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- EMDB-13002: Structure of human mitochondrial RNase P in complex with mitochon... -

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Basic information

Entry
Database: EMDB / ID: EMD-13002
TitleStructure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-Tyr
Map dataComposite map used for real space refinement.
Sample
  • Complex: Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate
    • Complex: Human mitochondrial RNase P complex with precursor mitochondrial tRNA-Tyr
      • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
      • Protein or peptide: Mitochondrial ribonuclease P catalytic subunit
      • Protein or peptide: tRNA methyltransferase 10 homolog C
      • RNA: Mitochondrial Precursor tRNA-Tyr
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsRNA Processing / Mitochondria / Gene Expression / Transcription / Translation / RNA BINDING PROTEIN
Function / homology
Function and homology information


mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / mitochondrial tRNA methylation ...mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / mitochondrial tRNA methylation / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA processing in the mitochondrion / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / tRNA modification in the mitochondrion / 7alpha-hydroxysteroid dehydrogenase / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / testosterone dehydrogenase [NAD(P)+] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / ribonuclease P / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / bile acid biosynthetic process / : / steroid catabolic process / positive regulation of mitochondrial translation / ribonuclease P activity / tRNA 5'-leader removal / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / Mitochondrial protein degradation / mitochondrion organization / Transferases; Transferring one-carbon groups; Methyltransferases / fatty acid metabolic process / lipid metabolic process / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mitochondrial ribonuclease P catalytic subunit / tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / Protein-only RNase P, C-terminal / Protein-only RNase P / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase ...Mitochondrial ribonuclease P catalytic subunit / tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / Protein-only RNase P, C-terminal / Protein-only RNase P / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / Tetratricopeptide-like helical domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Mitochondrial ribonuclease P catalytic subunit / tRNA methyltransferase 10 homolog C / 3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBhatta A / Dienemann C
Funding support Germany, 6 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)SFB1190 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
European Research Council (ERC)CHROMATRANS 693023 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural basis of RNA processing by human mitochondrial RNase P.
Authors: Arjun Bhatta / Christian Dienemann / Patrick Cramer / Hauke S Hillen /
Abstract: Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In ...Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing. Subunits TRMT10C and SDR5C1 form a subcomplex that binds conserved mitochondrial tRNA elements, including the anticodon loop, and positions the tRNA for methylation. The endonuclease PRORP is recruited and activated through interactions with its PPR and nuclease domains to ensure precise pre-tRNA cleavage. The structure provides the molecular basis for the first step of RNA processing in human mitochondria.
History
DepositionMay 26, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7onu
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13002.png

Downloads & links

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Map

FileDownload / File: emd_13002.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map used for real space refinement.
Voxel sizeX=Y=Z: 0.834 Å
Density
Contour LevelBy AUTHOR: 5.0 / Movie #1: 6
Minimum - Maximum-25.522234000000001 - 52.377856999999999
Average (Standard dev.)0.0056845625 (±1.1014985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.6004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8340.8340.834
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z333.600333.600333.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-25.52252.3780.006

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Supplemental data

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Mask #1

Fileemd_13002_msk_1.map
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Mask #2

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Mask #3

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Additional map: Half map 1 for focused refinement map.

Fileemd_13002_additional_1.map
AnnotationHalf map 1 for focused refinement map.
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Additional map: Post-processed map4.

Fileemd_13002_additional_10.map
AnnotationPost-processed map4.
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Additional map: Half map 2 for focused refinement map.

Fileemd_13002_additional_2.map
AnnotationHalf map 2 for focused refinement map.
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Additional map: MRPP3-Focused refinement map.

Fileemd_13002_additional_3.map
AnnotationMRPP3-Focused refinement map.
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Additional map: Global refinement post-processed map (Map 1).

Fileemd_13002_additional_4.map
AnnotationGlobal refinement post-processed map (Map 1).
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Additional map: Half map 2 for map3.

Fileemd_13002_additional_5.map
AnnotationHalf map 2 for map3.
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Additional map: Half map 2 for map4.

Fileemd_13002_additional_6.map
AnnotationHalf map 2 for map4.
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Additional map: Half map 1 for map4.

Fileemd_13002_additional_7.map
AnnotationHalf map 1 for map4.
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Additional map: Post-processed map3.

Fileemd_13002_additional_8.map
AnnotationPost-processed map3.
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Fileemd_13002_additional_9.map
AnnotationHalf map 1 for map3.
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Half map: #2

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Sample components

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Entire : Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate

EntireName: Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate
Components
  • Complex: Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate
    • Complex: Human mitochondrial RNase P complex with precursor mitochondrial tRNA-Tyr
      • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
      • Protein or peptide: Mitochondrial ribonuclease P catalytic subunit
      • Protein or peptide: tRNA methyltransferase 10 homolog C
      • RNA: Mitochondrial Precursor tRNA-Tyr
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate

SupramoleculeName: Human mitochondrial RNase P complex with precursor tRNA-Tyr substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 254 KDa

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Supramolecule #2: Human mitochondrial RNase P complex with precursor mitochondrial ...

SupramoleculeName: Human mitochondrial RNase P complex with precursor mitochondrial tRNA-Tyr
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 3-hydroxyacyl-CoA dehydrogenase type-2

MacromoleculeName: 3-hydroxyacyl-CoA dehydrogenase type-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: 3-hydroxyacyl-CoA dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.947021 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAAACRSVKG LVAVITGGAS GLGLATAERL VGQGASAVLL DLPNSGGEAQ AKKLGNNCVF APADVTSEKD VQTALALAKG KFGRVDVAV NCAGIAVASK TYNLKKGQTH TLEDFQRVLD VNLMGTFNVI RLVAGEMGQN EPDQGGQRGV IINTASVAAF E GQVGQAAY ...String:
MAAACRSVKG LVAVITGGAS GLGLATAERL VGQGASAVLL DLPNSGGEAQ AKKLGNNCVF APADVTSEKD VQTALALAKG KFGRVDVAV NCAGIAVASK TYNLKKGQTH TLEDFQRVLD VNLMGTFNVI RLVAGEMGQN EPDQGGQRGV IINTASVAAF E GQVGQAAY SASKGGIVGM TLPIARDLAP IGIRVMTIAP GLFGTPLLTS LPEKVCNFLA SQVPFPSRLG DPAEYAHLVQ AI IENPFLN GEVIRLDGAI RMQP

UniProtKB: 3-hydroxyacyl-CoA dehydrogenase type-2

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Macromolecule #2: Mitochondrial ribonuclease P catalytic subunit

MacromoleculeName: Mitochondrial ribonuclease P catalytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.458379 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SNAFSLKTMS PQNTKATNLI AKARYLRKDE GSNKQVYSVP HFFLAGAAKE RSQMNSQTED HALAPVRNTI QLPTQPLNSE EWDKLKEDL KENTGKTSFE SWIISQMAGC HSSIDVAKSL LAWVAAKNNG IVSYDLLVKY LYLCVFHMQT SEVIDVFEIM K ARYKTLEP ...String:
SNAFSLKTMS PQNTKATNLI AKARYLRKDE GSNKQVYSVP HFFLAGAAKE RSQMNSQTED HALAPVRNTI QLPTQPLNSE EWDKLKEDL KENTGKTSFE SWIISQMAGC HSSIDVAKSL LAWVAAKNNG IVSYDLLVKY LYLCVFHMQT SEVIDVFEIM K ARYKTLEP RGYSLLIRGL IHSDRWREAL LLLEDIKKVI TPSKKNYNDC IQGALLHQDV NTAWNLYQEL LGHDIVPMLE TL KAFFDFG KDIKDDNYSN KLLDILSYLR NNQLYPGESF AHSIKTWFES VPGKQWKGQF TTVRKSGQCS GCGKTIESIQ LSP EEYECL KGKIMRDVID GGDQYRKTTP QELKRFENFI KSRPPFDVVI DGLNVAKMFP KVRESQLLLN VVSQLAKRNL RLLV LGRKH MLRRSSQWSR DEMEEVQKQA SCFFADDISE DDPFLLYATL HSGNHCRFIT RDLMRDHKAC LPDAKTQRLF FKWQQ GHQL AIVNRFPGSK LTFQRILSYD TVVQTTGDSW HIPYDEDLVE RCSCEVPTKW LCLHQKT

UniProtKB: Mitochondrial ribonuclease P catalytic subunit

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Macromolecule #3: tRNA methyltransferase 10 homolog C

MacromoleculeName: tRNA methyltransferase 10 homolog C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.942477 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SNAMSSKIPA VTYPKNESTP PSEELELDKW KTTMKSSVQE ECVSTISSSK DEDPLAATRE FIEMWRLLGR EVPEHITEEE LKTLMECVS NTAKKKYLKY LYTKEKVKKA RQIKKEMKAA AREEAKNIKL LETTEEDKQK NFLFLRLWDR NMDIAMGWKG A QAMQFGQP ...String:
SNAMSSKIPA VTYPKNESTP PSEELELDKW KTTMKSSVQE ECVSTISSSK DEDPLAATRE FIEMWRLLGR EVPEHITEEE LKTLMECVS NTAKKKYLKY LYTKEKVKKA RQIKKEMKAA AREEAKNIKL LETTEEDKQK NFLFLRLWDR NMDIAMGWKG A QAMQFGQP LVFDMAYENY MKRKELQNTV SQLLESEGWN RRNVDPFHIY FCNLKIDGAL HRELVKRYQE KWDKLLLTST EK SHVDLFP KDSIIYLTAD SPNVMTTFRH DKVYVIGSFV DKSMQPGTSL AKAKRLNLAT ECLPLDKYLQ WEIGNKNLTL DQM IRILLC LKNNGNWQEA LQFVPKRKHT GFLEISQHSQ EFINRLKKAK T

UniProtKB: tRNA methyltransferase 10 homolog C

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Macromolecule #4: Mitochondrial Precursor tRNA-Tyr

MacromoleculeName: Mitochondrial Precursor tRNA-Tyr / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.490605 KDa
SequenceString:
GAGAAUAGUC AACGGUCGGC GAACAUCAGU GGGGGUGAGG UAAAAUGGCU GAGUGAAGCA UUGGACUGUA AAUCUAAAGA CAGGGGUUA GGCCUCUUUU UACCAGCUCC GAGGUGAUUU UCAAGCUCG

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Macromolecule #5: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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
Component:
ConcentrationFormulaName
150.0 mmol/LNaClSodium Chloride
40.0 mmol/LC8H17N2O4SNaNa-HEPES (Sodium 4-(2-hydroxyethyl)-1-piperazineethanesulfonate)
0.25 mmol/LC10H16N2O8NaEthylenediaminetetraacetic acid disodium salt
2.0 mmol/mLC4H10O2S2Dithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: 6150677
Startup modelType of model: OTHER
Details: Model for MRPP1/MRPP2-pre-tRNAtyr previously generated using a dataset collected on 200 keV Glacios Cryo-TEM.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 88081
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.11.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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