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- EMDB-61198: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer) -

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Entry
Database: EMDB / ID: EMD-61198
TitleCryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
Map data
Sample
  • Complex: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
    • Protein or peptide: Cullin-2
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
    • Protein or peptide: Poly-UNK
    • Protein or peptide: Poly-UNK
  • Ligand: ZINC ION
Keywordsubiquitination E3 ligase / Cryo-EM / PROTEIN BINDING
Function / homology
Function and homology information


tRNA import into mitochondrion / TOM complex / regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein-transporting ATPase activity ...tRNA import into mitochondrion / TOM complex / regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein-transporting ATPase activity / branching involved in prostate gland morphogenesis / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Mitochondrial protein import / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / target-directed miRNA degradation / elongin complex / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / regulation of extrinsic apoptotic signaling pathway via death domain receptors / death receptor binding / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / protein targeting to mitochondrion / SCF ubiquitin ligase complex / negative regulation of type I interferon production / Cul2-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / protein import into mitochondrial matrix / cullin family protein binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / protein monoubiquitination / ubiquitin ligase complex / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Formation of HIV elongation complex in the absence of HIV Tat / Nuclear events stimulated by ALK signaling in cancer / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / sperm midpiece / transcription-coupled nucleotide-excision repair / RNA Polymerase II Pre-transcription Events / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / post-translational protein modification / Regulation of BACH1 activity / T cell activation / transcription corepressor binding / PINK1-PRKN Mediated Mitophagy / cell periphery / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Degradation of DVL / cellular response to amino acid stimulus / transcription elongation by RNA polymerase II / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Inactivation of CSF3 (G-CSF) signaling / DNA Damage Recognition in GG-NER / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants
Similarity search - Function
Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. ...Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Elongin-C / Elongin B / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ankyrin repeat / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Ankyrin repeat-containing domain superfamily / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-2 / Elongin-C / Elongin-B / Mitochondrial import receptor subunit TOM20 homolog / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsZhao S / Xu C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2025
Title: TOM20-driven E3 ligase recruitment regulates mitochondrial dynamics through PLD6.
Authors: Anat Raiff / Shidong Zhao / Aizat Bekturova / Colin Zenge / Shir Mazor / Xinyan Chen / Wenwen Ru / Yaara Makaros / Tslil Ast / Alban Ordureau / Chao Xu / Itay Koren /
Abstract: Mitochondrial homeostasis is maintained through complex regulatory mechanisms, including the balance of mitochondrial dynamics involving fusion and fission processes. A central player in this ...Mitochondrial homeostasis is maintained through complex regulatory mechanisms, including the balance of mitochondrial dynamics involving fusion and fission processes. A central player in this regulation is the ubiquitin-proteasome system (UPS), which controls the degradation of pivotal mitochondrial proteins. In this study, we identified cullin-RING E3 ligase 2 (CRL2) and its substrate receptor, FEM1B, as critical regulators of mitochondrial dynamics. Through proteomic analysis, we demonstrate here that FEM1B controls the turnover of PLD6, a key regulator of mitochondrial dynamics. Using structural and biochemical approaches, we show that FEM1B physically interacts with PLD6 and that this interaction is facilitated by the direct association of FEM1B with the mitochondrial import receptor TOM20. Ablation of FEM1B or disruption of the FEM1B-TOM20 interaction impairs PLD6 degradation and induces mitochondrial defects, phenocopying PLD6 overexpression. These findings underscore the importance of FEM1B in maintaining mitochondrial morphology and provide further mechanistic insights into how the UPS regulates mitochondrial homeostasis.
History
DepositionAug 18, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61198.png

Downloads & links

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Map

FileDownload / File: emd_61198.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 640 pix.
= 524.8 Å		0.82 Å/pix.
x 640 pix.
= 524.8 Å		0.82 Å/pix.
x 640 pix.
= 524.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.24823381 - 0.6066203
Average (Standard dev.)0.0003574097 (±0.010797104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 524.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61198_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_61198_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)

EntireName: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
Components
  • Complex: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
    • Protein or peptide: Cullin-2
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
    • Protein or peptide: Poly-UNK
    • Protein or peptide: Poly-UNK
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)

