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- EMDB-59440: murine RNF213 (Y434A) (focused refinement of CBM20 domain) -

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Basic information

Entry
Database: EMDB / ID: EMD-59440
Titlemurine RNF213 (Y434A) (focused refinement of CBM20 domain)
Map datamurine RNF213 (Y434A) (focused refinement of CBM20 domain)
Sample
  • Complex: Murine RNF213 (Y434A)
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
KeywordsE3 ubiquitin ligase / AAA+ ATPase / CBM20 / SUGAR BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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
DepositionAug 16, 2026-
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_59440.png

Downloads & links

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Map

FileDownload / File: emd_59440.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmurine RNF213 (Y434A) (focused refinement of CBM20 domain)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 450 pix.
= 488.835 Å		1.09 Å/pix.
x 450 pix.
= 488.835 Å		1.09 Å/pix.
x 450 pix.
= 488.835 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0863 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.03815392 - 0.060757905
Average (Standard dev.)-0.000010230745 (±0.00040321815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 488.83502 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: murine RNF213 (Y434A) (focused refinement of CBM20 domain) - half 1

Fileemd_59440_half_map_1.map
Annotationmurine RNF213 (Y434A) (focused refinement of CBM20 domain) - half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: murine RNF213 (Y434A) (focused refinement of CBM20 domain) - half 2

Fileemd_59440_half_map_2.map
Annotationmurine RNF213 (Y434A) (focused refinement of CBM20 domain) - half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Murine RNF213 (Y434A)

EntireName: Murine RNF213 (Y434A)
Components
  • Complex: Murine RNF213 (Y434A)
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213

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Supramolecule #1: Murine RNF213 (Y434A)

SupramoleculeName: Murine RNF213 (Y434A) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 / Details: Y434A mutant / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 519.31075 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAMS MECPQCGHVS SEKAPKFCSE CGQKLPSAAT VQGDLKNDNT LVVSSTPEGK TEQGAVLREE EVLLSSTDPG KELEKPEESD SNASWTTQMS KKEKRRRKRQ GTISSSEAPS SGLWSLDMPP SPGSHNSALP ...String:
MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAMS MECPQCGHVS SEKAPKFCSE CGQKLPSAAT VQGDLKNDNT LVVSSTPEGK TEQGAVLREE EVLLSSTDPG KELEKPEESD SNASWTTQMS KKEKRRRKRQ GTISSSEAPS SGLWSLDMPP SPGSHNSALP QNQAQQGGAA SQPGHPLDTE NMPMEDGFVH TEGSGSPLQG QAAERTDAQS NLAPSDLAEV KDLNTSKPSV DKGLPLDGGP ALSAFKGHPK MTDASQKAPL PESKGETSGQ EKKVPPIDAA ASPVKTAGKE TGEDVRKPKP SPVSPVASKH GDQEAELKGK LATPVRKSNE GGNTQPEDQR KPGEGRNFAA AVKTQQAAAP QQAAAPEPTS AFNPRDTVTV YFHAIVSRHF GFNPEEHKVY VRGGEGLGQK GWTDACEMYC TQDLHDLGSL VEGKMDIPRQ SLDKPIPYKY VIHRGGSSKD TVEAEFIYEQ AQKKGEHVNR CLRVVSTSLG NGDWHQYDDI ICMRSTGFFQ QAKNRILDST RKELLKGKKQ AAVVMLDRIF SVLQPWSDIN LQSFMTQFLQ FYSVVREPMI HDGRARKWTS LQYEEKEVWT NLWEHVKKQM APFLEGKSGE SLPADCPVRS KLTLGLSILF MVEAAEFTVP KKDLDSLCYL LIPSAGSPEA LHSDLSPVLR IRQRWRIYLT NLCLRCIDER CDRWLGILPL LHTCMQKSPP KKNSKSQPED TWAGLEGISF SEFRDKAPTR SQPLQFMQSK MALLRVDEYL FRSWLSVVPL ESLSSYLENS IDYLSDVPVR VLDCLQGISY RLPGLRKISN QNMKKDVENV FKMLMHLVDI YQHRIFGENL LQIYLTECLT LHETVCNITA NHQFFEIPAL SAELICKLLE LSPPGHTDEG LPEKSYEDLV TSTLQEALAT TRNWLRSLFK SRMLSISSAY VRLTYSEEMA VWRRLVEIGF PEKHGWKGSL LGDMEGRLKQ EPPRLQISFF CSSQCRDGGL HDSVSRSFEK CVIEAVSSAC QSQTSVLEGL SCQDLQKFGT LLSAVITKSW PVHNGEPVFD VDEIFKYLLK WPDVRQLFEL CGTNEKIIDN ITEEGRQLMA TAESVFQKVA GELENGTIVV GQLELILEHQ SQFLDIWNLN RRRLPSQEKA CDVRSLLKRR RDDLLFLKQE KRYVESLLRQ LGRVKHLVQV DFGNIEIIHS QDLSNKKLNE AVIKLPNSSS YKRETHYCLS PDIREMASKL DSLKDSHIFQ DFWQETAESL NTLDKDPREL KVSLPEVLEY LYNPCYDNFY TLYENLKSGK ITFAEVDAIF KDFVDKYDEL KNDLKFMCTM NPQDQKGWIS ERVGQIKEYH TLHQAVSSAK VILQVRRALG VTGDFSVLNP LLNFADSFED FGNEKLDQIS PQFIKAKQLL QDISEPRQRC LEELARQTEL VAWLHKALED INELKVFVDL ASISAGENDI DVDRVACFHD AVQGYASLLY KMDERTNFSD FMNHLQELWR ALDNDQHLPD KLKDSARNLE WLKTVKESHG SVELSSLSLA TAINSRGVYV IEAPKDGQKI SPDTVLRLLL PDGHGYPEAL RTYSTEELKE LLNKLMLMSG KKDHNSNTEV EKFSEVFSNM QRLVHVFIKL HCAGNMLFRT WTAKVYCCPD GGIFMNFGLE LLSQLTEKGD VIQLLGALCR QMEDFLDNWK TVVAQKRAEH FYLNFYTAEQ LVYLSSELRK PRPSEAALMM LSFIKGKCTV QDLVQATSAC ESKADRYCLR EVMKKLPQQL LSEPSLMGKL QVIMMQSLVY MSAFLPHCLD LDALGRCLAH LATMGGTPVE RPLPKGLQAG QPNLILCGHS EVLPAALAIY MQAPRQPLPT FDEVLLCTPA TTIEEVELLL RRCLTSGSQG HKVYSLLFAD QLSYEVGCQA EEFFQSLCTR AHREDYQLVI LCDAAREHCY IPSTFSQYKV PLVPQAPLPN IQAYLQSHYQ VPKRLLSAAT VFRDGLCVGI VTSERAGVGK SLYVNTLHTK LKAKLRDETV PLKIIRLTEP HLDENQVLSA LLPFLKEKYQ KMPVIFHIDI STSVQTGIPI FLFKLLILQY LMDINGKIWR RSPGHLYLVE IPQGLSVQPK RSSKLNARAP LFKFLDLFPK VTCRPPKEVI DMELTPERSH TDPAMDPVEF CSEAFQRPYQ YLKRFHQQQN LDTFQYEKGS VEGSPEECLQ HFLIYCGLIN PSWSELRNFA WFLNCQLKDC EASIFCKSAF TGDTLRGFKN FVVTFMILMA RDFATPTLHT SDQSPGRQSV TIGEVVEEDL APFSLRKRWE SEPHPYVFFN GDHMTMTFIG FHLETNNNGY VDAINPSNGK VIKKDVMTKE LFDGLRLQRV PFNIDFDNLP RYEKLERLCL ALGIEWPIDP DETYELTTDN MLKILAIEMR FRCGIPVIIM GETGCGKTRL IKFLSDLKRG SVEAETMKLV KVHGGTTPSM IYSKVKEAER TAFSNKAQHK LDTILFFDEA NTTEAVSCIK EILCDRTVDG EHLHEDSGLH IIAACNPYRK HSQEMILRLE SAGLGYRVSA EETADRLGSI PLRQLVYRVH ALPPSLIPLV WDFGQLNDSA EKLYIQQIVQ RLVDSVSVNP SETCVIADVL SASQMFMRKR ENECGFVSLR DVERCVKVFR WFHDHSDMLL KELDKFLHES SDSTHTFERD PVLWSLVMAI GVCYHASLEE KASYRTAIAR CFPKPYNSSR AILDEVTHVQ DLFLRGAPIR TNIARNLALK ENVFMMVICI ELKIPLFLVG KPGSSKSLAK IIVADAMQGQ AAFSELFRCL KQVHLVSFQC SPHSTPQGII STFKQCARFQ QGKDLGQYVS VVVLDEVGLA EDSPKMPLKT LHPLLEDGCI EDDPAPYKKV GFVGISNWAL DPAKMNRGIF VSRGSPNEKE LIESAEGICS SDRLVQDKIR GYFAPFAKAY ETVCQKQDKE FFGLRDYYSL IKMVFAKAKA SKRGLSPQDI THAVLRNFSG KDNIQALSIF TASLPEARYK EEVSTVELIK QNIYPGPQAS SRGLDGAESR YLLVLTRNYV ALQILQQTFF EGQQPEIIFG SSFPQDQEYT QICRNINRVK ICMETGKMVV LLNLQNLYES LYDALNQYYV YLGGQKYVDL GLGTHRVKCR VHTAFRLIVI EEKDVVYKQF PVPLINRLEK HYLDMNTVLQ PWQKSIVQEL QQWAHEFADV KADQFIARHK YSPADVFIGY HSDACASVVL QAVERQGCRD LTEELYRKVS EEARSILLDC ATPDAVVRLS GSSLGSFTAK QLSQEYYYAQ QHNSFVDFLQ AHLRMTHHEC RAVFTEITTF SRLLTGNDCD VLASELRGLA SKPVVLSLQQ YDTEYSFLKD VRSWLTNPGK RKVLVIQADF DDGTRSAQLV ASAKYTAINE INKTQGTKDF VFVYFVTKLS RMGSGTSYVG FHGGLWRSVH IDDLRRSTIM ASDVTKLQNV TISQLFKPED KPEQEEMEIE TSQSKELAEE QMEVEDSEEM KKASDPRSCD CSQFLDTTRL VQSCVQGAVG MLRDQNESCA RNMRRVTILL DLLNEDNTRN ASFLRESKMR LHVLLNKQEE NQVRSLKEWV TREAANQDAL QEAGTFRHTL WKRVQDVVTP ILASMIAHID RDGNLELLAQ PDSPAWVQDL WMFIYSDIKF LNISLVLNNT RSNSEMSFIL VQSHMNLLKD AYNAVPFSWR IRDYLEELWV QAQYITDTEG LSKKFVEIFQ KTPLGVFLAQ FPVAQQQKLL QSYLKDFLLL TMKVSSREEL MFLQMALWSC LRELQEASGT PDETYKFPLS LPWVHLAFQH FRTRLQNFSR ILTIHPQVLS SLSQAAEKHS LAGCEMTLDA FAAMACAEML KGDLLKPSPK AWLQLVKNLS TPLELVCSEG YLCDSGSMTR SVIQEVRALW NRIFSIALFV EHVLLGTESH IPELSPLVTT YVSLLDKCLE EDSNLKTCRP FVAVMTTLCD CKDKASKKFS RFGIQPCFIC HGDAQDPVCL PCDHVYCLRC IQTWLIPGQM MCPYCLTDLP DKFSPTVSQD HRKAIEKHAQ FRHMCNSFFV DLVSTMCFKD NTPPEKSVID TLLSLLFVQK ELLRDASQKH REHTKSLSPF DDVVDQTPVI RSVLLKLLLK YSFHEVKDYI QNYLTQLEKK AFLTEDKTEL YLLFISCLED SVHQKTSAGC RNLEQVLREE GHFLRTYSPG LQGQEPVRIA SVEYLQEVAR VRLCLDLAAD FLSELQEGSE LAEDKRRFLK HVEEFCTRVN NDWHRVYLVR KLSSQRGMEF VQSFSKQGHP CQWVFPRKVI AQQKDHVSLM DRYLVHGNEY KAVRDATAKA VLECKTLDIG NALMACRSPK PQQTAYLLLA LYTEVAALYR SPNGSLHPEA KQLEAVNKFI KESKILSDPN IRCFARSLVD NTLPLLKIRS ANSILKGTVT EMAVHVATIL LCGHNQILKP LRNLAFYPVN MANAFLPTMP EDLLVHARTW RGLENVTWYT CPRGHPCSVG ECGRPMQEST CLDCGLPVGG LNHTPHEGFS AIRNNEDRTQ TGHVLGSPQS SGVAEVSDRG QSPVVFILTR LLTHLAMLVG ATHNPQALTV IIKPWVQDPQ GFLQQHIQRD LEQLTKMLGR SADETIHVVH LILSSLLRVQ SHGVLNFNAE LSTKGCRNNW EKHFETLLLR ELKHLDKNLP AINALISQDE RISSNPVTKI IYGDPATFLP HLPQKSIIHC SKIWSCRRKI TVEYLQHIVE QKNGKETVPV LWHFLQKEAE LRLVKFLPEI LALQRDLVKQ FQNVSRVEYS SIRGFIHSHS SDGLRKLLHD RITIFLSTWN ALRRSLETNG EIKLPKDYCC SDLDLDAEFE VILPRRQGLG LCGTALVSYL ISLHNNMVYT VQKFSNEDNS YSVDISEVAD LHVISYEVER DLNPLILSNC QYQVQQGGET SQEFDLEKIQ RQISSRFLQG KPRLTLKGIP TLVYRRDWNY EHLFMDIKNK MAQSSLPNLA ISTISGQLQS YSDACEALSI IEITLGFLST AGGDPGMDLN VYIEEVLRMC DQTAQVLKAF SRCQLRHIIA LWQFLSAHKS EQRLRLNKEL FREIDVQYKE ELSTQHQRLL GTFLNEAGLD AFLLELHEMI VLKLKGPRAA NSFNPNWSLK DTLVSYMETK DSDILSEVES QFPEEILMSS CISVWKIAAT RKWDRQSR

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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: 32.53 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: 1.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 176026
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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