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- EMDB-23931: Cryo-EM structure of human HUWE1 (d169-189 variant) -

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Basic information

Entry
Database: EMDB / ID: EMD-23931
TitleCryo-EM structure of human HUWE1 (d169-189 variant)
Map datamain map from Relion PostProcess
Sample
  • Organelle or cellular component: E3 ubiquitin-protein ligase HUWE1 (d169-189 variant)
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1
Function / homology
Function and homology information


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 / 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
HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE domain ...HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsHunkeler M / Fischer ES
Funding support United States, Switzerland, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA2144608 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA218278 United States
Swiss National Science Foundation174331 Switzerland
Swiss National Science Foundation191053 Switzerland
Other privateDRR-50-18 United States
CitationJournal: Mol Cell / Year: 2021
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
DepositionMay 4, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23931.png

Downloads & links

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Map

FileDownload / File: emd_23931.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map from Relion PostProcess
Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 0.048 / Movie #1: 0.048
Minimum - Maximum-0.06730821 - 0.1670167
Average (Standard dev.)0.00057165534 (±0.0058445632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z306.000306.000306.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0670.1670.001

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Supplemental data

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Mask #1

Fileemd_23931_msk_1.map
Projections & Slices
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Additional map: filtered map from Relion locres

Fileemd_23931_additional_1.map
Annotationfiltered map from Relion locres
Projections & Slices
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Additional map: main map postprocessed with deepEMhancer (wideTarget)

Fileemd_23931_additional_2.map
Annotationmain map postprocessed with deepEMhancer (wideTarget)
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Half map: half map 2 from Relion refine

Fileemd_23931_half_map_1.map
Annotationhalf map 2 from Relion refine
Projections & Slices
AxesZYX

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Half map: half map 2 from Relion refine

Fileemd_23931_half_map_2.map
Annotationhalf map 2 from Relion refine
Projections & Slices
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Sample components

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Entire : E3 ubiquitin-protein ligase HUWE1 (d169-189 variant)

EntireName: E3 ubiquitin-protein ligase HUWE1 (d169-189 variant)
Components
  • Organelle or cellular component: E3 ubiquitin-protein ligase HUWE1 (d169-189 variant)
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1

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Supramolecule #1: E3 ubiquitin-protein ligase HUWE1 (d169-189 variant)

SupramoleculeName: E3 ubiquitin-protein ligase HUWE1 (d169-189 variant) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: patient mutation variant d169-189
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 480 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: expi293 / Recombinant plasmid: pDEST

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Macromolecule #1: E3 ubiquitin-protein ligase HUWE1

MacromoleculeName: E3 ubiquitin-protein ligase HUWE1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 QHLAEKYPPS ATTLHFEFYA DPGAEVKIEK RTTSNTLHYI HIEQLDKISE SPSEIMESLT KMYSIPKDKQ MLLFTHIRLA HGFSNHRKRL QAVQARLHAI SILVYSNALQ ESANSILYNG LIEELVDVLQ ITDKQLMEIK AASLRTLTSI VHLERTPKLS SIIDCTGTAS YHGFLPVLVR NCIQAMIDPS MDPYPHQFAT ALFSFLYHLA SYDAGGEALV SCGMMEALLK VIKFLGDEQD QITFVTRAVR VVDLITNLDM AAFQSHSGLS IFIYRLEHEV DLCRKECPFV IKPKIQRPNT TQEGEEMETD MDGVQCIPQR AALLKSMLNF LKKAIQDPAF SDGIRHVMDG SLPTSLKHII SNAEYYGPSL FLLATEVVTV FVFQEPSLLS SLQDNGLTDV MLHALLIKDV PATREVLGSL PNVFSALCLN ARGLQSFVQC QPFERLFKVL LSPDYLPAMR RRRSSDPLGD TASNLGSAVD ELMRHQPTLK TDATTAIIKL LEEICNLGRD PKYICQKPSI QKADGTATAP PPRSNHAAEE ASSEDEEEEE VQAMQSFNST QQNETEPNQQ VVGTEERIPI PLMDYILNVM KFVESILSNN TTDDHCQEFV NQKGLLPLVT ILGLPNLPID FPTSAACQAV AGVCKSILTL SHEPKVLQEG LLQLDSILSS LEPLHRPIES PGGSVLLREL ACAGNVADAT LSAQATPLLH ALTAAHAYIM MFVHTCRVGQ SEIRSISVNQ WGSQLGLSVL SKLSQLYCSL VWESTVLLSL CTPNSLPSGC EFGQADMQKL VPKDEKAGTT QGGKRSDGEQ DGAAGSMDAS TQGLLEGIGL DGDTLAPMET DEPTASDSKG KSKITPAMAA RIKQIKPLLS ASSRLGRALA ELFGLLVKLC VGSPVRQRRS HHAASTTTAP TPAARSTASA LTKLLTKGLS WQPPPYTPTP RFRLTFFICS VGFTSPMLFD ERKYPYHLML QKFLCSGGHN ALFETFNWAL SMGGKVPVSE GLEHSDLPDG TGEFLDAWLM LVEKMVNPTT VLESPHSLPA KLPGGVQNFP QFSALRFLVV TQKAAFTCIK NLWNRKPLKV YGGRMAESML AILCHILRGE PVIRERLSKE KEGSRGEEDT GQEEGGSRRE PQVNQQQLQQ LMDMGFTREH AMEALLNTST MEQATEYLLT HPPPIMGGVV RDLSMSEEDQ MMRAIAMSLG QDIPMDQRAE SPEEVACRKE EEERKAREKQ EEEEAKCLEK FQDADPLEQD ELHTFTDTML PGCFHLLDEL PDTVYRVCDL IMTAIKRNGA DYRDMILKQV VNQVWEAADV LIKAALPLTT SDTKTVSEWI SQMATLPQAS NLATRILLLT LLFEELKLPC AWVVESSGIL NVLIKLLEVV QPCLQAAKEQ KEVQTPKWIT PVLLLIDFYE KTAISSKRRA QMTKYLQSNS NNWRWFDDRS GRWCSYSASN NSTIDSAWKS GETSVRFTAG RRRYTVQFTT MVQVNEETGN RRPVMLTLLR VPRLNKNSKN SNGQELEKTL EESKEMDIKR KENKGNDTPL ALESTNTEKE TSLEETKIGE ILIQGLTEDM VTVLIRACVS MLGVPVDPDT LHATLRLCLR LTRDHKYAMM FAELKSTRMI LNLTQSSGFN GFTPLVTLLL RHIIEDPCTL RHTMEKVVRS AATSGAGSTT SGVVSGSLGS REINYILRVL GPAACRNPDI FTEVANCCIR IALPAPRGSG TASDDEFENL RIKGPNAVQL VKTTPLKPSP LPVIPDTIKE VIYDMLNALA AYHAPEEADK SDPKPGVMTQ EVGQLLQDMG DDVYQQYRSL TRQSSDFDTQ SGFSINSQVF AADGASTETS ASGTSQGEAS TPEESRDGKK DKEGDRASEE GKQKGKGSKP LMPTSTILRL LAELVRSYVG IATLIANYSY TVGQSELIKE DCSVLAFVLD HLLPHTQNAE DKDTPALARL FLASLAAAGS GTDAQVALVN EVKAALGRAL AMAESTEKHA RLQAVMCIIS TIMESCPSTS SFYSSATAKT QHNGMNNIIR LFLKKGLVND LARVPHSLDL SSPNMANTVN AALKPLETLS RIVNQPSSLF GSKSASSKNK SEQDAQGASQ DSSSNQQDPG EPGEAEVQEE DHDVTQTEVA DGDIMDGEAE TDSVVIAGQP EVLSSQEMQV ENELEDLIDE LLERDGGSGN STIIVSRSGE DESQEDVLMD EAPSNLSQAS TLQANREDSM NILDPEDEEE HTQEEDSSGS NEDEDDSQDE EEEEEEDEED DQEDDEGEEG DEDDDDDGSE MELDEDYPDM NASPLVRFER FDREDDLIIE FDNMFSSATD IPPSPGNIPT THPLMVRHAD HSSLTLGSGS STTRLTQGIG RSQRTLRQLT ANTGHTIHVH YPGNRQPNPP LILQRLLGPS AAADILQLSS SLPLQSRGRA RLLVGNDDVH IIARSDDELL DDFFHDQSTA TSQAGTLSSI PTALTRWTEE CKVLDAESMH DCVSVVKVSI VNHLEFLRDE ELEERREKRR KQLAEEETKI TDKGKEDKEN RDQSAQCTAS KSNDSTEQNL SDGTPMPDSY PTTPSSTDAA TSESKETLGT LQSSQQQPTL PTPPALGEVP QELQSPAGEG GSSTQLLMPV EPEELGPTRP SGEAETTQME LSPAPTITSL SPERAEDSDA LTAVSSQLEG SPMDTSSLAS CTLEEAVGDT SAAGSSEQPR AGSSTPGDAP PAVAEVQGRS DGSGESAQPP EDSSPPASSE SSSTRDSAVA ISGADSRGIL EEPLPSTSSE EEDPLAGISL PEGVDPSFLA ALPDDIRREV LQNQLGIRPP TRTAPSTNSS APAVVGNPGV TEVSPEFLAA LPPAIQEEVL AQQRAEQQRR ELAQNASSDT PMDPVTFIQT LPSDLRRSVL EDMEDSVLAV MPPDIAAEAQ ALRREQEARQ RQLMHERLFG HSSTSALSAI LRSPAFTSRL SGNRGVQYTR LAVQRGGTFQ MGGSSSHNRP SGSNVDTLLR LRGRLLLDHE ALSCLLVLLF VDEPKLNTSR LHRVLRNLCY HAQTRHWVIR SLLSILQRSS ESELCIETPK LTTSEEKGKK SSKSCGSSSH ENRPLDLLHK MESKSSNQLS WLSVSMDAAL GCRTNIFQIQ RSGGRKHTEK HASGGSTVHI HPQAAPVVCR HVLDTLIQLA KVFPSHFTQQ RTKETNCESD RERGNKACSP CSSQSSSSGI CTDFWDLLVK LDNMNVSRKG KNSVKSVPVS AGGEGETSPY SLEASPLGQL MNMLSHPVIR RSSLLTEKLL RLLSLISIAL PENKVSEAQA NSGSGASSTT TATSTTSTTT TTAASTTPTP PTAPTPVTSA PALVAATAIS TIVVAASTTV TTPTTATTTV SISPTTKGSK SPAKVSDGGS SSTDFKMVSS GLTENQLQLS VEVLTSHSCS EEGLEDAANV LLQLSRGDSG TRDTVLKLLL NGARHLGYTL CKQIGTLLAE LREYNLEQQR RAQCETLSPD GLPEEQPQTT KLKGKMQSRF DMAENVVIVA SQKRPLGGRE LQLPSMSMLT SKTSTQKFFL RVLQVIIQLR DDTRRANKKA KQTGRLGSSG LGSASSIQAA VRQLEAEADA IIQMVREGQR ARRQQQAATS ESSQSEASVR REESPMDVDQ PSPSAQDTQS IASDGTPQGE KEKEERPPEL PLLSEQLSLD ELWDMLGECL KELEESHDQH AVLVLQPAVE AFFLVHATER ESKPPVRDTR ESQLAHIKDE PPPLSPAPLT PATPSSLDPF FSREPSSMHI SSSLPPDTQK FLRFAETHRT VLNQILRQST THLADGPFAV LVDYIRVLDF DVKRKYFRQE LERLDEGLRK EDMAVHVRRD HVFEDSYREL HRKSPEEMKN RLYIVFEGEE GQDAGGLLRE WYMIISREMF NPMYALFRTS PGDRVTYTIN PSSHCNPNHL SYFKFVGRIV AKAVYDNRLL ECYFTRSFYK HILGKSVRYT DMESEDYHFY QGLVYLLEND VSTLGYDLTF STEVQEFGVC EVRDLKPNGA NILVTEENKK EYVHLVCQMR MTGAIRKQLA AFLEGFYEII PKRLISIFTE QELELLISGL PTIDIDDLKS NTEYHKYQSN SIQIQWFWRA LRSFDQADRA KFLQFVTGTS KVPLQGFAAL EGMNGIQKFQ IHRDDRSTDR LPSAHTCFNQ LDLPAYESFE KLRHMLLLAI QECSEGFGLA

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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

Concentration1.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4S(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
150.0 mMNaClSodium chlorideSodium chloride
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 91 % / Chamber temperature: 283 K / Instrument: LEICA EM GP / Details: CHAPSO detergent added to final conc. of 1 mM..
DetailsMonodisperse.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -2.2 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsData collection in counting mode
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3862 / Average exposure time: 6.0 sec. / Average electron dose: 54.86 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 992194
CTF correctionSoftware: (Name: CTFFIND, RELION) / Details: standard correction in Relion
Startup modelType of model: OTHER / Details: de novo model generated in cryoSPARCv2
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION / Details: Relion
Final 3D classificationNumber classes: 6 / Avg.num./class: 53000 / Software - Name: RELION / Details: final class with 19% of particles
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: as implemented in relion / Number images used: 60560
FSC plot (resolution estimation)

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