SupramoleculeName: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 / Details: CUL2-FEM1B BOUND WITH TOM20
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.11475 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SASWSHPQFE KGGGSGGGSG TSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHV RHLHKRVLES EEQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNGGG PLMEIGELAL DMWRKLMVEP L QAILIRML ...String:
SASWSHPQFE KGGGSGGGSG TSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHV RHLHKRVLES EEQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNGGG PLMEIGELAL DMWRKLMVEP L QAILIRML LREIKNDRGG EDPNQKVIHG VINSFVHVEQ YKKKFPLKFY QEIFESPFLT ETGEYYKQEA SNLLQESNCS QY MEKVLGR LKDEEIRCRK YLHPSSYTKV IHECQQRMVA DHLQFLHAEC HNIIRQEKKN DMANMYVLLR AVSTGLPHMI QEL QNHIHD EGLRATSNLT QENMPTLFVE SVLEVHGKFV QLINTVLNGD QHFMSALDKA LTSVVNYREP KSVCKAPELL AKYC DNLLK KSAKGMTENE VEDRLTSFIT VFKYIDDKDV FQKFYARMLA KRLIHGLSMS MDSEEAMINK LKQACGYEFT SKLHR MYTD MSVSADLNNK FNNFIKNQDT VIDLGISFQI YVLQAGAWPL TQAPSSTFAI PQELEKSVQM FELFYSQHFS GRKLTW LHY LCTGEVKMNY LGKPYVAMVT TYQMAVLLAF NNSETVSYKE LQDSTQMNEK ELTKTIKSLL DVKMINHDSE KEDIDAE SS FSLNMNFSSK RTKFKITTSM QKDTPQEMEQ TRSAVDEDRK MYLQAAIVRI MKARKVLRHN ALIQEVISQS RARFNPSI S MIKKCIEVLI DKQYIERSQA SADEYSYVA

UniProtKB: Cullin-2

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Macromolecule #2: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.84342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC

UniProtKB: Elongin-C

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Macromolecule #3: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.348964 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GGSMDVFLMI RRHKTTIFTD AKESSTVFEL KRIVEGILKR PPDEQRLYKD DQLLDDGKTL GECGFTSQTA RPQAPATVGL AFRADDTFE ALCIEPFSSP PELPDVMKPQ DSGSSANEQA VQ

UniProtKB: Elongin-B

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Macromolecule #4: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.19683 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SHMGAGKKRF EVKKWNAVAL WAWDIVVDNC AICRNHIMDL CIECQANQAS ATSEECTVAW GVCNHAFHFH CISRWLKTRQ VCPLDNREW EFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #5: Protein fem-1 homolog B

MacromoleculeName: Protein fem-1 homolog B / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.355062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEGLAGYVYK AASEGKVLTL AALLLNRSES DIRYLLGYVS QQGGQRSTPL IIAARNGHAK VVRLLLEHYR VQTQQTGTVR FDGYVIDGA TALWCAAGAG HFEVVKLLVS HGANVNHTTV TNSTPLRAAC FDGRLDIVKY LVENNANISI ANKYDNTCLM I AAYKGHTD ...String:
MEGLAGYVYK AASEGKVLTL AALLLNRSES DIRYLLGYVS QQGGQRSTPL IIAARNGHAK VVRLLLEHYR VQTQQTGTVR FDGYVIDGA TALWCAAGAG HFEVVKLLVS HGANVNHTTV TNSTPLRAAC FDGRLDIVKY LVENNANISI ANKYDNTCLM I AAYKGHTD VVRYLLEQRA DPNAKAHCGA TALHFAAEAG HIDIVKELIK WRAAIVVNGH GMTPLKVAAE SCKADVVELL LS HADCDRR SRIEALELLG ASFANDRENY DIIKTYHYLY LAMLERFQDG DNILEKEVLP PIHAYGNRTE CRNPQELESI RQD RDALHM EGLIVRERIL GADNIDVSHP IIYRGAVYAD NMEFEQCIKL WLHALHLRQK GNRNTHKDLL RFAQVFSQMI HLNE TVKAP DIECVLRCSV LEIEQSMNRV KNISDADVHN AMDNYECNLY TFLYLVCIST KTQCSEEDQC KINKQIYNLI HLDPR TREG FTLLHLAVNS NTPVDDFHTN DVCSFPNALV TKLLLDCGAE VNAVDNEGNS ALHIIVQYNR PISDFLTLHS IIISLV EAG AHTDMTNKQN KTPLDKSTTG VSEILLKTQM KMSLKCLAAR AVRANDINYQ DQIPRTLEEF VGFH

UniProtKB: Protein fem-1 homolog B

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Macromolecule #6: Mitochondrial import receptor subunit TOM20 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM20 homolog / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.839889 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DRKRRSDPNF KNRLRERRKK QKLAKERAGL SKLPDLKDAE AVQKFFLEEI QLGEELLAQG EYEKGVDHLT NAIAVCGQPQ QLLQVLQQT LPPPVFQMLL TKLPTISQRI VSAQSLAEDD VE

UniProtKB: Mitochondrial import receptor subunit TOM20 homolog

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Macromolecule #7: Poly-UNK

MacromoleculeName: Poly-UNK / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 869.063 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #8: Poly-UNK

MacromoleculeName: Poly-UNK / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 698.854 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 55.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.8 µm
Sample stageCooling holder cryogen: NITROGEN
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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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