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- EMDB-71720: HUWE1(CS)-Ubiquitin bound to the HECT domain -

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Basic information

Entry
Database: EMDB / ID: EMD-71720
TitleHUWE1(CS)-Ubiquitin bound to the HECT domain
Map dataComposite HUWE1(CS)-Ub map, sharpened
Sample
  • Complex: HUWE1-Ubiquitin complex
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1
    • Protein or peptide: Ubiquitin
KeywordsUbiquitin complex / HUWE1 / E3 ligase / LIGASE
Function / homology
Function and homology information


negative regulation of peroxisome proliferator activated receptor signaling pathway / histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / protein branched polyubiquitination / positive regulation of type 2 mitophagy / HECT-type E3 ubiquitin transferase / : / ubiquitin-ubiquitin ligase activity / Golgi organization / protein monoubiquitination ...negative regulation of peroxisome proliferator activated receptor signaling pathway / histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / protein branched polyubiquitination / positive regulation of type 2 mitophagy / HECT-type E3 ubiquitin transferase / : / ubiquitin-ubiquitin ligase activity / Golgi organization / protein monoubiquitination / protein K48-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of protein ubiquitination / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of innate immune responses to cytosolic DNA / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / circadian regulation of gene expression / TNFR1-induced NF-kappa-B signaling pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Ubiquitin-dependent degradation of Cyclin D / Peroxisomal protein import / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Stabilization of p53 / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Termination of translesion DNA synthesis / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / EGFR downregulation / Regulation of TNFR1 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
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 / WWE domain superfamily / WWE domain / WWE domain profile. ...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 / WWE domain superfamily / WWE domain / WWE domain profile. / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / Ubiquitin-binding motif (UBM) 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsYatskevich S / Juszkiewicz S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Molecular mechanism of HUWE1-HAPSTR1-USP7-mediated ubiquitin chain amplification on nuclear proteins
Authors: Yatskevich S
History
DepositionJul 16, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71720.png

Downloads & links

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Map

FileReleased
AnnotationComposite HUWE1(CS)-Ub map, sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 213 pix.
= 311.406 Å		1.46 Å/pix.
x 213 pix.
= 311.406 Å		1.46 Å/pix.
x 213 pix.
= 311.406 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.462 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.165
Minimum - Maximum-0.70364153 - 2.1370797
Average (Standard dev.)0.008962422 (±0.038235825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-2-1-1
Dimensions213213213
Spacing213213213
CellA=B=C: 311.406 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Composite HUWE1(CS)-Ub map, unsharpened

Fileemd_71720_additional_1.map
AnnotationComposite HUWE1(CS)-Ub map, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus HUWE1(CS)-Ub map, sharpened

Fileemd_71720_additional_2.map
AnnotationConsensus HUWE1(CS)-Ub map, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus HUWE1(CS)-Ub map, unsharpened

Fileemd_71720_additional_3.map
AnnotationConsensus HUWE1(CS)-Ub map, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement of HUWE1(HECT) domain with bound Ubiquitin,...

Fileemd_71720_additional_4.map
AnnotationLocal refinement of HUWE1(HECT) domain with bound Ubiquitin, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement of HUWE1(HECT) domain with bound Ubiquitin,...

Fileemd_71720_additional_5.map
AnnotationLocal refinement of HUWE1(HECT) domain with bound Ubiquitin, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HUWE1-Ubiquitin complex

EntireName: HUWE1-Ubiquitin complex
Components
  • Complex: HUWE1-Ubiquitin complex
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1
    • Protein or peptide: Ubiquitin

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Supramolecule #1: HUWE1-Ubiquitin complex

SupramoleculeName: HUWE1-Ubiquitin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 482.408281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKVDRTKLKK TPTEAPADCR ALIDKLKVCN DEQLLLELQQ IKTWNIGKCE LYHWVDLLDR FDGILADAGQ TVENMSWMLV CDRPEREQL KMLLLAVLNF TALLIEYSFS RHLYSSIEHL TTLLASSDMQ VVLAVLNLLY VFSKRSNYIT RLGSDKRTPL L TRLQHLAE ...String:
MKVDRTKLKK TPTEAPADCR ALIDKLKVCN DEQLLLELQQ IKTWNIGKCE LYHWVDLLDR FDGILADAGQ TVENMSWMLV CDRPEREQL KMLLLAVLNF TALLIEYSFS RHLYSSIEHL TTLLASSDMQ VVLAVLNLLY VFSKRSNYIT RLGSDKRTPL L TRLQHLAE SWGGKENGFG LAECCRDLHM MKYPPSATTL HFEFYADPGA EVKIEKRTTS NTLHYIHIEQ LDKISESPSE IM ESLTKMY SIPKDKQMLL FTHIRLAHGF SNHRKRLQAV QARLHAISIL VYSNALQESA NSILYNGLIE ELVDVLQITD KQL MEIKAA SLRTLTSIVH LERTPKLSSI IDCTGTASYH GFLPVLVRNC IQAMIDPSMD PYPHQFATAL FSFLYHLASY DAGG EALVS CGMMEALLKV IKFLGDEQDQ ITFVTRAVRV VDLITNLDMA AFQSHSGLSI FIYRLEHEVD LCRKECPFVI KPKIQ RPNT TQEGEEMETD MDGVQCIPQR AALLKSMLNF LKKAIQDPAF SDGIRHVMDG SLPTSLKHII SNAEYYGPSL FLLATE VVT VFVFQEPSLL SSLQDNGLTD VMLHALLIKD VPATREVLGS LPNVFSALCL NARGLQSFVQ CQPFERLFKV LLSPDYL PA MRRRRSSDPL GDTASNLGSA VDELMRHQPT LKTDATTAII KLLEEICNLG RDPKYICQKP SIQKADGTAT APPPRSNH A AEEASSEDEE EEEVQAMQSF NSTQQNETEP NQQVVGTEER IPIPLMDYIL NVMKFVESIL SNNTTDDHCQ EFVNQKGLL PLVTILGLPN LPIDFPTSAA CQAVAGVCKS ILTLSHEPKV LQEGLLQLDS ILSSLEPLHR PIESPGGSVL LRELACAGNV ADATLSAQA TPLLHALTAA HAYIMMFVHT CRVGQSEIRS ISVNQWGSQL GLSVLSKLSQ LYCSLVWEST VLLSLCTPNS L PSGCEFGQ ADMQKLVPKD EKAGTTQGGK RSDGEQDGAA GSMDASTQGL LEGIGLDGDT LAPMETDEPT ASDSKGKSKI TP AMAARIK QIKPLLSASS RLGRALAELF GLLVKLCVGS PVRQRRSHHA ASTTTAPTPA ARSTASALTK LLTKGLSWQP PPY TPTPRF RLTFFICSVG FTSPMLFDER KYPYHLMLQK FLCSGGHNAL FETFNWALSM GGKVPVSEGL EHSDLPDGTG EFLD AWLML VEKMVNPTTV LESPHSLPAK LPGGVQNFPQ FSALRFLVVT QKAAFTCIKN LWNRKPLKVY GGRMAESMLA ILCHI LRGE PVIRERLSKE KEGSRGEEDT GQEEGGSRRE PQVNQQQLQQ LMDMGFTREH AMEALLNTST MEQATEYLLT HPPPIM GGV VRDLSMSEED QMMRAIAMSL GQDIPMDQRA ESPEEVACRK EEEERKAREK QEEEEAKCLE KFQDADPLEQ DELHTFT DT MLPGCFHLLD ELPDTVYRVC DLIMTAIKRN GADYRDMILK QVVNQVWEAA DVLIKAALPL TTSDTKTVSE WISQMATL P QASNLATRIL LLTLLFEELK LPCAWVVESS GILNVLIKLL EVVQPCLQAA KEQKEVQTPK WITPVLLLID FYEKTAISS KRRAQMTKYL QSNSNNWRWF DDRSGRWCSY SASNNSTIDS AWKSGETSVR FTAGRRRYTV QFTTMVQVNE ETGNRRPVML TLLRVPRLN KNSKNSNGQE LEKTLEESKE MDIKRKENKG NDTPLALEST NTEKETSLEE TKIGEILIQG LTEDMVTVLI R ACVSMLGV PVDPDTLHAT LRLCLRLTRD HKYAMMFAEL KSTRMILNLT QSSGFNGFTP LVTLLLRHII EDPCTLRHTM EK VVRSAAT SGAGSTTSGV VSGSLGSREI NYILRVLGPA ACRNPDIFTE VANCCIRIAL PAPRGSGTAS DDEFENLRIK GPN AVQLVK TTPLKPSPLP VIPDTIKEVI YDMLNALAAY HAPEEADKSD PKPGVMTQEV GQLLQDMGDD VYQQYRSLTR QSSD FDTQS GFSINSQVFA ADGASTETSA SGTSQGEAST PEESRDGKKD KEGDRASEEG KQKGKGSKPL MPTSTILRLL AELVR SYVG IATLIANYSY TVGQSELIKE DCSVLAFVLD HLLPHTQNAE DKDTPALARL FLASLAAAGS GTDAQVALVN EVKAAL GRA LAMAESTEKH ARLQAVMCII