[English] 日本語

- EMDB-50914: Structure of human RNF213 bound to the secreted effector IpaH2.5 ... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri | |||||||||
![]() | Composite cryoEM map of IpaH2.5-RNF213 complex, produced from a combination of locally refined sharpened maps | |||||||||
![]() |
| |||||||||
![]() | RNF213 / IpaH2.5 / IpaH / E3 ligase / RING / LRR / NEL / secreted effector / Shigella / inhibitor / complex / AAA ATPase / ANTIMICROBIAL PROTEIN | |||||||||
Function / homology | ![]() lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / regulation of lipid metabolic process / protein K63-linked ubiquitination ...lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / regulation of lipid metabolic process / protein K63-linked ubiquitination / protein autoubiquitination / lipid droplet / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Signaling by ALK fusions and activated point mutants / Antigen processing: Ubiquitination & Proteasome degradation / toxin activity / ubiquitin-dependent protein catabolic process / angiogenesis / host cell cytoplasm / protein ubiquitination / defense response to bacterium / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / nucleolus / ATP hydrolysis activity / extracellular region / ATP binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Naydenova K / Randow F | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213 Authors: Naydenova K / Boyle KB / Pathe C / Pothukuchi P / Crespillo-Casado A / Otten EG / Hammoudi P-M / Randow F | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 220 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
Images | ![]() | 132.7 KB | ||
Filedesc metadata | ![]() | 9.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 359.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 358.9 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9g09MC ![]() 9g08C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Composite cryoEM map of IpaH2.5-RNF213 complex, produced from a combination of locally refined sharpened maps | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2375 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
Sample components
-Entire : E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shi...
Entire | Name: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri |
---|---|
Components |
|
-Supramolecule #1: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shi...
Supramolecule | Name: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: ![]() |
-Macromolecule #1: E3 ubiquitin-protein ligase IpaH2.5
Macromolecule | Name: E3 ubiquitin-protein ligase IpaH2.5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 63.651699 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIKSTNIQVI GSGIMHQINN IHSLTLFSLP VSLSPSCNEY YLKVWSEWER NGTPGEQRNI AFNRLKICLQ NQEAELNLSE LDLKTLPDL PPQITTLEIR KNLLTHLPDL PPMLKVIHAQ FNQLESLPAL PETLEELNAG DNKIKELPFL PENLTHLRVH N NRLHILPL ...String: MIKSTNIQVI GSGIMHQINN IHSLTLFSLP VSLSPSCNEY YLKVWSEWER NGTPGEQRNI AFNRLKICLQ NQEAELNLSE LDLKTLPDL PPQITTLEIR KNLLTHLPDL PPMLKVIHAQ FNQLESLPAL PETLEELNAG DNKIKELPFL PENLTHLRVH N NRLHILPL LPPELKLLVV SGNRLDSIPP FPDKLEGLAL ANNFIEQLPE LPFSMNRAVL MNNNLTTLPE SVLRLAQNAF VN VAGNPLS GHTMRTLQQI TTGPDYSGPQ IFFSMGNSAT ISAPEHSLAD AVTAWFPENK QSDVSQIWHA FEHEEHANTF SAF LDRLSD TVSARNTSGF REQVAAWLEK LSASAELRQQ SFAVAADATE SCEDRVALTW NNLRKTLLVH QASEGLFDND TGAL LSLGR EMFRLEILED IARDKVRTLH FVDEIEVYLA FQTMLAEKLQ LSTAVKEMRF YGVSGVTAND LRTAEAMVRS REENE FTDW FSLWGPWHAV LKRTEADRWA QAEEQKYEML ENEYSQRVAD RLKASGLSGD ADAEREAGAQ VMRETEQQIY RQLTDE VLA UniProtKB: E3 ubiquitin-protein ligase IpaH2.5 |
-Macromolecule #2: E3 ubiquitin-protein ligase RNF213
Macromolecule | Name: E3 ubiquitin-protein ligase RNF213 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 596.45025 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 PRTADNFNDI 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 |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP |
---|---|
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 |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 |
---|---|
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 23344 / Average exposure time: 1.75 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213053 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |