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- EMDB-52570: Cryo-EM structure of mouse RNF213 (WB3/WB4 + ATP) -

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Basic information

Entry
Database: EMDB / ID: EMD-52570
TitleCryo-EM structure of mouse RNF213 (WB3/WB4 + ATP)
Map data
Sample
  • Complex: RNF213
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsE3 ligase / ubiquitin / AAA ATPase / LIGASE
Function / homology
Function and homology information


lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / regulation of lipid metabolic process / protein K63-linked ubiquitination / immune system process ...lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / regulation of lipid metabolic process / protein K63-linked ubiquitination / immune system process / 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 / ubiquitin protein ligase activity / angiogenesis / ubiquitin-dependent protein catabolic process / defense response to bacterium / protein ubiquitination / ATP hydrolysis activity / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
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. ...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: 4.5 Å
AuthorsGrabarczyk DB / Ahel J / Clausen T
Funding support Austria, 1 items
OrganizationGrant numberCountry
Austrian Research Promotion Agency852936 Austria
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 16, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52570.png

Downloads & links

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Map

FileDownload / File: emd_52570.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 352 pix.
= 373.12 Å		1.06 Å/pix.
x 352 pix.
= 373.12 Å		1.06 Å/pix.
x 352 pix.
= 373.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00484
Minimum - Maximum-0.006717144 - 0.02109338
Average (Standard dev.)-0.00011564775 (±0.00096835085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 373.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52570_msk_1.map
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Additional map: #1

Fileemd_52570_additional_1.map
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Half map: #2

Fileemd_52570_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_52570_half_map_2.map
Projections & Slices
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Sample components