STIMESCPST SSFYSSATAK TQHNGMNNII RLFLKKGLVN DLARVPHSLD LSSPNMA NT VNAALKPLET LSRIVNQPSS LFGSKSASSK NKSEQDAQGA SQDSSSNQQD PGEPGEAEVQ EEDHDVTQTE VADGDIMD G EAETDSVVIA GQPEVLSSQE MQVENELEDL IDELLERDGG SGNSTIIVSR SGEDESQEDV LMDEAPSNLS QASTLQANR EDSMNILDPE DEEEHTQEED SSGSNEDEDD SQDEEEEEEE DEEDDQEDDE GEEGDEDDDD DGSEMELDED YPDMNASPLV RFERFDRED DLIIEFDNMF SSATDIPPSP GNIPTTHPLM VRHADHSSLT LGSGSSTTRL TQGIGRSQRT LRQLTANTGH T IHVHYPGN RQPNPPLILQ RLLGPSAAAD ILQLSSSLPL QSRGRARLLV GNDDVHIIAR SDDELLDDFF HDQSTATSQA GT LSSIPTA LTRWTEECKV LDAESMHDCV SVVKVSIVNH LEFLRDEELE ERREKRRKQL AEEETKITDK GKEDKENRDQ SAQ CTASKS NDSTEQNLSD GTPMPDSYPT TPSSTDAATS ESKETLGTLQ SSQQQPTLPT PPALGEVPQE LQSPAGEGGS STQL LMPVE PEELGPTRPS GEAETTQMEL SPAPTITSLS PERAEDSDAL TAVSSQLEGS PMDTSSLASC TLEEAVGDTS AAGSS EQPR AGSSTPGDAP PAVAEVQGRS DGSGESAQPP EDSSPPASSE SSSTRDSAVA ISGADSRGIL EEPLPSTSSE EEDPLA GIS LPEGVDPSFL AALPDDIRRE VLQNQLGIRP PTRTAPSTNS SAPAVVGNPG VTEVSPEFLA ALPPAIQEEV LAQQRAE QQ RRELAQNASS DTPMDPVTFI QTLPSDLRRS VLEDMEDSVL AVMPPDIAAE AQALRREQEA RQRQLMHERL FGHSSTSA L SAILRSPAFT SRLSGNRGVQ YTRLAVQRGG TFQMGGSSSH NRPSGSNVDT LLRLRGRLLL DHEALSCLLV LLFVDEPKL NTSRLHRVLR NLCYHAQTRH WVIRSLLSIL QRSSESELCI ETPKLTTSEE KGKKSSKSCG SSSHENRPLD LLHKMESKSS NQLSWLSVS MDAALGCRTN IFQIQRSGGR KHTEKHASGG STVHIHPQAA PVVCRHVLDT LIQLAKVFPS HFTQQRTKET N CESDRERG NKACSPCSSQ SSSSGICTDF WDLLVKLDNM NVSRKGKNSV KSVPVSAGGE GETSPYSLEA SPLGQLMNML SH PVIRRSS LLTEKLLRLL SLISIALPEN KVSEAQANSG SGASSTTTAT STTSTTTTTA ASTTPTPPTA PTPVTSAPAL VAA TAISTI VVAASTTVTT PTTATTTVSI SPTTKGSKSP AKVSDGGSSS TDFKMVSSGL TENQLQLSVE VLTSHSCSEE GLED AANVL LQLSRGDSGT RDTVLKLLLN GARHLGYTLC KQIGTLLAEL REYNLEQQRR AQCETLSPDG LPEEQPQTTK LKGKM QSRF DMAENVVIVA SQKRPLGGRE LQLPSMSMLT SKTSTQKFFL RVLQVIIQLR DDTRRANKKA KQTGRLGSSG LGSASS IQA AVRQLEAEAD AIIQMVREGQ RARRQQQAAT SESSQSEASV RREESPMDVD QPSPSAQDTQ SIASDGTPQG EKEKEER PP ELPLLSEQLS LDELWDMLGE CLKELEESHD QHAVLVLQPA VEAFFLVHAT ERESKPPVRD TRESQLAHIK DEPPPLSP A PLTPATPSSL DPFFSREPSS MHISSSLPPD TQKFLRFAET HRTVLNQILR QSTTHLADGP FAVLVDYIRV LDFDVKRKY FRQELERLDE GLRKEDMAVH VRRDHVFEDS YRELHRKSPE EMKNRLYIVF EGEEGQDAGG LLREWYMIIS REMFNPMYAL FRTSPGDRV TYTINPSSHC NPNHLSYFKF VGRIVAKAVY DNRLLECYFT RSFYKHILGK SVRYTDMESE DYHFYQGLVY L LENDVSTL GYDLTFSTEV QEFGVCEVRD LKPNGANILV TEENKKEYVH LVCQMRMTGA IRKQLAAFLE GFYEIIPKRL IS IFTEQEL ELLISGLPTI DIDDLKSNTE YHKYQSNSIQ IQWFWRALRS FDQADRAKFL QFVTGTSKVP LQGFAALEGM NGI QKFQIH RDDRSTDRLP SAHTSFNQLD LPAYESFEKL RHMLLLAIQE CSEGFGLA

UniProtKB: E3 ubiquitin-protein ligase HUWE1

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Macromolecule #2: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7jq9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105530
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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