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- EMDB-19653: Structure of the E3 ubiquitin ligase RNF213, determined by cryoEM -

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Basic information

Entry
Database: EMDB / ID: EMD-19653
TitleStructure of the E3 ubiquitin ligase RNF213, determined by cryoEM
Map dataComposite unsharpened cryoEM map of RNF213, produced by a combination of local refinements of sub-domains, and used for model building and refinement
Sample
  • Complex: Human RNF213
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsE3 ubiquitin ligase / ATPase / carbohydrate-binding domain / RING domain / RZ domain / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / 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 / Suppression of apoptosis / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / 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 / Signaling by ALK fusions and activated point mutants / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / angiogenesis / protein ubiquitination / defense response to bacterium / nucleolus / ATP hydrolysis activity / zinc ion binding / ATP binding / membrane / 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) / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type ...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) / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsNaydenova K / Randow F
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)U105170648 United Kingdom
Wellcome Trust222503/Z/21/Z United Kingdom
CitationJournal: EMBO Rep / Year: 2024
Title: Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213.
Authors: Ana Crespillo-Casado / Prathyush Pothukuchi / Katerina Naydenova / Matthew C J Yip / Janet M Young / Jerome Boulanger / Vimisha Dharamdasani / Ceara Harper / Pierre-Mehdi Hammoudi / Elsje G ...Authors: Ana Crespillo-Casado / Prathyush Pothukuchi / Katerina Naydenova / Matthew C J Yip / Janet M Young / Jerome Boulanger / Vimisha Dharamdasani / Ceara Harper / Pierre-Mehdi Hammoudi / Elsje G Otten / Keith Boyle / Mayuri Gogoi / Harmit S Malik / Felix Randow /
Abstract: Innate immunity senses microbial ligands known as pathogen-associated molecular patterns (PAMPs). Except for nucleic acids, PAMPs are exceedingly taxa-specific, thus enabling pattern recognition ...Innate immunity senses microbial ligands known as pathogen-associated molecular patterns (PAMPs). Except for nucleic acids, PAMPs are exceedingly taxa-specific, thus enabling pattern recognition receptors to detect cognate pathogens while ignoring others. How the E3 ubiquitin ligase RNF213 can respond to phylogenetically distant pathogens, including Gram-negative Salmonella, Gram-positive Listeria, and eukaryotic Toxoplasma, remains unknown. Here we report that the evolutionary history of RNF213 is indicative of repeated adaptation to diverse pathogen target structures, especially in and around its newly identified CBM20 carbohydrate-binding domain, which we have resolved by cryo-EM. We find that RNF213 forms coats on phylogenetically distant pathogens. ATP hydrolysis by RNF213's dynein-like domain is essential for coat formation on all three pathogens studied as is RZ finger-mediated E3 ligase activity for bacteria. Coat formation is not diffusion-limited but instead relies on rate-limiting initiation events and subsequent cooperative incorporation of further RNF213 molecules. We conclude that RNF213 responds to evolutionarily distant pathogens through enzymatically amplified cooperative recruitment.
History
DepositionFeb 16, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19653.png

Downloads & links

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Map

FileDownload / File: emd_19653.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite unsharpened cryoEM map of RNF213, produced by a combination of local refinements of sub-domains, and used for model building and refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 512 pix.
= 471.552 Å		0.92 Å/pix.
x 512 pix.
= 471.552 Å		0.92 Å/pix.
x 512 pix.
= 471.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.0022551 - 0.05472094
Average (Standard dev.)0.0004352499 (±0.0008523008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 471.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human RNF213

EntireName: Human RNF213
Components
  • Complex: Human 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: Human RNF213

SupramoleculeName: Human RNF213 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: E3 ubiquitin ligase RNF213, human, N1045D natural variant
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 590 KDa

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Macromolecule #1: E3 ubiquitin-protein ligase RNF213

MacromoleculeName: E3 ubiquitin-protein ligase RNF213 / type: protein_or_peptide / ID: 1
Details: N-terminally Strep-II tagged human RNF213, N1045D natural variant
Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 596.45125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAMS MECPSCQHVS KEETPKFCSQ CGERLPPAAP IADSENNNST MASASEGEM ECGQELKEEG GPCLFPGSDS WQENPEEPCS KASWTVQESK KKKRKKKKKG NKSASSELAS LPLSPASPCH L TLLSNPWP ...String:
MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAMS MECPSCQHVS KEETPKFCSQ CGERLPPAAP IADSENNNST MASASEGEM ECGQELKEEG GPCLFPGSDS WQENPEEPCS KASWTVQESK KKKRKKKKKG NKSASSELAS LPLSPASPCH L TLLSNPWP QDTALPHSQA QQSGPTGQPS QPPGTATTPL EGDGLSAPTE VGDSPLQAQA LGEAGVATGS EAQSSPQFQD HT EGEDQDA SIPSGGRGLS QEGTGPPTSA GEGHSRTEDA AQELLLPESK GGSSEPGTEL QTTEQQAGAS ASMAVDAVAE PAN AVKGAG KEMKEKTQRM KQPPATTPPF KTHCQEAETK TKDEMAAAEE KVGKNEQGEP EDLKKPEGKN RSAAAVKNEK EQKN QEADV QEVKASTLSP GGGVTVFFHA IISLHFPFNP DLHKVFIRGG EEFGESKWDS NICELHYTRD LGHDRVLVEG IVCIS KKHL DKYIPYKYVI YNGESFEYEF IYKHQQKKGE YVNRCLFIKS SLLGSGDWHQ YYDIVYMKPH GRLQKVMNHI TDGPRK DLV KGKQIAAALM LDSTFSILQT WDTINLNSFF TQFEQFCFVL QQPMIYEGQA QLWTDLQYRE KEVKRYLWQH LKKHVVP LP DGKSTDFLPV DCPVRSKLKT GLIVLFVVEK IELLLEGSLD WLCHLLTSDA SSPDEFHRDL SHILGIPQSW RLYLVNLC Q RCMDTRTYTW LGALPVLHCC MELAPRHKDA WRQPEDTWAA LEGLSFSPFR EQMLDTSSLL QFMREKQHLL SIDEPLFRS WFSLLPLSHL VMYMENFIEH LGRFPAHILD CLSGIYYRLP GLEQVLNTQD VQDVQNVQNI LEMLLRLLDT YRDKIPEEAL SPSYLTVCL KLHEAICSST KLLKFYELPA LSAEIVCRMI RLLSLVDSAG QRDETGNNSV QTVFQGTLAA TKRWLREVFT K NMLTSSGA SFTYVKEIEV WRRLVEIQFP AEHGWKESLL GDMEWRLTKE EPLSQITAYC NSCWDTKGLE DSVAKTFEKC II EAVSSAC QSQTSILQGF SYSDLRKFGI VLSAVITKSW PRTADNFDDI LKHLLTLADV KHVFRLCGTD EKILANVTED AKR LIAVAD SVLTKVVGDL LSGTILVGQL ELIIKHKNQF LDIWQLREKS LSPQDEQCAV EEALDWRREE LLLLKKEKRC VDSL LKMCG NVKHLIQVDF GVLAVRHSQD LSSKRLNDTV TVRLSTSSNS QRATHYHLSS QVQEMAGKID LLRDSHIFQL FWREA AEPL SEPKEDQEAA ELLSEPEEES ERHILELEEV YDYLYQPSYR KFIKLHQDLK SGEVTLAEID VIFKDFVNKY TDLDSE LKI MCTVDHQDQR DWIKDRVEQI KEYHHLHQAV HAAKVILQVK ESLGLNGDFS VLNTLLNFTD NFDDFRRETL DQINQEL IQ AKKLLQDISE ARCKGLQALS LRKEFICWVR EALGGINELK VFVDLASISA GENDIDVDRV ACFHDAVQGY ASLLFKLD P SVDFSAFMKH LKKLWKALDK DQYLPRKLCD SARNLEWLKT VNESHGSVER SSLTLATAIN QRGIYVIQAP KGGQKISPD TVLHLILPES PGSHEESREY SLEEVKELLN KLMLMSGKKD RNNTEVERFS EVFCSVQRLS QAFIDLHSAG NMLFRTWIAM AYCSPKQGV SLQMDFGLDL VTELKEGGDV TELLAALCRQ MEHFLDSWKR FVTQKRMEHF YLNFYTAEQL VYLSTELRKQ P PSDAALTM LSFIKSNCTL RDVLRASVGC GSEAARYRMR RVMEELPLML LSEFSLVDKL RIIMEQSMRC LPAFLPDCLD LE TLGHCLA HLAGMGGSPV ERCLPRGLQV GQPNLVVCGH SEVLPAALAV YMQTPSQPLP TYDEVLLCTP ATTFEEVALL LRR CLTLGS LGHKVYSLLF ADQLSYEVAR QAEELFHNLC TQQHREDYQL VMVCDGDWEH CYLPSAFSQH KVFVTPQAPL EAIQ AYLAG HYRVPKQTLS AAAVFNDRLC VGIVASERAG VGKSLYVKRL HDKMKMQLNV KNVPLKTIRL IDPQVDESRV LGALL PFLD AQYQKVPVLF HLDVTSSVQT GIWVFLFKLL ILQYLMDING KMWLRNPCHL YIVEILERRT SVPSRSSSAL RTRVPQ FSF LDIFPKVTCR PPKEVIDMEL SALRSDTEPG MDLWEFCSET FQRPYQYLRR FNQNQDLDTF QYQEGSVEGT PEECLQH FL FHCGVINPSW SELRNFARFL NYQLRDCEAS LFCNPSFIGD TLRGFKKFVV TFMIFMARDF ATPSLHTSDQ SPGKHMVT M DGVREEDLAP FSLRKRWESE PHPYVFFNDD HTTMTFIGFH LQPNINGSVD AISHLTGKVI KRDVMTRDLY QGLLLQRVP FNVDFDKLPR HKKLERLCLT LGIPQATDPD KTYELTTDNM LKILAIEMRF RCGIPVIIMG ETGCGKTRLI KFLSDLRRGG TNADTIKLV KVHGGTTADM IYSRVREAEN VAFANKDQHQ LDTILFFDEA NTTEAISCIK EVLCDHMVDG QPLAEDSGLH I IAACNPYR KHSEEMICRL ESAGLGYRVS MEETADRLGS IPLRQLVYRV HALPPSLIPL VWDFGQLSDV AEKLYIQQIV QR LVESISL DENGTRVITE VLCASQGFMR KTEDECSFVS LRDVERCVKV FRWFHEHSAM LLAQLNAFLS KSSVSKNHTE RDP VLWSLM LAIGVCYHAS LEKKDSYRKA IARFFPKPYD DSRLLLDEIT RAQDLFLDGV PLRKTIAKNL ALKENVFMMV VCIE LKIPL FLVGKPGSSK SLAKTIVADA MQGPAAYSDL FRSLKQVHLV SFQCSPHSTP QGIISTFRQC ARFQQGKDLQ QYVSV VVLD EVGLAEDSPK MPLKTLHPLL EDGCIEDDPA PHKKVGFVGI SNWALDPAKM NRGIFVSRGS PNETELIESA KGICSS DIL VQDRVQGYFA SFAKAYETVC KRQDKEFFGL RDYYSLIKMV FAAAKASNRK PSPQDIAQAV LRNFSGKDDI QALDIFL AN LPEAKCSEEV SPMQLIKQNI FGPSQKVPGG EQEDAESRYL LVLTKNYVAL QILQQTFFEG DQQPEIIFGS GFPKDQEY T QLCRNINRVK ICMETGKMVL LLNLQNLYES LYDALNQYYV HLGGQKYVDL GLGTHRVKCR VHPNFRLIVI EEKDVVYKH FPIPLINRLE KHYLDINTVL EKWQKSIVEE LCAWVEKFIN VKAHHFQKRH KYSPSDVFIG YHSDACASVV LQVIERQGPR ALTEELHQK VSEEAKSILL NCATPDAVVR LSAYSLGGFA AEWLSQEYFH RQRHNSFADF LQAHLHTADL ERHAIFTEIT T FSRLLTSH DCEILESEVT GRAPKPTLLW LQQFDTEYSF LKEVRNCLTN TAKCKILIFQ TDFEDGIRSA QLIASAKYSV IN EINKIRE NEDRIFVYFI TKLSRVGRGT AYVGFHGGLW QSVHIDDLRR STLMVSDVTR LQHVTISQLF APGDLPELGL EHR AEDGHE EAMETEASTS GEVAEVAEEA METESSEKVG KETSELGGSD VSILDTTRLL RSCVQSAVGM LRDQNESCTR NMRR VVLLL GLLNEDDACH ASFLRVSKMR LSVFLKKQEE SQFHPLEWLA REACNQDALQ EAGTFRHTLW