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- EMDB-48083: Import stalled PINK1 TOM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-48083
TitleImport stalled PINK1 TOM complex
Map dataMain map
Sample
  • Complex: Import stalled PINK1 TOM complex
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
    • Protein or peptide: Non-selective voltage-gated ion channel VDAC2
    • Protein or peptide: Mitochondrial import receptor subunit TOM40 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM5 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM7 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM6 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM22 homolog
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsPINK1 / TOM complex / VDAC / TRANSLOCASE
Function / homology
Function and homology information


positive regulation of free ubiquitin chain polymerization / positive regulation of synaptic transmission, dopaminergic / tRNA import into mitochondrion / TOM complex / positive regulation of cristae formation / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / mitochondrial outer membrane permeabilization / : / Mitochondrial calcium ion transport ...positive regulation of free ubiquitin chain polymerization / positive regulation of synaptic transmission, dopaminergic / tRNA import into mitochondrion / TOM complex / positive regulation of cristae formation / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / mitochondrial outer membrane permeabilization / : / Mitochondrial calcium ion transport / mitochondrion to lysosome vesicle-mediated transport / maintenance of protein location in mitochondrion / mitochondrion targeting sequence binding / : / mitochondrial outer membrane translocase complex / cellular response to hydrogen sulfide / protein kinase B binding / Lewy body / phospholipid scramblase activity / regulation of autophagy of mitochondrion / ceramide binding / regulation of synaptic vesicle transport / TORC2 signaling / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of mitochondrial electron transport, NADH to ubiquinone / regulation of oxidative phosphorylation / regulation of hydrogen peroxide metabolic process / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / C3HC4-type RING finger domain binding / protein-transporting ATPase activity / regulation of cellular response to oxidative stress / migrasome / dopamine secretion / voltage-gated monoatomic ion channel activity / negative regulation of autophagosome assembly / positive regulation of dopamine secretion / binding of sperm to zona pellucida / autophagy of mitochondrion / phosphatidylcholine binding / oxysterol binding / positive regulation of type 2 mitophagy / Mitochondrial protein import / cellular response to toxic substance / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrion organization / monoatomic anion transport / negative regulation of JNK cascade / regulation of reactive oxygen species metabolic process / : / peptidase activator activity / : / phospholipid translocation / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / astrocyte projection / cholesterol binding / positive regulation of mitochondrial fission / negative regulation of macroautophagy / porin activity / negative regulation of mitophagy / pore complex / FOXO-mediated transcription of cell death genes / negative regulation of intrinsic apoptotic signaling pathway / protein import into mitochondrial matrix / positive regulation of release of cytochrome c from mitochondria / positive regulation of ATP biosynthetic process / hemopoiesis / negative regulation of reactive oxygen species metabolic process / mitochondrial nucleoid / positive regulation of macroautophagy / regulation of protein ubiquitination / protein transmembrane transporter activity / negative regulation of mitochondrial fission / regulation of protein-containing complex assembly / mitophagy / monoatomic ion transport / sperm midpiece / regulation of proteasomal protein catabolic process / acrosomal vesicle / positive regulation of protein ubiquitination / positive regulation of translation / response to ischemia / cell periphery / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / respiratory electron transport chain / mitochondrion organization / macroautophagy / regulation of protein stability / mitochondrial intermembrane space / mitochondrial membrane / kinase binding / kinase activity / unfolded protein binding / growth cone / cell body / response to oxidative stress / cellular response to oxidative stress
Similarity search - Function
PINK1, protein kinase domain / Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor ...PINK1, protein kinase domain / Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / : / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM40 homolog / Non-selective voltage-gated ion channel VDAC2 / Mitochondrial import receptor subunit TOM20 homolog / Mitochondrial import receptor subunit TOM5 homolog / Mitochondrial import receptor subunit TOM6 homolog / Serine/threonine-protein kinase PINK1, mitochondrial / Mitochondrial import receptor subunit TOM22 homolog / Mitochondrial import receptor subunit TOM7 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKirk NS / Glukhova A / Callegari S / Komander D
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1178122 Australia
Other private
CitationJournal: Science / Year: 2025
Title: Structure of human PINK1 at a mitochondrial TOM-VDAC array.
Authors: Sylvie Callegari / Nicholas S Kirk / Zhong Yan Gan / Toby Dite / Simon A Cobbold / Andrew Leis / Laura F Dagley / Alisa Glukhova / David Komander /
Abstract: Mutations in the ubiquitin kinase PINK1 cause early-onset Parkinson's disease, but how PINK1 is stabilized at depolarized mitochondrial translocase complexes has remained poorly understood. We ...Mutations in the ubiquitin kinase PINK1 cause early-onset Parkinson's disease, but how PINK1 is stabilized at depolarized mitochondrial translocase complexes has remained poorly understood. We determined a 3.1-angstrom resolution cryo-electron microscopy structure of dimeric human PINK1 stabilized at an endogenous array of mitochondrial translocase of the outer membrane (TOM) and voltage-dependent anion channel (VDAC) complexes. Symmetric arrangement of two TOM core complexes around a central VDAC2 dimer is facilitated by TOM5 and TOM20, both of which also bind PINK1 kinase C-lobes. PINK1 enters mitochondria through the proximal TOM40 barrel of the TOM core complex, guided by TOM7 and TOM22. Our structure explains how human PINK1 is stabilized at the TOM complex and regulated by oxidation, uncovers a previously unknown TOM-VDAC assembly, and reveals how a physiological substrate traverses TOM40 during translocation.
History
DepositionNov 26, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48083.png

Downloads & links

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Map

FileDownload / File: emd_48083.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.872 Å		0.83 Å/pix.
x 384 pix.
= 319.872 Å		0.83 Å/pix.
x 384 pix.
= 319.872 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.10502413 - 0.23208478
Average (Standard dev.)0.00004904298 (±0.0075290017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.872 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional map, reconstructed without symmetry operations.

Fileemd_48083_additional_1.map
AnnotationAdditional map, reconstructed without symmetry operations.
Projections & Slices
AxesZYX

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Half map: Half map B

Fileemd_48083_half_map_1.map
AnnotationHalf map B
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_48083_half_map_2.map
AnnotationHalf map A
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Sample components

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Entire : Import stalled PINK1 TOM complex

EntireName: Import stalled PINK1 TOM complex
Components
  • Complex: Import stalled PINK1 TOM complex
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
    • Protein or peptide: Non-selective voltage-gated ion channel VDAC2
    • Protein or peptide: Mitochondrial import receptor subunit TOM40 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM5 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM7 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM6 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM22 homolog
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Import stalled PINK1 TOM complex

SupramoleculeName: Import stalled PINK1 TOM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #8, #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: Mitochondrial import receptor subunit TOM20 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM20 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.319862 KDa
SequenceString:
MVGRNSAIAA GVCGALFIGY CIYFDRKRRS DPNFKNRLRE RRKKQKLAKE RAGLSKLPDL KDAEAVQKFF LEEIQLGEEL LAQGEYEKG VDHLTNAIAV CGQPQQLLQV LQQTLPPPVF QMLLTKLPTI SQRIVSAQSL AEDDVE

UniProtKB: Mitochondrial import receptor subunit TOM20 homolog

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Macromolecule #2: Non-selective voltage-gated ion channel VDAC2

MacromoleculeName: Non-selective voltage-gated ion channel VDAC2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.600445 KDa
SequenceString: MATHGQTCAR PMCIPPSYAD LGKAARDIFN KGFGFGLVKL DVKTKSCSGV EFSTSGSSNT DTGKVTGTLE TKYKWCEYGL TFTEKWNTD NTLGTEIAIE DQICQGLKLT FDTTFSPNTG KKSGKIKSSY KRECINLGCD VDFDFAGPAI HGSAVFGYEG W LAGYQMTF ...String:
MATHGQTCAR PMCIPPSYAD LGKAARDIFN KGFGFGLVKL DVKTKSCSGV EFSTSGSSNT DTGKVTGTLE TKYKWCEYGL TFTEKWNTD NTLGTEIAIE DQICQGLKLT FDTTFSPNTG KKSGKIKSSY KRECINLGCD VDFDFAGPAI HGSAVFGYEG W LAGYQMTF DSAKSKLTRN NFAVGYRTGD FQLHTNVNDG TEFGGSIYQK VCEDLDTSVN LAWTSGTNCT RFGIAAKYQL DP TASISAK VNNSSLIGVG YTQTLRPGVK LTLSALVDGK SINAGGHKVG LALELEA

