVYR VHALPPSLIP LVWDFGQLND SAEKLYIQQI VQRLVDSVSV NPSETCVIAD VLSASQMFMR KRENECGFVS LR DVERCVK VFRWFHDHSD MLLKELDKFL HESSDSTHTF ERDPVLWSLV MAIGVCYHAS LEEKASYRTA IARCFPKPYN SSR AILDEV THVQDLFLRG APIRTNIARN LALKENVFMM VICIELKIPL FLVGKPGSSK SLAKIIVADA MQGQAAFSEL FRCL KQVHL VSFQCSPHST PQGIISTFKQ CARFQQGKDL GQYVSVVVLD EVGLAEDSPK MPLKTLHPLL EDGCIEDDPA PYKKV GFVG ISNWALDPAK MNRGIFVSRG SPNEKELIES AEGICSSDRL VQDKIRGYFA PFAKAYETVC QKQDKEFFGL RDYYSL IKM VFAKAKASKR GLSPQDITHA VLRNFSGKDN IQALSIFTAS LPEARYKEEV STVELIKQNI YPGPQASSRG LDGAESR YL LVLTRNYVAL QILQQTFFEG QQPEIIFGSS FPQDQEYTQI CRNINRVKIC METGKMVVLL NLQNLYESLY DALNQYYV Y LGGQKYVDLG LGTHRVKCRV HTAFRLIVIE EKDVVYKQFP VPLINRLEKH YLDMNTVLQP WQKSIVQELQ QWAHEFADV KADQFIARHK YSPADVFIGY HSDACASVVL QAVERQGCRD LTEELYRKVS EEARSILLDC ATPDAVVRLS GSSLGSFTAK QLSQEYYYA QQHNSFVDFL QAHLRMTHHE CRAVFTEITT FSRLLTGNDC DVLASELRGL ASKPVVLSLQ QYDTEYSFLK D VRSWLTNP GKRKVLVIQA DFDDGTRSAQ LVASAKYTAI NEINKTQGTK DFVFVYFVTK LSRMGSGTSY VGFHGGLWRS VH IDDLRRS TIMASDVTKL QNVTISQLFK PEDKPEQEEM EIETSQSKEL AEEQMEVEDS EEMKKASDPR SCDCSQFLDT TRL VQSCVQ GAVGMLRDQN ESCARNMRRV TILLDLLNED NTRNASFLRE SKMRLHVLLN KQEENQVRSL KEWVTREAAN QDAL QEAGT FRHTLWKRVQ DVVTPILASM IAHIDRDGNL ELLAQPDSPA WVQDLWMFIY SDIKFLNISL VLNNTRSNSE MSFIL VQSH MNLLKDAYNA VPFSWRIRDY LEELWVQAQY ITDTEGLSKK FVEIFQKTPL GVFLAQFPVA QQQKLLQSYL KDFLLL TMK VSSREELMFL QMALWSCLRE LQEASGTPDE TYKFPLSLPW VHLAFQHFRT RLQNFSRILT IHPQVLSSLS QAAEKHS LA GCEMTLDAFA AMACAEMLKG DLLKPSPKAW LQLVKNLSTP LELVCSEGYL CDSGSMTRSV IQEVRALWNR IFSIALFV E HVLLGTESHI PELSPLVTTY VSLLDKCLEE DSNLKTCRPF VAVMTTLCDC KDKASKKFSR FGIQPCFICH GDAQDPVCL PCDHVYCLRC IQTWLIPGQM MCPYCLTDLP DKFSPTVSQD HRKAIEKHAQ FRHMCNSFFV DLVSTMCFKD NTPPEKSVID TLLSLLFVQ KELLRDASQK HREHTKSLSP FDDVVDQTPV IRSVLLKLLL KYSFHEVKDY IQNYLTQLEK KAFLTEDKTE L YLLFISCL EDSVHQKTSA GCRNLEQVLR EEGHFLRTYS PGLQGQEPVR IASVEYLQEV ARVRLCLDLA ADFLSELQEG SE LAEDKRR FLKHVEEFCT RVNNDWHRVY LVRKLSSQRG MEFVQSFSKQ GHPCQWVFPR KVIAQQKDHV SLMDRYLVHG NEY KAVRDA TAKAVLECKT LDIGNALMAC RSPKPQQTAY LLLALYTEVA ALYRSPNGSL HPEAKQLEAV NKFIKESKIL SDPN IRCFA RSLVDNTLPL LKIRSANSIL KGTVTEMAVH VATILLCGHN QILKPLRNLA FYPVNMANAF LPTMPEDLLV HARTW RGLE NVTWYTCPRG HPCSVGECGR PMQESTCLDC GLPVGGLNHT PHEGFSAIRN NEDRTQTGHV LGSPQSSGVA EVSDRG QSP VVFILTRLLT HLAMLVGATH NPQALTVIIK PWVQDPQGFL QQHIQRDLEQ LTKMLGRSAD ETIHVVHLIL SSLLRVQ SH GVLNFNAELS TKGCRNNWEK HFETLLLREL KHLDKNLPAI NALISQDERI SSNPVTKIIY GDPATFLPHL PQKSIIHC S KIWSCRRKIT VEYLQHIVEQ KNGKETVPVL WHFLQKEAEL RLVKFLPEIL ALQRDLVKQF QNVSRVEYSS IRGFIHSHS SDGLRKLLHD RITIFLSTWN ALRRSLETNG EIKLPKDYCC SDLDLDAEFE VILPRRQGLG LCGTALVSYL ISLHNNMVYT VQKFSNEDN SYSVDISEVA DLHVISYEVE RDLNPLILSN CQYQVQQGGE TSQEFDLEKI QRQISSRFLQ GKPRLTLKGI P TLVYRRDW NYEHLFMDIK NKMAQSSLPN LAISTISGQL QSYSDACEAL SIIEITLGFL STAGGDPGMD LNVYIEEVLR MC DQTAQVL KAFSRCQLRH IIALWQFLSA HKSEQRLRLN KELFREIDVQ YKEELSTQHQ RLLGTFLNEA GLDAFLLELH EMI VLKLKG PRAANSFNPN WSLKDTLVSY METKDSDILS EVESQFPEEI LMSSCISVWK IAATRKWDRQ SR

UniProtKB: E3 ubiquitin-protein ligase RNF213

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 31.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 557952
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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