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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22429 | ||||||||||||||||||
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Title | Cryo-EM structure of human HUWE1 (focused on WWE) | ||||||||||||||||||
![]() | map from refinement after classification focused on WWE | ||||||||||||||||||
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Function / homology | ![]() negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / cell differentiation / Golgi membrane / Neutrophil degranulation / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
![]() | Hunkeler M / Fischer ES | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition. Authors: Moritz Hunkeler / Cyrus Y Jin / Michelle W Ma / Julie K Monda / Daan Overwijn / Eric J Bennett / Eric S Fischer / ![]() Abstract: HECT ubiquitin ligases play essential roles in metazoan development and physiology. The HECT ligase HUWE1 is central to the cellular stress response by mediating degradation of key death or survival ...HECT ubiquitin ligases play essential roles in metazoan development and physiology. The HECT ligase HUWE1 is central to the cellular stress response by mediating degradation of key death or survival factors, including Mcl1, p53, DDIT4, and Myc. Although mutations in HUWE1 and related HECT ligases are widely implicated in human disease, our molecular understanding remains limited. Here we present a comprehensive investigation of full-length HUWE1, deepening our understanding of this class of enzymes. The N-terminal ∼3,900 amino acids of HUWE1 are indispensable for proper ligase function, and our cryo-EM structures of HUWE1 offer a complete molecular picture of this large HECT ubiquitin ligase. HUWE1 forms an alpha solenoid-shaped assembly with a central pore decorated with protein interaction modules. Structures of HUWE1 variants linked to neurodevelopmental disorders as well as of HUWE1 bound to a model substrate link the functions of this essential enzyme to its three-dimensional organization. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.1 KB 32.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.9 KB | Display | ![]() |
Images | ![]() | 35.9 KB | ||
Masks | ![]() | 184 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() ![]() | 162.5 MB 12.9 MB 11.4 MB 145.4 MB 145.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mweMC ![]() 7jq9C ![]() 7mopC ![]() 7mwdC ![]() 7mwfC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map from refinement after classification focused on WWE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: main map postprocessed with deepEMhancer
File | emd_22429_additional_1.map | ||||||||||||
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Annotation | main map postprocessed with deepEMhancer | ||||||||||||
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-Additional map: main map blurred to B=-20A2
File | emd_22429_additional_2.map | ||||||||||||
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Annotation | main map blurred to B=-20A2 | ||||||||||||
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-Additional map: main map blurred to B=10A2
File | emd_22429_additional_3.map | ||||||||||||
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Annotation | main map blurred to B=10A2 | ||||||||||||
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Density Histograms |
-Half map: half map 1
File | emd_22429_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_22429_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : E3 ubiquitin-protein ligase HUWE1
Entire | Name: E3 ubiquitin-protein ligase HUWE1 |
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Components |
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-Supramolecule #1: E3 ubiquitin-protein ligase HUWE1
Supramolecule | Name: E3 ubiquitin-protein ligase HUWE1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: full length, crosslinked with BS3, refinement after classification focused on WWE domain |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 480 KDa |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: E3 ubiquitin-protein ligase HUWE1
Macromolecule | Name: E3 ubiquitin-protein ligase HUWE1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: MDYKDDDDKL AAANSSIDLI STSLYKKAGF KGTNSVDMKV DRTKLKKTPT EAPADCRALI DKLKVCNDEQ LLLELQQIKT WNIGKCELYH WVDLLDRFDG ILADAGQTVE NMSWMLVCDR PEREQLKMLL LAVLNFTALL IEYSFSRHLY SSIEHLTTLL ASSDMQVVLA ...String: MDYKDDDDKL AAANSSIDLI STSLYKKAGF KGTNSVDMKV DRTKLKKTPT EAPADCRALI DKLKVCNDEQ LLLELQQIKT WNIGKCELYH WVDLLDRFDG ILADAGQTVE NMSWMLVCDR PEREQLKMLL LAVLNFTALL IEYSFSRHLY SSIEHLTTLL ASSDMQVVLA VLNLLYVFSK RSNYITRLGS DKRTPLLTRL QHLAESWGGK ENGFGLAECC RDLHMMKYPP SATTLHFEFY ADPGAEVKIE KRTTSNTLHY IHIEQLDKIS ESPSEIMESL TKMYSIPKDK QMLLFTHIRL AHGFSNHRKR LQAVQARLHA ISILVYSNAL QESANSILYN GLIEELVDVL QITDKQLMEI KAASLRTLTS IVHLERTPKL SSIIDCTGTA SYHGFLPVLV RNCIQAMIDP SMDPYPHQFA TALFSFLYHL ASYDAGGEAL VSCGMMEALL KVIKFLGDEQ DQITFVTRAV RVVDLITNLD MAAFQSHSGL SIFIYRLEHE VDLCRKECPF VIKPKIQRPN TTQEGEEMET DMDGVQCIPQ RAALLKSMLN FLKKAIQDPA FSDGIRHVMD GSLPTSLKHI ISNAEYYGPS LFLLATEVVT VFVFQEPSLL SSLQDNGLTD VMLHALLIKD VPATREVLGS LPNVFSALCL NARGLQSFVQ CQPFERLFKV LLSPDYLPAM RRRRSSDPLG DTASNLGSAV DELMRHQPTL KTDATTAIIK LLEEICNLGR DPKYICQKPS IQKADGTATA PPPRSNHAAE EASSEDEEEE EVQAMQSFNS TQQNETEPNQ QVVGTEERIP IPLMDYILNV MKFVESILSN NTTDDHCQEF VNQKGLLPLV TILGLPNLPI DFPTSAACQA VAGVCKSILT LSHEPKVLQE GLLQLDSILS SLEPLHRPIE SPGGSVLLRE LACAGNVADA TLSAQATPLL HALTAAHAYI MMFVHTCRVG QSEIRSISVN QWGSQLGLSV LSKLSQLYCS LVWESTVLLS LCTPNSLPSG CEFGQADMQK LVPKDEKAGT TQGGKRSDGE QDGAAGSMDA STQGLLEGIG LDGDTLAPME TDEPTASDSK GKSKITPAMA ARIKQIKPLL SASSRLGRAL AELFGLLVKL CVGSPVRQRR SHHAASTTTA PTPAARSTAS ALTKLLTKGL SWQPPPYTPT PRFRLTFFIC SVGFTSPMLF DERKYPYHLM LQKFLCSGGH NALFETFNWA LSMGGKVPVS EGLEHSDLPD GTGEFLDAWL MLVEKMVNPT TVLESPHSLP AKLPGGVQNF PQFSALRFLV VTQKAAFTCI KNLWNRKPLK VYGGRMAESM LAILCHILRG EPVIRERLSK EKEGSRGEED TGQEEGGSRR EPQVNQQQLQ QLMDMGFTRE HAMEALLNTS TMEQATEYLL THPPPIMGGV VRDLSMSEED QMMRAIAMSL GQDIPMDQRA ESPEEVACRK EEEERKAREK QEEEEAKCLE KFQDADPLEQ DELHTFTDTM LPGCFHLLDE LPDTVYRVCD LIMTAIKRNG ADYRDMILKQ VVNQVWEAAD VLIKAALPLT TSDTKTVSEW ISQMATLPQA SNLATRILLL TLLFEELKLP CAWVVESSGI LNVLIKLLEV VQPCLQAAKE QKEVQTPKWI TPVLLLIDFY EKTAISSKRR AQMTKYLQSN SNNWRWFDDR SGRWCSYSAS NNSTIDSAWK SGETSVRFTA GRRRYTVQFT TMVQVNEETG NRRPVMLTLL RVPRLNKNSK NSNGQELEKT LEESKEMDIK RKENKGNDTP LALESTNTEK ETSLEETKIG EILIQGLTED MVTVLIRACV SMLGVPVDPD TLHATLRLCL RLTRDHKYAM MFAELKSTRM ILNLTQSSGF NGFTPLVTLL LRHIIEDPCT LRHTMEKVVR SAATSGAGST TSGVVSGSLG SREINYILRV