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- EMDB-72719: Cryo-EM structure of the apical region of subpellicular microtubu... -

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Basic information

Entry
Database: EMDB / ID: EMD-72719
TitleCryo-EM structure of the apical region of subpellicular microtubule (SPMT) from Toxoplasma gondii (8-nm repeat)
Map data
Sample
  • Complex: conoid fiber from Toxoplasma gondii (24-nm repeat)
    • Protein or peptide: x 8 types
  • Ligand: x 3 types
KeywordsTubulin / Microtubule / Microtubule Inner Protein / Microtubule-associated Protein / Toxoplasma gondii / conoid / conoid fiber / subpellicular microtubule / SPMT / STRUCTURAL PROTEIN
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / microtubule-based process / negative regulation of protein ubiquitination / structural constituent of cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / hydrolase activity ...thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / microtubule-based process / negative regulation of protein ubiquitination / structural constituent of cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / hydrolase activity / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Stabilizer of axonemal microtubules 1/2 / Thioredoxin-like / Thioredoxin-like fold / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...Stabilizer of axonemal microtubules 1/2 / Thioredoxin-like / Thioredoxin-like fold / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Thioredoxin-like superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / PDI family protein / Microtubule associated protein SPM1 / Uncharacterized protein / Tubulin beta chain / Tubulin alpha chain / PDI family protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZeng J / Zhang R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI179885 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Atomic models of the Toxoplasma cell invasion machinery
Authors: Zeng J / Fu Y / Qian P / Niu Q / Beatty WL / Brown A / Sibley LD / Zhang R
History
DepositionSep 15, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72719.png

Downloads & links

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Map

FileDownload / File: emd_72719.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 400 pix.
= 536. Å		1.34 Å/pix.
x 400 pix.
= 536. Å		1.34 Å/pix.
x 400 pix.
= 536. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum0.0 - 2.1866078
Average (Standard dev.)0.009882546 (±0.06683993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 536.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72719_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72719_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72719_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : conoid fiber from Toxoplasma gondii (24-nm repeat)

EntireName: conoid fiber from Toxoplasma gondii (24-nm repeat)
Components
  • Complex: conoid fiber from Toxoplasma gondii (24-nm repeat)
    • Protein or peptide: Microtubule associated protein SPM1
    • Protein or peptide: TLAP3 (apical cap protein AC5), TGME49_235380
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: TLAP4 (thioredoxin-like associated protein), TGME49_201760
    • Protein or peptide: TLAP2 (thioredoxin-like associated protein), TGME49_232130
    • Protein or peptide: TRXL1, TGME49_232410
    • Protein or peptide: TRXL2, TGME49_225790
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: conoid fiber from Toxoplasma gondii (24-nm repeat)

SupramoleculeName: conoid fiber from Toxoplasma gondii (24-nm repeat) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Toxoplasma gondii (eukaryote)

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Macromolecule #1: Microtubule associated protein SPM1

MacromoleculeName: Microtubule associated protein SPM1 / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 38.84575 KDa
SequenceString: MSGGNSNTPK KLPSEEGSDY GYPQKPQKYL PKSEQAEPDY SACCKGNDAY KGASHGTVQF SHPEEAQKYA GAAAGAETIQ RGRERVAAD RQPRAAGDVP ARRLHLSDVD EAHRGQSPSR HPGYCVEELC TCGMHKCIPS RAPVPFTGST QYRQEFVPKP L PPPTQVSQ ...String:
MSGGNSNTPK KLPSEEGSDY GYPQKPQKYL PKSEQAEPDY SACCKGNDAY KGASHGTVQF SHPEEAQKYA GAAAGAETIQ RGRERVAAD RQPRAAGDVP ARRLHLSDVD EAHRGQSPSR HPGYCVEELC TCGMHKCIPS RAPVPFTGST QYRQEFVPKP L PPPTQVSQ VTLPPSLPFE AESSYRTEFV AKPLPPPAKF SEVKLPPTLP FHGESAYRTD YVPKPLPEVA KPVEVKLPPT LP FNAQSCY RSEYVAKPLP PPVQTVEVKL PPSLPFEGST HYRDEFQVKP LPPATKVTEV KLPPSLPFDA TSMYRSDYVA KSN PICPVS KLPQYPAATY PQNHVFWDPD TKQWY

UniProtKB: Microtubule associated protein SPM1

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Macromolecule #2: TLAP3 (apical cap protein AC5), TGME49_235380

MacromoleculeName: TLAP3 (apical cap protein AC5), TGME49_235380 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 65.286098 KDa
SequenceString: MPRPGVFELN YGEESRHSPV PKDPSTVTYG DASVGVVHHP LPAAGMYRQP CAFPHGSGFS KQSNETAFPD YPSTEHVAQR YVPPMDDKR QWAGHTSYYA PATMEQRGYQ DARYFGAELM PKSQGGENPQ NHPIMPSEAA EYGPRKPDCG RLIAAPHEGQ V NNLSQVDG ...String:
MPRPGVFELN YGEESRHSPV PKDPSTVTYG DASVGVVHHP LPAAGMYRQP CAFPHGSGFS KQSNETAFPD YPSTEHVAQR YVPPMDDKR QWAGHTSYYA PATMEQRGYQ DARYFGAELM PKSQGGENPQ NHPIMPSEAA EYGPRKPDCG RLIAAPHEGQ V NNLSQVDG RICGTLPVID NQSFQVEPCF RAPTIATGIP RLQTMKGRDA FAQDATRQRA LQGHRTADLL KTPFDYDLFH RT RLPPSAG ASIQAAGKEI DWSEKKLFRK AVVSTVFASD QVAERLRQDL PSPNTRDGQR TNADHGNRRN WSENIESLLR QAT PVESSA ENDPIFTAKV EERSFDSSLL YHGCRHLKKR SAFGHTPDAV AQLLRSSAEA GKGERPLVPS RPSRPSQHDS TQLK RVLSY HPDPEADSKG CFEQRARLRR SQLVTAKNSC RWGVNVFGYD LSPPRRNRLY ALRDHLDSKL VPNQSTDDAT HIKPR HTNV LSTSLHMSKL VPVTDLSPRP SFRYHADTGS LDATLLPVDA VPQERIGRRL ISPPESSLQS NFVPSHEEVG RHKRFL VNS RDSLQGNMIP IVKECTRRRK

UniProtKB: Uncharacterized protein

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Macromolecule #3: Tubulin alpha chain

MacromoleculeName: Tubulin alpha chain / type: protein_or_peptide / ID: 3 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 50.166645 KDa
SequenceString: MREVISIHVG QAGIQIGNAC WELFCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCVFLDL EPTVVDEVRT GTYRHLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLSL DRIRKLADNC TGLQGFLMFN AVGGGTGSGL GCLLLERLSV D YGKKSKLN ...String:
MREVISIHVG QAGIQIGNAC WELFCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCVFLDL EPTVVDEVRT GTYRHLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLSL DRIRKLADNC TGLQGFLMFN AVGGGTGSGL GCLLLERLSV D YGKKSKLN FCSWPSPQVS TAVVEPYNSV LSTHSLLEHT DVAVMLDNEA IYDICRRNLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDVTEFQT NLVPYPRIHF MLSSYAPIIS AEKAYHEQLS VAEITNSAFE PASMMAKCDP RHGKYMACCL MYR GDVVPK DVNAAVATIK TKRTIQFVDW CPTGFKCGIN YQPPTVVPGG DLAKVMRAVC MISNSTAIAE VFSRMDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDYEEV GIETAEGEGE EEGYGDEY

UniProtKB: Tubulin alpha chain

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Macromolecule #4: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 4 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 50.119121 KDa
SequenceString: MREIVHVQGG QCGNQIGAKF WEVISDEHGI DPTGTYCGDS DLQLERINVF YNEATGGRFV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKVREEY P DRIMETFS ...String:
MREIVHVQGG QCGNQIGAKF WEVISDEHGI DPTGTYCGDS DLQLERINVF YNEATGGRFV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKVREEY P DRIMETFS VFPSPKVSDT VVEPYNATLS VHQLVENADE VQVIDNEALY DICFRTLKLT TPTYGDLNHL VSAAMSGVTC CL RFPGQLN SDLRKLAVNL IPFPRLHFFL IGFAPLTSRG SQQYRALSVP ELTQQMFDAK NMMCASDPRH GRYLTASAMF RGR MSTKEV DEQMLNVQNK NSSYFVEWIP NNMKSSVCDI PPKGLKMSVT FVGNSTAIQE MFKRVSDQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE FDEEEGEMGA EEGA

UniProtKB: Tubulin beta chain

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Macromolecule #5: TLAP4 (thioredoxin-like associated protein), TGME49_201760