UniProtKB: Non-selective voltage-gated ion channel VDAC2

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Macromolecule #3: Mitochondrial import receptor subunit TOM40 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM40 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.926926 KDa
SequenceString: MGNVLAASSP PAGPPPPPAP ALVGLPPPPP SPPGFTLPPL GGSLGAGTST SRSSERTPGA ATASASGAAE DGACGCLPNP GTFEECHRK CKELFPIQME GVKLTVNKGL SNHFQVNHTV ALSTIGESNY HFGVTYVGTK QLSPTEAFPV LVGDMDNSGS L NAQVIHQL ...String:
MGNVLAASSP PAGPPPPPAP ALVGLPPPPP SPPGFTLPPL GGSLGAGTST SRSSERTPGA ATASASGAAE DGACGCLPNP GTFEECHRK CKELFPIQME GVKLTVNKGL SNHFQVNHTV ALSTIGESNY HFGVTYVGTK QLSPTEAFPV LVGDMDNSGS L NAQVIHQL GPGLRSKMAI QTQQSKFVNW QVDGEYRGSD FTAAVTLGNP DVLVGSGILV AHYLQSITPC LALGGELVYH RR PGEEGTV MSLAGKYTLN NWLATVTLGQ AGMHATYYHK ASDQLQVGVE FEASTRMQDT SVSFGYQLDL PKANLLFKGS VDS NWIVGA TLEKKLPPLP LTLALGAFLN HRKNKFQCGF GLTIG

UniProtKB: Mitochondrial import receptor subunit TOM40 homolog

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Macromolecule #4: Mitochondrial import receptor subunit TOM5 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM5 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.045318 KDa
SequenceString:
MFRIEGLAPK LDPEEMKRKM REDVISSIRN FLIYVALLRV TPFILKKLDS I

UniProtKB: Mitochondrial import receptor subunit TOM5 homolog

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Macromolecule #5: Mitochondrial import receptor subunit TOM7 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM7 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.256473 KDa
SequenceString:
MVKLSKEAKQ RLQQLFKGSQ FAIRWGFIPL VIYLGFKRGA DPGMPEPTVL SLLWG

UniProtKB: Mitochondrial import receptor subunit TOM7 homolog

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Macromolecule #6: Mitochondrial import receptor subunit TOM6 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM6 homolog / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.007988 KDa
SequenceString:
MASSTVPVSA AGSANETPEI PDNVGDWLRG VYRFATDRND FRRNLILNLG LFAAGVWLAR NLSDIDLMAP QPGV

UniProtKB: Mitochondrial import receptor subunit TOM6 homolog

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Macromolecule #7: Mitochondrial import receptor subunit TOM22 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM22 homolog / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.532528 KDa
SequenceString:
MAAAVAAAGA GEPQSPDELL PKGDAEKPEE ELEEDDDEEL DETLSERLWG LTEMFPERVR SAAGATFDLS LFVAQKMYRF SRAALWIGT TSFMILVLPV VFETEKLQME QQQQLQQRQI LLGPNTGLSG GMPGALPSLP GKI

UniProtKB: Mitochondrial import receptor subunit TOM22 homolog

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Macromolecule #8: Serine/threonine-protein kinase PINK1, mitochondrial

MacromoleculeName: Serine/threonine-protein kinase PINK1, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.561562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVRQALGRG LQLGRALLLR FTGKPGRAYG LGRPGPAAGC VRGERPGWAA GPGAEPRRVG LGLPNRLRFF RQSVAGLAAR LQRQFVVRA WGCAGPCGRA VFLAFGLGLG LIEEKQAESR RAVSACQEIQ AIFTQKSKPG PDPLDTRRLQ GFRLEEYLIG Q SIGKGCSA ...String:
MAVRQALGRG LQLGRALLLR FTGKPGRAYG LGRPGPAAGC VRGERPGWAA GPGAEPRRVG LGLPNRLRFF RQSVAGLAAR LQRQFVVRA WGCAGPCGRA VFLAFGLGLG LIEEKQAESR RAVSACQEIQ AIFTQKSKPG PDPLDTRRLQ GFRLEEYLIG Q SIGKGCSA AVYEATMPTL PQNLEVTKST GLLPGRGPGT SAPGEGQERA PGAPAFPLAI KMMWNISAGS SSEAILNTMS QE LVPASRV ALAGEYGAVT YRKSKRGPKQ LAPHPNIIRV LRAFTSSVPL LPGALVDYPD VLPSRLHPEG LGHGRTLFLV MKN YPCTLR QYLCVNTPSP RLAAMMLLQL LEGVDHLVQQ GIAHRDLKSD NILVELDPDG CPWLVIADFG CCLADESIGL QLPF SSWYV DRGGNGCLMA PEVSTARPGP RAVIDYSKAD AWAVGAIAYE IFGLVNPFYG QGKAHLESRS YQEAQLPALP ESVPP DVRQ LVRALLQREA SKRPSARVAA NVLHLSLWGE HILALKNLKL DKMVGWLLQQ SAATLLANRL TEKCCVETKM KMLFLA NLE CETLCQAALL LCSWRAALDY KDHDGDYKDH DIDYKDDDDK

UniProtKB: Serine/threonine-protein kinase PINK1, mitochondrial

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Macromolecule #9: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 9 / Number of copies: 17 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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

Concentration4 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.4 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: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 347000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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