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- EMDB-22427: Cryo-EM structure of human HUWE1 -

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Basic information

Entry
Database: EMDB / ID: EMD-22427
TitleCryo-EM structure of human HUWE1
Map dataCryo-EM structure of human HUWE1
Sample
  • Organelle or cellular component: E3 ubiquitin-protein ligase HUWE1
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1
KeywordsUbiquitin / Quality Control / E3 ligase / protein degradation / TRANSFERASE
Function / homology
Function and homology information


histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / : / 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 ...histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / : / 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
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) / WWE domain / UBA-like domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain superfamily ...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) / WWE domain / UBA-like domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / 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 / 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: 3.1 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
DepositionAug 10, 2020-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jq9
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22427.png

Downloads & links

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Map

FileDownload / File: emd_22427.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human HUWE1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 364 pix.
= 300.3 Å		0.83 Å/pix.
x 364 pix.
= 300.3 Å		0.83 Å/pix.
x 364 pix.
= 300.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.0676397 - 0.12725288
Average (Standard dev.)0.00017041744 (±0.0023082066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 300.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z364364364
origin x/y/z0.0000.0000.000
length x/y/z300.300300.300300.300
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS364364364
D min/max/mean-0.0680.1270.000

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Supplemental data

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Mask #1

Fileemd_22427_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: main map postprocessed with deepEMhancer

Fileemd_22427_additional_1.map
Annotationmain map postprocessed with deepEMhancer
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: main map blurred to B=10A2

Fileemd_22427_additional_2.map
Annotationmain map blurred to B=10A2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_22427_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_22427_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E3 ubiquitin-protein ligase HUWE1

EntireName: E3 ubiquitin-protein ligase HUWE1
Components
  • Organelle or cellular component: E3 ubiquitin-protein ligase HUWE1
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1

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Supramolecule #1: E3 ubiquitin-protein ligase HUWE1

SupramoleculeName: E3 ubiquitin-protein ligase HUWE1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: full length, crosslinked with BS3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: E3 ubiquitin-protein ligase HUWE1

MacromoleculeName: E3 ubiquitin-protein ligase HUWE1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 486.409531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKL AAANSSIDLI STSLYKKAGF KGTNSVDMKV DRTKLKKTPT EAPADCRALI DKLKVCNDEQ LLLELQQIKT WNIGKCELY HWVDLLDRFD GILADAGQTV ENMSWMLVCD RPEREQLKML LLAVLNFTAL LIEYSFSRHL YSSIEHLTTL L ASSDMQVV ...String:
MDYKDDDDKL AAANSSIDLI STSLYKKAGF KGTNSVDMKV DRTKLKKTPT EAPADCRALI DKLKVCNDEQ LLLELQQIKT WNIGKCELY HWVDLLDRFD GILADAGQTV ENMSWMLVCD RPEREQLKML LLAVLNFTAL LIEYSFSRHL YSSIEHLTTL L ASSDMQVV LAVLNLLYVF SKRSNYITRL GSDKRTPLLT RLQHLAESWG GKENGFGLAE CCRDLHMMKY PPSATTLHFE FY ADPGAEV KIEKRTTSNT LHYIHIEQLD KISESPSEIM ESLTKMYSIP KDKQMLLFTH IRLAHGFSNH RKRLQAVQAR LHA ISILVY SNALQESANS ILYNGLIEEL VDVLQITDKQ LMEIKAASLR TLTSIVHLER TPKLSSIIDC TGTASYHGFL PVLV RNCIQ AMIDPSMDPY PHQFATALFS FLYHLASYDA GGEALVSCGM MEALLKVIKF LGDEQDQITF VTRAVRVVDL ITNLD MAAF QSHSGLSIFI YRLEHEVDLC RKECPFVIKP KIQRPNTTQE GEEMETDMDG VQCIPQRAAL LKSMLNFLKK AIQDPA FSD GIRHVMDGSL PTSLKHIISN AEYYGPSLFL LATEVVTVFV FQEPSLLSSL QDNGLTDVML HALLIKDVPA TREVLGS LP NVFSALCLNA RGLQSFVQCQ PFERLFKVLL SPDYLPAMRR RRSSDPLGDT ASNLGSAVDE LMRHQPTLKT DATTAIIK L LEEICNLGRD PKYICQKPSI QKADGTATAP PPRSNHAAEE ASSEDEEEEE VQAMQSFNST QQNETEPNQQ VVGTEERIP IPLMDYILNV MKFVESILSN NTTDDHCQEF VNQKGLLPLV TILGLPNLPI DFPTSAACQA VAGVCKSILT LSHEPKVLQE GLLQLDSIL SSLEPLHRPI ESPGGSVLLR ELACAGNVAD ATLSAQATPL LHALTAAHAY IMMFVHTCRV GQSEIRSISV N QWGSQLGL SVLSKLSQLY CSLVWESTVL LSLCTPNSLP SGCEFGQADM QKLVPKDEKA GTTQGGKRSD GEQDGAAGSM DA STQGLLE GIGLDGDTLA PMETDEPTAS DSKGKSKITP AMAARIKQIK PLLSASSRLG RALAELFGLL VKLCVGSPVR QRR SHHAAS TTTAPTPAAR STASALTKLL TKGLSWQPPP YTPTPRFRLT FFICSVGFTS PMLFDERKYP YHLMLQKFLC SGGH NALFE TFNWALSMGG KVPVSEGLEH SDLPDGTGEF LDAWLMLVEK MVNPTTVLES PHSLPAKLPG GVQNFPQFSA LRFLV VTQK AAFTCIKNLW NRKPLKVYGG RMAESMLAIL CHILRGEPVI RERLSKEKEG SRGEEDTGQE EGGSRREPQV NQQQLQ QLM DMGFTREHAM EALLNTSTME QATEYLLTHP PPIMGGVVRD LSMSEEDQMM RAIAMSLGQD IPMDQRAESP EEVACRK EE EERKAREKQE EEEAKCLEKF QDADPLEQDE LHTFTDTMLP GCFHLLDELP DTVYRVCDLI MTAIKRNGAD YRDMILKQ V VNQVWEAADV LIKAALPLTT SDTKTVSEWI SQMATLPQAS NLATRILLLT LLFEELKLPC AWVVESSGIL NVLIKLLEV VQPCLQAAKE QKEVQTPKWI TPVLLLIDFY EKTAISSKRR AQMTKYLQSN SNNWRWFDDR SGRWCSYSAS NNSTIDSAWK SGETSVRFT AGRRRYTVQF TTMVQVNEET GNRRPVMLTL LRVPRLNKNS KNSNGQELEK TLEESKEMDI KRKENKGNDT P LALESTNT EKETSLEETK IGEILIQGLT EDMVTVLIRA CVSMLGVPVD PDTLHATLRL CLRLTRDHKY AMMFAELKST RM ILNLTQS SGFNGFTPLV TLLLRHIIED PCTLRHTMEK VVRSAATSGA GSTTSGVVSG SLGSREINYI LRVLGPAACR NPD IFTEVA NCCIRIALPA PRGSGTASDD EFENLRIKGP NAVQLVKTTP LKPSPLPVIP DTIKEVIYDM LNALAAYHAP EEAD KSDPK PGVMTQEVGQ LLQDMGDDVY QQYRSLTRQS SDFDTQSGFS INSQVFAADG ASTETSASGT SQGEASTPEE SRDGK KDKE GDRASEEGKQ KGKGSKPLMP TSTILRLLAE LVRSYVGIAT LIANYSYTVG QSELIKEDCS VLAFVLDHLL PHTQNA EDK DTPALARLFL ASLAAAGSGT DAQVALVNEV KAALGRALAM AESTEKHARL QAVMCIISTI MESCPSTSSF YSSATAK TQ HNGMNNIIRL FLKKGLVNDL ARVPHSLDLS SPNMANTVNA ALKPLETLSR IVNQPSSLFG SKSASSKNKS EQDAQGAS Q DSSSNQQDPG EPGEAEVQEE DHDVTQTEVA DGDIMDGEAE TDSVVIAGQP EVLSSQEMQV ENELEDLIDE LLERDGGSG NSTIIVSRSG EDESQEDVLM DEAPSNLSQA STLQANREDS MNILDPEDEE EHTQEEDSSG SNEDEDDSQD EEEEEEEDEE DDQEDDEGE EGDEDDDDDG SEMELDEDYP DMNASPLVRF ERFDREDDLI IEFDNMFSSA TDIPPSPGNI PTTHPLMVRH A DHSSLTLG SGSSTTRLTQ GIGRSQRTLR QLTANTGHTI HVHYPGNRQP NPPLILQRLL GPSAAADILQ LSSSLPLQSR GR ARLLVGN DDVHIIARSD DELLDDFFHD QSTATSQAGT LSSIPTALTR WTEECKVLDA ESMHDCVSVV KVSIVNHLEF LRD EELEER REKRRKQLAE EETKITDKGK EDKENRDQSA QCTASKSNDS TEQNLSDGTP MPDSYPTTPS STDAATSESK ETLG TLQSS QQQPTLPTPP ALGEVPQELQ SPAGEGGSST QLLMPVEPEE LGPTRPSGEA ETTQMELSPA PTITSLSPER AEDSD ALTA VSSQLEGSPM DTSSLASCTL EEAVGDTSAA GSSEQPRAGS STPGDAPPAV AEVQGRSDGS GESAQPPEDS SPPASS ESS STRDSAVAIS GADSRGILEE PLPSTSSEEE DPLAGISLPE GVDPSFLAAL PDDIRREVLQ NQLGIRPPTR TAPSTNS SA PAVVGNPGVT EVSPEFLAAL PPAIQEEVLA QQRAEQQRRE LAQNASSDTP MDPVTFIQTL PSDLRRSVLE DMEDSVLA V MPPDIAAEAQ ALRREQEARQ RQLMHERLFG HSSTSALSAI LRSPAFTSRL SGNRGVQYTR LAVQRGGTFQ MGGSSSHNR PSGSNVDTLL RLRGRLLLDH EALSCLLVLL FVDEPKLNTS RLHRVLRNLC YHAQTRHWVI RSLLSILQRS SESELCIETP KLTTSEEKG KKSSKSCGSS SHENRPLDLL HKMESKSSNQ LSWLSVSMDA ALGCRTNIFQ IQRSGGRKHT EKHASGGSTV H IHPQAAPV VCRHVLDTLI QLAKVFPSHF TQQRTKETNC ESDRERGNKA CSPCSSQSSS SGICTDFWDL LVKLDNMNVS RK GKNSVKS VPVSAGGEGE TSPYSLEASP LGQLMNMLSH PVIRRSSLLT EKLLRLLSLI SIALPENKVS EAQANSGSGA SST TTATST TSTTTTTAAS TTPTPPTAPT PVTSAPALVA ATAISTIVVA ASTTVTTPTT ATTTVSISPT TKGSKSPAKV SDGG SSSTD FKMVSSGLTE NQLQLSVEVL TSHSCSEEGL EDAANVLLQL SRGDSGTRDT VLKLLLNGAR HLGYTLCKQI GTLLA ELRE YNLEQQRRAQ CETLSPDGLP EEQPQTTKLK GKMQSRFDMA ENVVIVASQK RPLGGRELQL PSMSMLTSKT STQKFF LRV LQVIIQLRDD TRRANKKAKQ TGRLGSSGLG SASSIQAAVR QLEAEADAII QMVREGQRAR RQQQAATSES SQSEASV RR EESPMDVDQP SPSAQDTQSI ASDGTPQGEK EKEERPPELP LLSEQLSLDE LWDMLGECLK ELEESHDQHA VLVLQPAV E AFFLVHATER ESKPPVRDTR ESQLAHIKDE PPPLSPAPLT PATPSSLDPF FSREPSSMHI SSSLPPDTQK FLRFAETHR TVLNQILRQS TTHLADGPFA VLVDYIRVLD FDVKRKYFRQ ELERLDEGLR KEDMAVHVRR DHVFEDSYRE LHRKSPEEMK NRLYIVFEG EEGQDAGGLL REWYMIISRE MFNPMYALFR TSPGDRVTYT INPSSHCNPN HLSYFKFVGR IVAKAVYDNR L LECYFTRS FYKHILGKSV RYTDMESEDY HFYQGLVYLL ENDVSTLGYD LTFSTEVQEF GVCEVRDLKP NGANILVTEE NK KEYVHLV CQMRMTGAIR KQLAAFLEGF YEIIPKRLIS IFTEQELELL ISGLPTIDID DLKSNTEYHK YQSNSIQIQW FWR ALRSFD QADRAKFLQF VTGTSKVPLQ GFAALEGMNG IQKFQIHRDD RSTDRLPSAH TCFNQLDLPA YESFEKLRHM LLLA IQECS EGFGLA

UniProtKB: E3 ubiquitin-protein ligase HUWE1

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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

Concentration0.9 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4S(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
150.0 mMNaClSodium 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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen 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..
DetailsSample crosslinked with BS3. Monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsData collection in counting mode, using multi-shot scheme (4 holes per stage position, 3 movies per hole)
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 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

Particle selectionNumber selected: 2110785
Startup modelType of model: OTHER / Details: de novo model generated in cryoSPARCv2
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: as implemented in relion / Number images used: 762898
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION / Details: Relion
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Avg.num./class: 250000 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 60.88 / Target criteria: CC
Output model

PDB-7jq9:
Cryo-EM structure of human HUWE1

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