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Entire : RNF213

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

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Supramolecule #1: RNF213

SupramoleculeName: 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: 586.543562 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MECPQCGHVS SEKAPKFCSE CGQKLPSAAT VQGDLKNDNT LVVSSTPEGK TEQGAVLREE EVLLSSTDPG KELEKPEESD SNASWTTQM SKKEKRRRKR QGTISSSEAP SSGLWSLDMP PSPGSHNSAL PQNQAQQGGA ASQPGHPLDT ENMPMEDGFV H TEGSGSPL ...String:
MECPQCGHVS SEKAPKFCSE CGQKLPSAAT VQGDLKNDNT LVVSSTPEGK TEQGAVLREE EVLLSSTDPG KELEKPEESD SNASWTTQM SKKEKRRRKR QGTISSSEAP SSGLWSLDMP PSPGSHNSAL PQNQAQQGGA ASQPGHPLDT ENMPMEDGFV H TEGSGSPL QGQAAERTDA QSNLAPSDLA EVKDLNTSKP SVDKGLPLDG GPALSAFKGH PKMTDASQKA PLPESKGETS GQ EKKVPPI DAAASPVKTA GKETGEDVRK PKPSPVSPVA SKHGDQEAEL KGKLATPVRK SNEGGNTQPE DQRKPGEGRN FAA AVKTQQ AAAPQQAAAP EPTSAFNPRD TVTVYFHAIV SRHFGFNPEE HKVYVRGGEG LGQKGWTDAC EMYCTQDLHD LGSL VEGKM DIPRQSLDKP IPYKYVIHRG GSSKDTVEYE FIYEQAQKKG EHVNRCLRVV STSLGNGDWH QYDDIICMRS TGFFQ QAKN RILDSTRKEL LKGKKQAAVV MLDRIFSVLQ PWSDINLQSF MTQFLQFYSV VREPMIHDGR ARKWTSLQYE EKEVWT NLW EHVKKQMAPF LEGKSGESLP ADCPVRSKLT LGLSILFMVE AAEFTVPKKD LDSLCYLLIP SAGSPEALHS DLSPVLR IR QRWRIYLTNL CLRCIDERCD RWLGILPLLH TCMQKSPPKK NSKSQPEDTW AGLEGISFSE FRDKAPTRSQ PLQFMQSK M ALLRVDEYLF RSWLSVVPLE SLSSYLENSI DYLSDVPVRV LDCLQGISYR LPGLRKISNQ NMKKDVENVF KMLMHLVDI YQHRIFGENL LQIYLTECLT LHETVCNITA NHQFFEIPAL SAELICKLLE LSPPGHTDEG LPEKSYEDLV TSTLQEALAT TRNWLRSLF KSRMLSISSA YVRLTYSEEM AVWRRLVEIG FPEKHGWKGS LLGDMEGRLK QEPPRLQISF FCSSQCRDGG L HDSVSRSF EKCVIEAVSS ACQSQTSVLE GLSCQDLQKF GTLLSAVITK SWPVHNGEPV FDVDEIFKYL LKWPDVRQLF EL CGTNEKI IDNITEEGRQ LMATAESVFQ KVAGELENGT IVVGQLELIL EHQSQFLDIW NLNRRRLPSQ EKACDVRSLL KRR RDDLLF LKQEKRYVES LLRQLGRVKH LVQVDFGNIE IIHSQDLSNK KLNEAVIKLP NSSSYKRETH YCLSPDIREM ASKL DSLKD SHIFQDFWQE TAESLNTLDK DPRELKVSLP EVLEYLYNPC YDNFYTLYEN LKSGKITFAE VDAIFKDFVD KYDEL KNDL KFMCTMNPQD QKGWISERVG QIKEYHTLHQ AVSSAKVILQ VRRALGVTGD FSVLNPLLNF ADSFEDFGNE KLDQIS PQF IKAKQLLQDI SEPRQRCLEE LARQTELVAW LHKALEDINE LKVFVDLASI SAGENDIDVD RVACFHDAVQ GYASLLY KM DERTNFSDFM NHLQELWRAL DNDQHLPDKL KDSARNLEWL KTVKESHGSV ELSSLSLATA INSRGVYVIE APKDGQKI S PDTVLRLLLP DGHGYPEALR TYSTEELKEL LNKLMLMSGK KDHNSNTEVE KFSEVFSNMQ RLVHVFIKLH CAGNMLFRT WTAKVYCCPD GGIFMNFGLE LLSQLTEKGD VIQLLGALCR QMEDFLDNWK TVVAQKRAEH FYLNFYTAEQ LVYLSSELRK PRPSEAALM MLSFIKGKCT VQDLVQATSA CESKADRYCL REVMKKLPQQ LLSEPSLMGK LQVIMMQSLV YMSAFLPHCL D LDALGRCL AHLATMGGTP VERPLPKGLQ AGQPNLILCG HSEVLPAALA IYMQAPRQPL PTFDEVLLCT PATTIEEVEL LL RRCLTSG SQGHKVYSLL FADQLSYEVG CQAEEFFQSL CTRAHREDYQ LVILCDAARE HCYIPSTFSQ YKVPLVPQAP LPN IQAYLQ SHYQVPKRLL SAATVFRDGL CVGIVTSERA GVGKSLYVNT LHTKLKAKLR DETVPLKIIR LTEPHLDENQ VLSA LLPFL KEKYQKMPVI FHIDISTSVQ TGIPIFLFKL LILQYLMDIN GKIWRRSPGH LYLVEIPQGL SVQPKRSSKL NARAP LFKF LDLFPKVTCR PPKEVIDMEL TPERSHTDPA MDPVEFCSEA FQRPYQYLKR FHQQQNLDTF QYEKGSVEGS PEECLQ HFL IYCGLINPSW SELRNFAWFL NCQLKDCEAS IFCKSAFTGD TLRGFKNFVV TFMILMARDF ATPTLHTSDQ SPGRQSV TI GEVVEEDLAP FSLRKRWESE PHPYVFFNGD HMTMTFIGFH LETNNNGYVD AINPSNGKVI KKDVMTKELF DGLRLQRV P FNIDFDNLPR YEKLERLCLA LGIEWPIDPD ETYELTTDNM LKILAIEMRF RCGIPVIIMG ETGCGKTRLI KFLSDLKRG SVEAETMKLV KVHGGTTPSM IYSKVKEAER TAFSNKAQHK LDTILFFDQA NTTEAVSCIK EILCDRTVDG EHLHEDSGLH IIAACNPYR KHSQEMILRL ESAGLGYRVS AEETADRLGS IPLRQLVYRV HALPPSLIPL VWDFGQLNDS AEKLYIQQIV Q RLVDSVSV NPSETCVIAD VLSASQMFMR KRENECGFVS LRDVERCVKV FRWFHDHSDM LLKELDKFLH ESSDSTHTFE RD PVLWSLV MAIGVCYHAS LEEKASYRTA IARCFPKPYN SSRAILDEVT HVQDLFLRGA PIRTNIARNL ALKENVFMMV ICI ELKIPL FLVGKPGSSK SLAKIIVADA MQGQAAFSEL FRCLKQVHLV SFQCSPHSTP QGIISTFKQC ARFQQGKDLG QYVS VVVLD QVGLAEDSPK MPLKTLHPLL EDGCIEDDPA PYKKVGFVGI SNWALDPAKM NRGIFVSRGS PNEKELIESA EGICS SDRL VQDKIRGYFA PFAKAYETVC QKQDKEFFGL RDYYSLIKMV FAKAKASKRG LSPQDITHAV LRNFSGKDNI QALSIF TAS LPEARYKEEV STVELIKQNI YPGPQASSRG LDGAESRYLL VLTRNYVALQ ILQQTFFEGQ QPEIIFGSSF PQDQEYT QI CRNINRVKIC METGKMVVLL NLQNLYESLY DALNQYYVYL GGQKYVDLGL GTHRVKCRVH TAFRLIVIEE KDVVYKQF P VPLINRLEKH YLDMNTVLQP WQKSIVQELQ QWAHEFADVK ADQFIARHKY SPADVFIGYH SDACASVVLQ AVERQGCRD LTEELYRKVS EEARSILLDC ATPDAVVRLS GSSLGSFTAK QLSQEYYYAQ QHNSFVDFLQ AHLRMTHHEC RAVFTEITTF SRLLTGNDC DVLASELRGL ASKPVVLSLQ QYDTEYSFLK DVRSWLTNPG KRKVLVIQAD FDDGTRSAQL VASAKYTAIN E INKTQGTK DFVFVYFVTK LSRMGSGTSY VGFHGGLWRS VHIDDLRRST IMASDVTKLQ NVTISQLFKP EDKPEQEEME IE TSQSKEL AEEQMEVEDS EEMKKASDPR SCDCSQFLDT TRLVQSCVQG AVGMLRDQNE SCARNMRRVT ILLDLLNEDN TRN ASFLRE SKMRLHVLLN KQEENQVRSL KEWVTREAAN QDALQEAGTF RHTLWKRVQD VVTPILASMI AHIDRDGNLE LLAQ PDSPA WVQDLWMFIY SDIKFLNISL VLNNTRSNSE MSFILVQSHM NLLKDAYNAV PFSWRIRDYL EELWVQAQYI TDTEG LSKK FVEIFQKTPL GVFLAQFPVA QQQKLLQSYL KDFLLLTMKV SSREELMFLQ MALWSCLREL QEASGTPDET YKFPLS LPW VHLAFQHFRT RLQNFSRILT IHPQVLSSLS QAAEKHSLAG CEMTLDAFAA MACAEMLKGD LLKPSPKAWL QLVKNLS TP LELVCSEGYL CDSGSMTRSV IQEVRALWNR IFSIALFVEH VLLGTESHIP ELSPLVTTYV SLLDKCLEED SNLKTCRP F VAVMTTLCDC KDKASKKFSR FGIQPCFICH GDAQDPVCLP CDHVYCLRCI QTWLIPGQMM CPYCLTDLPD KFSPTVSQD HRKAIEKHAQ FRHMCNSFFV DLVSTMCFKD NTPPEKSVID TLLSLLFVQK ELLRDASQKH REHTKSLSPF DDVVDQTPVI RSVLLKLLL KYSFHEVKDY IQNYLTQLEK KAFLTEDKTE LYLLFISCLE DSVHQKTSAG CRNLEQVLRE EGHFLRTYSP G LQGQEPVR IASVEYLQEV ARVRLCLDLA ADFLSELQEG SELAEDKRRF LKHVEEFCTR VNNDWHRVYL VRKLSSQRGM EF VQSFSKQ GHPCQWVFPR KVIAQQKDHV SLMDRYLVHG NEYKAVRDAT AKAVLECKTL DIGNALMACR SPKPQQTAYL LLA LYTEVA ALYRSPNGSL HPEAKQLEAV NKFIKESKIL SDPNIRCFAR SLVDNTLPLL KIRSANSILK GTVTEMAVHV ATIL LCGHN QILKPLRNLA FYPVNMANAF LPTMPEDLLV HARTWRGLEN VTWYTCPRGH PCSVGECGRP MQESTCLDCG LPVGG LNHT PHEGFSAIRN NEDRTQTGHV LGSPQSSGVA EVSDRGQSPV VFILTRLLTH LAMLVGATHN PQALTVIIKP WVQDPQ GFL QQHIQRDLEQ LTKMLGRSAD ETIHVVHLIL SSLLRVQSHG VLNFNAELST KGCRNNWEKH FETLLLRELK HLDKNLP AI NALISQDERI SSNPVTKIIY GDPATFLPHL PQKSIIHCSK IWSCRRKITV EYLQHIVEQK NGKETVPVLW HFLQKEAE L RLVKFLPEIL ALQRDLVKQF QNVSRVEYSS IRGFIHSHSS DGLRKLLHDR ITIFLSTWNA LRRSLETNGE IKLPKDYCC SDLDLDAEFE VILPRRQGLG LCGTALVSYL ISLHNNMVYT VQKFSNEDNS YSVDISEVAD LHVISYEVER DLNPLILSNC QYQVQQGGE TSQEFDLEKI QRQISSRFLQ GKPRLTLKGI PTLVYRRDWN YEHLFMDIKN KMAQSSLPNL AISTISGQLQ S YSDACEAL SIIEITLGFL STAGGDPGMD LNVYIEEVLR MCDQTAQVLK AFSRCQLRHI IALWQFLSAH KSEQRLRLNK EL FREIDVQ YKEELSTQHQ RLLGTFLNEA GLDAFLLELH EMIVLKLKGP RAANSFNPNW SLKDTLVSYM ETKDSDILSE VES QFPEEI LMSSCISVWK IAATRKWDRQ SRGGGHHHHH HHHHH

UniProtKB: E3 ubiquitin-protein ligase RNF213

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / 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 #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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