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- EMDB-48084: Import stalled PINK1 TOM complex, symmetry expanded -

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Basic information

Entry
Database: EMDB / ID: EMD-48084
TitleImport stalled PINK1 TOM complex, symmetry expanded
Map dataMain map
Sample
  • Complex: Complex of VDAC, TOM core and PINK1
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
    • Protein or peptide: Voltage-dependent anion-selective channel protein 2
    • 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


negative regulation of protein polymerization / positive regulation of synaptic transmission, dopaminergic / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of free ubiquitin chain polymerization / positive regulation of cristae formation / tRNA import into mitochondrion / TOM complex / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / regulation of protein targeting to mitochondrion ...negative regulation of protein polymerization / positive regulation of synaptic transmission, dopaminergic / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of free ubiquitin chain polymerization / positive regulation of cristae formation / tRNA import into mitochondrion / TOM complex / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / regulation of protein targeting to mitochondrion / mitochondrial outer membrane permeabilization / mitochondrion to lysosome vesicle-mediated transport / Mitochondrial calcium ion transport / maintenance of protein location in mitochondrion / cellular response to hydrogen sulfide / mitochondrion targeting sequence binding / Lewy body / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / protein kinase B binding / establishment of protein localization to mitochondrion / phospholipid scramblase activity / TORC2 signaling / regulation of autophagy of mitochondrion / regulation of synaptic vesicle transport / ceramide binding / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of hydrogen peroxide metabolic process / regulation of oxidative phosphorylation / migrasome / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / protein import into mitochondrial matrix / peptidase activator activity / C3HC4-type RING finger domain binding / regulation of cellular response to oxidative stress / protein-transporting ATPase activity / dopamine secretion / positive regulation of dopamine secretion / voltage-gated monoatomic ion channel activity / negative regulation of autophagosome assembly / peptidyl-serine autophosphorylation / binding of sperm to zona pellucida / autophagy of mitochondrion / phosphatidylcholine binding / cellular response to toxic substance / positive regulation of type 2 mitophagy / astrocyte projection / Mitochondrial protein import / oxysterol binding / negative regulation of JNK cascade / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrion organization / monoatomic anion transport / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of reactive oxygen species metabolic process / phospholipid translocation / positive regulation of ubiquitin-protein transferase activity / cholesterol binding / negative regulation of macroautophagy / positive regulation of mitochondrial fission / porin activity / positive regulation of ATP biosynthetic process / response to muscle activity / negative regulation of mitophagy / pore complex / protein insertion into mitochondrial outer membrane / FOXO-mediated transcription of cell death genes / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / hemopoiesis / mitochondrial nucleoid / negative regulation of reactive oxygen species metabolic process / positive regulation of macroautophagy / protein transmembrane transporter activity / negative regulation of mitochondrial fission / regulation of protein ubiquitination / regulation of protein-containing complex assembly / mitophagy / monoatomic ion transport / positive regulation of peptidyl-serine phosphorylation / regulation of proteasomal protein catabolic process / sperm midpiece / acrosomal vesicle / regulation of mitochondrial membrane potential / positive regulation of translation / positive regulation of protein ubiquitination / response to ischemia / PINK1-PRKN Mediated Mitophagy / respiratory electron transport chain / cell periphery / mitochondrion organization / macroautophagy / mitochondrial membrane / regulation of protein stability / mitochondrial intermembrane space / kinase binding / kinase activity
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 / Protein import receptor MAS20, metazoan / 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 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / : / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / 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: 2.75 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 Australia
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_48084.png

Downloads & links

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Map

FileDownload / File: emd_48084.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
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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-0.09551215 - 0.23618957
Average (Standard dev.)0.00043873873 (±0.004906057)
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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Half map: Half map B

Fileemd_48084_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_48084_half_map_2.map
AnnotationHalf map A
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 : Complex of VDAC, TOM core and PINK1

EntireName: Complex of VDAC, TOM core and PINK1
Components
  • Complex: Complex of VDAC, TOM core and PINK1
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
    • Protein or peptide: Voltage-dependent anion-selective channel protein 2
    • 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: Complex of VDAC, TOM core and PINK1

SupramoleculeName: Complex of VDAC, TOM core and PINK1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: Serine/threonine-protein kinase PINK1, mitochondrial

MacromoleculeName: Serine/threonine-protein kinase PINK1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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 #2: Mitochondrial import receptor subunit TOM20 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM20 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: Voltage-dependent anion-selective channel protein 2

MacromoleculeName: Voltage-dependent anion-selective channel protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: Mitochondrial import receptor subunit TOM40 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM40 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 2 / 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 #5: Mitochondrial import receptor subunit TOM5 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM5 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 2 / 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 #6: Mitochondrial import receptor subunit TOM7 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM7 homolog / type: protein_or_peptide / ID: 6 / Number of copies: 2 / 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 #7: Mitochondrial import receptor subunit TOM6 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM6 homolog / type: protein_or_peptide / ID: 7 / Number of copies: 2 / 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 #8: Mitochondrial import receptor subunit TOM22 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM22 homolog / type: protein_or_peptide / ID: 8 / Number of copies: 2 / 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 #9: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 9 / Number of copies: 9 / 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

Concentration4.3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 10 for 2 s..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 16992 / Average exposure time: 3.34 sec. / 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 / 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: 5700000 / Details: Picked using low resolution templates
Startup modelType of model: OTHER / Details: Ab initio model, SGD algorithm
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 791000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7cp9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9eii:
Import stalled PINK1 TOM complex, symmetry expanded

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Atomic model buiding 2

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9eii:
Import stalled PINK1 TOM complex, symmetry expanded

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