MacromoleculeName: TLAP4 (thioredoxin-like associated protein), TGME49_201760
type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 37.36023 KDa
SequenceString: MERSGHLCKM EPWKQKVPQC LSLHGSNSLR GGKRTYNCNV LMDNWRNDRL DAHNDQKLTS WRIPHPLYTE LPQGSKYETH YRQSYDYED WARRPVRLSK YGLLGHDDSG AESWTTETRS EYEPPRLRRD QLKAAGQWPY GEDIYPRHVH GNEEFMCPHP M AIHVSRTH ...String:
MERSGHLCKM EPWKQKVPQC LSLHGSNSLR GGKRTYNCNV LMDNWRNDRL DAHNDQKLTS WRIPHPLYTE LPQGSKYETH YRQSYDYED WARRPVRLSK YGLLGHDDSG AESWTTETRS EYEPPRLRRD QLKAAGQWPY GEDIYPRHVH GNEEFMCPHP M AIHVSRTH REDYIRSLTP RPAYERPPAG VPSSSGRLPG VPPYANDPIS HHGGSQEQRH FCRMPCRNPS GSSSVQGTTG VD ARASPAG SPVFAGQVPA QVKQEGGECG QGYAGIAATE DGLVDHGNSQ TDRSAGQHCM LNASGGSERA HAAANTSTCP QRK ESDPQP TVSWAAVPCQ

UniProtKB: Uncharacterized protein

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Macromolecule #6: TLAP2 (thioredoxin-like associated protein), TGME49_232130

MacromoleculeName: TLAP2 (thioredoxin-like associated protein), TGME49_232130
type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 47.924449 KDa
SequenceString: MDPRGQPVGP ARPGVPPQMM RPQGGPPPGA FPGGPRGPAG APFGAPMGPG GPMGPPRGPG PQMGPPRGPG PQMGPPRGQQ GPPPPGVRG LMPGMTPQGP PGARPGMPPP GTMPMGPDGK LRMQPQTAPG APPAGMPGTG MPPQQVPRGP MGHVGGGTGG M PAPDARQP ...String:
MDPRGQPVGP ARPGVPPQMM RPQGGPPPGA FPGGPRGPAG APFGAPMGPG GPMGPPRGPG PQMGPPRGPG PQMGPPRGQQ GPPPPGVRG LMPGMTPQGP PGARPGMPPP GTMPMGPDGK LRMQPQTAPG APPAGMPGTG MPPQQVPRGP MGHVGGGTGG M PAPDARQP VPSKTDSHGL QQKDLAQRSR NLRTLEDDER SDHQFGEEIL NKGLQTFARL VALNDVGDLG AWNGYTWKSR RP PSVFFIN ITHDPEGRLW AVTESNEVGK LTVKGFKAIG HIGQEDVVDI TFDPKDGTLW AINRVGELLH WNGYTWDKKY HAG FHKLRA ATFDRKGNLW VVNTAGEIAM WDEEEQQWDL KKVPGATRLH TLAFDENNKL WVLGSHGELM LLAANRWVVY GWVG CWKFR DISFRWSKTA IEQLRAVRST GTVFGGRSSA LADRLPVPQG A

UniProtKB: Uncharacterized protein

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Macromolecule #7: TRXL1, TGME49_232410

MacromoleculeName: TRXL1, TGME49_232410 / type: protein_or_peptide / ID: 7 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 24.939332 KDa
SequenceString: MSQPVFASPL NVEKRRLNEE RALMQAQKAG GEGVNIQLPP NYGDMDLILF PEGSLKNSNN TVIPQSHLKG KSVALYFADG ADPKCASLL PFLLNYYRTM NEGGANQKIE IIFVSLDRDR EAFESHRAHM PWLSIDLENP LTEILKRHFR VMKEYEVPTY G YGSRTGVP ...String:
MSQPVFASPL NVEKRRLNEE RALMQAQKAG GEGVNIQLPP NYGDMDLILF PEGSLKNSNN TVIPQSHLKG KSVALYFADG ADPKCASLL PFLLNYYRTM NEGGANQKIE IIFVSLDRDR EAFESHRAHM PWLSIDLENP LTEILKRHFR VMKEYEVPTY G YGSRTGVP SVIVIGSDGR EAQFLPICSG LEEGDRALLR WDWRNTKFAS DQFHVRPTLL EQ

UniProtKB: PDI family protein

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Macromolecule #8: TRXL2, TGME49_225790

MacromoleculeName: TRXL2, TGME49_225790 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 21.687934 KDa
SequenceString:
MLAADCFFGP DVVKRTQQGN YVPVRPDHFA GVSVALFFAK AGHSKCAQIV PVVRQFYKTT NFSGEKAVIE IIYVSLDKDE QDFERVRAL MPWCSVEYKS CLRKKLIERY RVPNGELAFG TVRIPSTAIP LLIVIGPNGE EAGRMNFQQS DEFVLQRWDY R FNKWPGSA QRLRTLNDAT DPWKKRLPQN V

UniProtKB: PDI family protein

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Macromolecule #9: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 26 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #10: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 26 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 26 / 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 statefilament

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Sample preparation

BufferpH: 7.5
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 225207
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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