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- EMDB-22428: Cryo-EM structure of human HUWE1 (focused on HECT) -

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Basic information

Entry
Database: EMDB / ID: EMD-22428
TitleCryo-EM structure of human HUWE1 (focused on HECT)
Map datamap from refinement after classification focused on HECT domain
Sample
  • Organelle or cellular component: E3 ubiquitin-protein ligase HUWE1
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1
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: 3.7 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-
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: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7mwd
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22428.png

Downloads & links

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Map

FileDownload / File: emd_22428.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap from refinement after classification focused on HECT domain
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: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.04175356 - 0.09367054
Average (Standard dev.)0.0001846184 (±0.0021022726)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS364364364
D min/max/mean-0.0420.0940.000

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Supplemental data

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Mask #1

Fileemd_22428_msk_1.map
Projections & Slices
AxesZYX

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Additional map: main map blurred to B=10A2

Fileemd_22428_additional_1.map
Annotationmain map blurred to B=10A2
Projections & Slices
AxesZYX

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Additional map: main map blurred to B=-20A2

Fileemd_22428_additional_2.map
Annotationmain map blurred to B=-20A2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: half map 2

Fileemd_22428_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_22428_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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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, refinement after classification focused on HECT domain
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 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

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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: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / 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 colleciton 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
CTF correctionSoftware: (Name: CTFFIND, RELION) / Details: standard correction in Relion
Startup modelType of model: OTHER / Details: de novo model generated in cryoSPARCv2
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: as implemented in Relion / Number images used: 33078
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION / Details: Relion
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 8 / Avg.num./class: 40000 / Software - Name: RELION / Details: classification with mask focusing on HECT domain
FSC plot (resolution estimation)

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