KRVQGAVTPL LASMI SFID RDGNLELLTR PDTPPWARDL WMFIFSDTML LNIPLVMNNE RHKGEMAYIV VQNHMNLSEN ASNNVPFSWK IKDYLE ELW VQAQYITDAE GLPKKFVDIF QQTPLGRFLA QLHGEPQQEL LQCYLKDFIL LTMRVSTEEE LKFLQMALWS CTRKLKA AS EAPEEEVSLP WVHLAYQRFR SRLQNFSRIL TIYPQVLHSL MEARWNHELA GCEMTLDAFA AMACTEMLTR NTLKPSPQ A WLQLVKNLSM PLELICSDEH MQGSGSLAQA VIREVRAQWS RIFSTALFVE HVLLGTESRV PELQGLVTEH VFLLDKCLR ENSDVKTHGP FEAVMRTLCE CKETASKTLS RFGIQPCSIC LGDAKDPVCL PCDHVHCLRC LRAWFASEQM ICPYCLTALP DEFSPAVSQ AHREAIEKHA RFRQMCNSFF VDLVSTICFK DNAPPEKEVI ESLLSLLFVQ KGRLRDAAQR HCEHTKSLSP F NDVVDKTP VIRSVILKLL LKYSFHDVKD YIQEYLTLLK KKAFITEDKT ELYMLFINCL EDSILEKTSA YSRNDELNHL EE EGRFLKA YSPASRGREP ANEASVEYLQ EVARIRLCLD RAADFLSEPE GGPEMAKEKQ CYLQQVKQFC IRVENDWHRV YLV RKLSSQ RGMEFVQGLS KPGRPHQWVF PKDVVKQQGL RQDHPGQMDR YLVYGDEYKA LRDAVAKAVL ECKPLGIKTA LKAC KTPQS QQSAYFLLTL FREVAILYRS HNASLHPTPE QCEAVSKFIG ECKILSPPDI SRFATSLVDN SVPLLRAGPS DSNLD GTVT EMAIHAAAVL LCGQNELLEP LKNLAFSPAT MAHAFLPTMP EDLLAQARRW KGLERVHWYT CPNGHPCSVG ECGRPM EQS ICIDCHAPIG GIDHKPRDGF HLVKDKADRT QTGHVLGNPQ RRDVVTCDRG LPPVVFLLIR LLTHLALLLG ASQSSQA LI NIIKPPVRDP KGFLQQHILK DLEQLAKMLG HSADETIGVV HLVLRRLLQE QHQLSSRRLL NFDTELSTKE MRNNWEKE I AAVISPELEH LDKTLPTMNN LISQDKRISS NPVAKIIYGD PVTFLPHLPR KSVVHCSKIW SCRKRITVEY LQHIVEQKN GKERVPILWH FLQKEAELRL VKFLPEILAL QRDLVKQFQN VQQVEYSSIR GFLSKHSSDG LRQLLHNRIT VFLSTWNKLR RSLETNGEI NLPKDYCSTD LDLDTEFEIL LPRRRGLGLC ATALVSYLIR LHNEIVYAVE KLSKENNSYS VDAAEVTELH V ISYEVERD LTPLILSNCQ YQVEEGRETV QEFDLEKIQR QIVSRFLQGK PRLSLKGIPT LVYRHDWNYE HLFMDIKNKM AQ DSLPSSV ISAISGQLQS YSDACEVLSV VEVTLGFLST AGGDPNMQLN VYTQDILQMG DQTIHVLKAL NRCQLKHTIA LWQ FLSAHK SEQLLRLHKE PFGEISSRYK ADLSPENAKL LSTFLNQTGL DAFLLELHEM IILKLKNPQT QTEERFRPQW SLRD TLVSY MQTKESEILP EMASQFPEEI LLASCVSVWK TAAVLKWNRE MR

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: 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 #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: 1 / 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
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 4.86 sec. / Average electron dose: 29.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8s24:
Structure of the E3 ubiquitin ligase RNF213, determined by cryoEM

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