LGPAACRNPD IFTEVANCCI RIALPAPRGS GTASDDEFEN LRIKGPNAVQ LVKTTPLKPS PLPVIPDTIK EVIYDMLNAL AAYHAPEEAD KSDPKPGVMT QEVGQLLQDM GDDVYQQYRS LTRQSSDFDT QSGFSINSQV FAADGASTET SASGTSQGEA STPEESRDGK KDKEGDRASE EGKQKGKGSK PLMPTSTILR LLAELVRSYV GIATLIANYS YTVGQSELIK EDCSVLAFVL DHLLPHTQNA EDKDTPALAR LFLASLAAAG SGTDAQVALV NEVKAALGRA LAMAESTEKH ARLQAVMCII STIMESCPST SSFYSSATAK TQHNGMNNII RLFLKKGLVN DLARVPHSLD LSSPNMANTV NAALKPLETL SRIVNQPSSL FGSKSASSKN KSEQDAQGAS QDSSSNQQDP GEPGEAEVQE EDHDVTQTEV ADGDIMDGEA ETDSVVIAGQ PEVLSSQEMQ VENELEDLID ELLERDGGSG NSTIIVSRSG EDESQEDVLM DEAPSNLSQA STLQANREDS MNILDPEDEE EHTQEEDSSG SNEDEDDSQD EEEEEEEDEE DDQEDDEGEE GDEDDDDDGS EMELDEDYPD MNASPLVRFE RFDREDDLII EFDNMFSSAT DIPPSPGNIP TTHPLMVRHA DHSSLTLGSG SSTTRLTQGI GRSQRTLRQL TANTGHTIHV HYPGNRQPNP PLILQRLLGP SAAADILQLS SSLPLQSRGR ARLLVGNDDV HIIARSDDEL LDDFFHDQST ATSQAGTLSS IPTALTRWTE ECKVLDAESM HDCVSVVKVS IVNHLEFLRD EELEERREKR RKQLAEEETK ITDKGKEDKE NRDQSAQCTA SKSNDSTEQN LSDGTPMPDS YPTTPSSTDA ATSESKETLG TLQSSQQQPT LPTPPALGEV PQELQSPAGE GGSSTQLLMP VEPEELGPTR PSGEAETTQM ELSPAPTITS LSPERAEDSD ALTAVSSQLE GSPMDTSSLA SCTLEEAVGD TSAAGSSEQP RAGSSTPGDA PPAVAEVQGR SDGSGESAQP PEDSSPPASS ESSSTRDSAV AISGADSRGI LEEPLPSTSS EEEDPLAGIS LPEGVDPSFL AALPDDIRRE VLQNQLGIRP PTRTAPSTNS SAPAVVGNPG VTEVSPEFLA ALPPAIQEEV LAQQRAEQQR RELAQNASSD TPMDPVTFIQ TLPSDLRRSV LEDMEDSVLA VMPPDIAAEA QALRREQEAR QRQLMHERLF GHSSTSALSA ILRSPAFTSR LSGNRGVQYT RLAVQRGGTF QMGGSSSHNR PSGSNVDTLL RLRGRLLLDH EALSCLLVLL FVDEPKLNTS RLHRVLRNLC YHAQTRHWVI RSLLSILQRS SESELCIETP KLTTSEEKGK KSSKSCGSSS HENRPLDLLH KMESKSSNQL SWLSVSMDAA LGCRTNIFQI QRSGGRKHTE KHASGGSTVH IHPQAAPVVC RHVLDTLIQL AKVFPSHFTQ QRTKETNCES DRERGNKACS PCSSQSSSSG ICTDFWDLLV KLDNMNVSRK GKNSVKSVPV SAGGEGETSP YSLEASPLGQ LMNMLSHPVI RRSSLLTEKL LRLLSLISIA LPENKVSEAQ ANSGSGASST TTATSTTSTT TTTAASTTPT PPTAPTPVTS APALVAATAI STIVVAASTT VTTPTTATTT VSISPTTKGS KSPAKVSDGG SSSTDFKMVS SGLTENQLQL SVEVLTSHSC SEEGLEDAAN VLLQLSRGDS GTRDTVLKLL LNGARHLGYT LCKQIGTLLA ELREYNLEQQ RRAQCETLSP DGLPEEQPQT TKLKGKMQSR FDMAENVVIV ASQKRPLGGR ELQLPSMSML TSKTSTQKFF LRVLQVIIQL RDDTRRANKK AKQTGRLGSS GLGSASSIQA AVRQLEAEAD AIIQMVREGQ RARRQQQAAT SESSQSEASV RREESPMDVD QPSPSAQDTQ SIASDGTPQG EKEKEERPPE LPLLSEQLSL DELWDMLGEC LKELEESHDQ HAVLVLQPAV EAFFLVHATE RESKPPVRDT RESQLAHIKD EPPPLSPAPL TPATPSSLDP FFSREPSSMH ISSSLPPDTQ KFLRFAETHR TVLNQILRQS TTHLADGPFA VLVDYIRVLD FDVKRKYFRQ ELERLDEGLR KEDMAVHVRR DHVFEDSYRE LHRKSPEEMK NRLYIVFEGE EGQDAGGLLR EWYMIISREM FNPMYALFRT SPGDRVTYTI NPSSHCNPNH LSYFKFVGRI VAKAVYDNRL LECYFTRSFY KHILGKSVRY TDMESEDYHF YQGLVYLLEN DVSTLGYDLT FSTEVQEFGV CEVRDLKPNG ANILVTEENK KEYVHLVCQM RMTGAIRKQL AAFLEGFYEI IPKRLISIFT EQELELLISG LPTIDIDDLK SNTEYHKYQS NSIQIQWFWR ALRSFDQADR AKFLQFVTGT SKVPLQGFAA LEGMNGIQKF QIHRDDRSTD RLPSAHTCFN QLDLPAYESF EKLRHMLLLA IQECSEGFGL A |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP Details: CHAPSO detergent added to final conc. of 0.8 mM. Sample applied twice.. | |||||||||
Details | Sample crosslinked with BS3. Monodisperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Data colleciton in counting mode, using multi-shot scheme (4 holes per stage position, 3 movies per hole) |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 10390 / Average exposure time: 2.4 sec. / Average electron dose: 45.68 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |