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Yorodumi- EMDB-52571: Cryo-EM structure of mouse RNF213:UBE2L3 transthiolation intermed... -
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Open data
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Basic information
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| Title | Cryo-EM structure of mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized, and ATPgS | |||||||||
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Keywords | E3 ligase / ubiquitin / AAA ATPase / LIGASE | |||||||||
| Function / homology | Function and homology informationlipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / cell cycle phase transition / ubiquitin-protein transferase activator activity / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases ...lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / cell cycle phase transition / ubiquitin-protein transferase activator activity / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / : / cellular response to glucocorticoid stimulus / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / regulation of lipid metabolic process / protein K63-linked ubiquitination / immune system process / ubiquitin ligase complex / protein autoubiquitination / lipid droplet / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein modification process / Regulation of necroptotic cell death / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / angiogenesis / ubiquitin-dependent protein catabolic process / transcription coactivator activity / cell population proliferation / defense response to bacterium / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Grabarczyk DB / Ahel J / Clausen T | |||||||||
| Funding support | Austria, 1 items
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Citation | Journal: 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. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_52571.map.gz | 117.9 MB | EMDB map data format | |
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| Header (meta data) | emd-52571-v30.xml emd-52571.xml | 27.1 KB 27.1 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_52571_fsc.xml | 11.4 KB | Display | FSC data file |
| Images | emd_52571.png | 28.1 KB | ||
| Masks | emd_52571_msk_1.map | 127.4 MB | Mask map | |
| Filedesc metadata | emd-52571.cif.gz | 10 KB | ||
| Others | emd_52571_additional_1.map.gz emd_52571_half_map_1.map.gz emd_52571_half_map_2.map.gz | 119.3 MB 101.2 MB 101.1 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-52571 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-52571 | HTTPS FTP |
-Validation report
| Summary document | emd_52571_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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| Full document | emd_52571_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML | emd_52571_validation.xml.gz | 18.4 KB | Display | |
| Data in CIF | emd_52571_validation.cif.gz | 23.9 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-52571 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-52571 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9i1jMC ![]() 9i1iC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_52571.map.gz / Format: CCP4 / Size: 127.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.18 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_52571_msk_1.map | ||||||||||||
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-Additional map: AAA focused map
| File | emd_52571_additional_1.map | ||||||||||||
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| Annotation | AAA focused map | ||||||||||||
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-Half map: #2
| File | emd_52571_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_52571_half_map_2.map | ||||||||||||
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Sample components
-Entire : Mouse RNF213:UBE2L3 transthiolation intermediate
| Entire | Name: Mouse RNF213:UBE2L3 transthiolation intermediate |
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| Components |
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-Supramolecule #1: Mouse RNF213:UBE2L3 transthiolation intermediate
| Supramolecule | Name: Mouse RNF213:UBE2L3 transthiolation intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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| Source (natural) | Organism: ![]() |
-Macromolecule #1: E3 ubiquitin-protein ligase RNF213
| Macromolecule | Name: E3 ubiquitin-protein ligase RNF213 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 552.623375 KDa |
| Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
| Sequence | String: MASWSHPQFE KGSTSAFNPR DTVTVYFHAI VSRHFGFNPE EHKVYVRGGE GLGQKGWTDA CEMYCTQDLH DLGSLVEGKM DIPRQSLDK PIPYKYVIHR GGSSKDTVEY EFIYEQAQKK GEHVNRCLRV VSTSLGNGDW HQYDDIICMR STGFFQQAKN R ILDSTRKE ...String: MASWSHPQFE KGSTSAFNPR DTVTVYFHAI VSRHFGFNPE EHKVYVRGGE GLGQKGWTDA CEMYCTQDLH DLGSLVEGKM DIPRQSLDK PIPYKYVIHR GGSSKDTVEY EFIYEQAQKK GEHVNRCLRV VSTSLGNGDW HQYDDIICMR STGFFQQAKN R ILDSTRKE LLKGKKQAAV VMLDRIFSVL QPWSDINLQS FMTQFLQFYS VVREPMIHDG RARKWTSLQY EEKEVWTNLW EH VKKQMAP FLEGKSGESL PADCPVRSKL TLGLSILFMV EAAEFTVPKK DLDSLCYLLI PSAGSPEALH SDLSPVLRIR QRW RIYLTN LCLRCIDERC DRWLGILPLL HTCMQKSPPK KNSKSQPEDT WAGLEGISFS EFRDKAPTRS QPLQFMQSKM ALLR VDEYL FRSWLSVVPL ESLSSYLENS IDYLSDVPVR VLDCLQGISY RLPGLRKISN QNMKKDVENV FKMLMHLVDI YQHRI FGEN LLQIYLTECL TLHETVCNIT ANHQFFEIPA LSAELICKLL ELSPPGHTDE GLPEKSYEDL VTSTLQEALA TTRNWL RSL FKSRMLSISS AYVRLTYSEE MAVWRRLVEI GFPEKHGWKG SLLGDMEGRL KQEPPRLQIS FFCSSQCRDG GLHDSVS RS FEKCVIEAVS SACQSQTSVL EGLSCQDLQK FGTLLSAVIT KSWPVHNGEP VFDVDEIFKY LLKWPDVRQL FELCGTNE K IIDNITEEGR QLMATAESVF QKVAGELENG TIVVGQLELI LEHQSQFLDI WNLNRRRLPS QEKACDVRSL LKRRRDDLL FLKQEKRYVE SLLRQLGRVK HLVQVDFGNI EIIHSQDLSN KKLNEAVIKL PNSSSYKRET HYCLSPDIRE MASKLDSLKD SHIFQDFWQ ETAESLNTLD KDPRELKVSL PEVLEYLYNP CYDNFYTLYE NLKSGKITFA EVDAIFKDFV DKYDELKNDL K FMCTMNPQ DQKGWISERV GQIKEYHTLH QAVSSAKVIL QVRRALGVTG DFSVLNPLLN FADSFEDFGN EKLDQISPQF IK AKQLLQD ISEPRQRCLE ELARQTELVA WLHKALEDIN ELKVFVDLAS ISAGENDIDV DRVACFHDAV QGYASLLYKM DER TNFSDF MNHLQELWRA LDNDQHLPDK LKDSARNLEW LKTVKESHGS VELSSLSLAT AINSRGVYVI EAPKDGQKIS PDTV LRLLL PDGHGYPEAL RTYSTEELKE LLNKLMLMSG KKDHNSNTEV EKFSEVFSNM QRLVHVFIKL HCAGNMLFRT WTAKV YCCP DGGIFMNFGL ELLSQLTEKG DVIQLLGALC RQMEDFLDNW KTVVAQKRAE HFYLNFYTAE QLVYLSSELR KPRPSE AAL MMLSFIKGKC TVQDLVQATS ACESKADRYC LREVMKKLPQ QLLSEPSLMG KLQVIMMQSL VYMSAFLPHC LDLDALG RC LAHLATMGGT PVERPLPKGL QAGQPNLILC GHSEVLPAAL AIYMQAPRQP LPTFDEVLLC TPATTIEEVE LLLRRCLT S GSQGHKVYSL LFADQLSYEV GCQAEEFFQS LCTRAHREDY QLVILCDAAR EHCYIPSTFS QYKVPLVPQA PLPNIQAYL QSHYQVPKRL LSAATVFRDG LCVGIVTSER AGVGKSLYVN TLHTKLKAKL RDETVPLKII RLTEPHLDEN QVLSALLPFL KEKYQKMPV IFHIDISTSV QTGIPIFLFK LLILQYLMDI NGKIWRRSPG HLYLVEIPQG LSVQPKRSSK LNARAPLFKF L DLFPKVTC RPPKEVIDME LTPERSHTDP AMDPVEFCSE AFQRPYQYLK RFHQQQNLDT FQYEKGSVEG SPEECLQHFL IY CGLINPS WSELRNFAWF LNCQLKDCEA SIFCKSAFTG DTLRGFKNFV VTFMILMARD FATPTLHTSD QSPGRQSVTI GEV VEEDLA PFSLRKRWES EPHPYVFFNG DHMTMTFIGF HLETNNNGYV DAINPSNGKV IKKDVMTKEL FDGLRLQRVP FNID FDNLP RYEKLERLCL ALGIEWPIDP DETYELTTDN MLKILAIEMR FRCGIPVIIM GETGCGKTRL IKFLSDLKRG SVEAE TMKL VKVHGGTTPS MIYSKVKEAE RTAFSNKAQH KLDTILFFDE ANTTEAVSCI KEILCDRTVD GEHLHEDSGL HIIAAC NPY RKHSQEMILR LESAGLGYRV SAEETADRLG SIPLRQLVYR VHALPPSLIP LVWDFGQLND SAEKLYIQQI VQRLVDS VS VNPSETCVIA DVLSASQMFM RKRENECGFV SLRDVERCVK VFRWFHDHSD MLLKELDKFL HESSDSTHTF ERDPVLWS L VMAIGVCYHA SLEEKASYRT AIARCFPKPY NSSRAILDEV THVQDLFLRG APIRTNIARN LALKENVFMM VICIELKIP LFLVGKPGSS KSLAKIIVAD AMQGQAAFSE LFRCLKQVHL VSFQCSPHST PQGIISTFKQ CARFQQGKDL GQYVSVVVLD EVGLAEDSP KMPLKTLHPL LEDGCIEDDP APYKKVGFVG ISNWALDPAK MNRGIFVSRG SPNEKELIES AEGICSSDRL V QDKIRGYF APFAKAYETV CQKQDKEFFG LRDYYSLIKM VFAKAKASKR GLSPQDITHA VLRNFSGKDN IQALSIFTAS LP EARYKEE VSTVELIKQN IYPGPQASSR GLDGAESRYL LVLTRNYVAL QILQQTFFEG QQPEIIFGSS FPQDQEYTQI CRN INRVKI CMETGKMVVL LNLQNLYESL YDALNQYYVY LGGQKYVDLG LGTHRVKCRV HTAFRLIVIE EKDVVYKQFP VPLI NRLEK HYLDMNTVLQ PWQKSIVQEL QQWAHEFADV KADQFIARHK YSPADVFIGY HSDACASVVL QAVERQGCRD LTEEL YRKV SEEARSILLD CATPDAVVRL SGSSLGSFTA KQLSQEYYYA QQHNSFVDFL QAHLRMTHHE CRAVFTEITT FSRLLT GND CDVLASELRG LASKPVVLSL QQYDTEYSFL KDVRSWLTNP GKRKVLVIQA DFDDGTRSAQ LVASAKYTAI NEINKTQ GT KDFVFVYFVT KLSRMGSGTS YVGFHGGLWR SVHIDDLRRS TIMASDVTKL QNVTISQLFK PEDKPEQEEM EIETSQSK E LAEEQMEVED SEEMKKASDP RSCDCSQFLD TTRLVQSCVQ GAVGMLRDQN ESCARNMRRV TILLDLLNED NTRNASFLR ESKMRLHVLL NKQEENQVRS LKEWVTREAA NQDALQEAGT FRHTLWKRVQ DVVTPILASM IAHIDRDGNL ELLAQPDSPA WVQDLWMFI YSDIKFLNIS LVLNNTRSNS EMSFILVQSH MNLLKDAYNA VPFSWRIRDY LEELWVQAQY ITDTEGLSKK F VEIFQKTP LGVFLAQFPV AQQQKLLQSY LKDFLLLTMK VSSREELMFL QMALWSCLRE LQEASGTPDE TYKFPLSLPW VH LAFQHFR TRLQNFSRIL TIHPQVLSSL SQAAEKHSLA GCEMTLDAFA AMACAEMLKG DLLKPSPKAW LQLVKNLSTP LEL VCSEGY LCDSGSMTRS VIQEVRALWN RIFSIALFVE HVLLGTESHI PELSPLVTTY VSLLDKCLEE DSNLKTCRPF VAVM TTLCD CKDKASKKFS RFGIQPCFIC HGDAQDPVCL PCDHVYCLRC IQTWLIPGQM MCPYCLTDLP DKFSPTVSQD HRKAI EKHA QFRHMCNSFF VDLVSTMCFK DNTPPEKSVI DTLLSLLFVQ KELLRDASQK HREHTKSLSP FDDVVDQTPV IRSVLL KLL LKYSFHEVKD YIQNYLTQLE KKAFLTEDKT ELYLLFISCL EDSVHQKTSA GCRNLEQVLR EEGHFLRTYS PGLQGQE PV RIASVEYLQE VARVRLCLDL AADFLSELQE GSELAEDKRR FLKHVEEFCT RVNNDWHRVY LVRKLSSQRG MEFVQSFS K QGHPCQWVFP RKVIAQQKDH VSLMDRYLVH GNEYKAVRDA TAKAVLECKT LDIGNALMAC RSPKPQQTAY LLLALYTEV AALYRSPNGS LHPEAKQLEA VNKFIKESKI LSDPNIRCFA RSLVDNTLPL LKIRSANSIL KGTVTEMAVH VATILLCGHN QILKPLRNL AFYPVNMANA FLPTMPEDLL VHARTWRGLE NVTWYTCPRG HPCSVGECGR PMQESTCLDC GLPVGGLNHT P HEGFSAIR NNEDRTQTGH VLGSPQSSGV AEVSDRGQSP VVFILTRLLT HLAMLVGATH NPQALTVIIK PWVQDPQGFL QQ HIQRDLE QLTKMLGRSA DETIHVVHLI LSSLLRVQSH GVLNFNAELS TKGCRNNWEK HFETLLLREL KHLDKNLPAI NAL ISQDER ISSNPVTKII YGDPATFLPH LPQKSIIHCS KIWSCRRKIT VEYLQHIVEQ KNGKETVPVL WHFLQKEAEL RLVK FLPEI LALQRDLVKQ FQNVSRVEYS SIRGFIHSHS SDGLRKLLHD RITIFLSTWN ALRRSLETNG EIKLPKDYCC SDLDL DAEF EVILPRRQGL GLCGTALVSY LISLHNNMVY TVQKFSNEDN SYSVDISEVA DLHVISYEVE RDLNPLILSN CQYQVQ QGG ETSQEFDLEK IQRQISSRFL QGKPRLTLKG IPTLVYRRDW NYEHLFMDIK NKMAQSSLPN LAISTISGQL QSYSDAC EA LSIIEITLGF LSTAGGDPGM DLNVYIEEVL RMCDQTAQVL KAFSRCQLRH IIALWQFLSA HKSEQRLRLN KELFREID V QYKEELSTQH QRLLGTFLNE AGLDAFLLEL HEMIVLKLKG PRAANSFNPN WSLKDTLVSY METKDSDILS EVESQFPEE ILMSSCISVW KIAATRKWDR QSRGGGHHHH HHHHHH UniProtKB: E3 ubiquitin-protein ligase RNF213 |
-Macromolecule #2: Ubiquitin-conjugating enzyme E2 L3
| Macromolecule | Name: Ubiquitin-conjugating enzyme E2 L3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 19.197908 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: GWSHPQFEKP GSMAASRRLM KELEEIRKSG MKNFRNIQVD EANLLTWQGL IVPDNPPYDK GAFRIEINFP AEYPFKPPKI TFKTKIYHP NIDEKGQVCL PVISAENWKP ATKTDQVIQS LIALVNDPQP EHPLRADLAE EYSKDRKKFS KNAEEFTKKY G EKRPVD UniProtKB: Ubiquitin-conjugating enzyme E2 L3 |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
| Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP |
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| Molecular weight | Theoretical: 507.181 Da |
| Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #4: MAGNESIUM ION
| Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
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| Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ZINC ION
| Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
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| Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
| Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP |
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| Molecular weight | Theoretical: 427.201 Da |
| Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 8 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Austria, 1 items
Citation









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Trichoplusia ni (cabbage looper)


Processing
FIELD EMISSION GUN

