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- EMDB-10519: Structure of an archaeal ABCE1-bound ribosomal post-splitting complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10519
TitleStructure of an archaeal ABCE1-bound ribosomal post-splitting complex
Map datacomposite map of post-processed maps
Sample
  • Complex: 30S ABCE1 post-splitting complex
    • Complex: 30S small ribosomal subunit
      • RNA: x 1 types
      • Protein or peptide: x 28 types
    • Complex: ABCE1
      • Protein or peptide: x 1 types
  • Ligand: x 4 types
KeywordsABC Proteins / Ribosome Recycling / Translation / RIBOSOME
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosomal small subunit binding / translational termination / translational initiation / ribosome biogenesis / small ribosomal subunit / tRNA binding / oxidoreductase activity / rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / ribosomal small subunit binding / translational termination / translational initiation / ribosome biogenesis / small ribosomal subunit / tRNA binding / oxidoreductase activity / rRNA binding / ribosome / structural constituent of ribosome / iron ion binding / translation / ribonucleoprotein complex / ATP hydrolysis activity / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea ...Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / RLI1 / Ribosomal protein S8e, archaeal / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Ribosomal protein L7Ae, archaea / 4Fe-4S binding domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Ribosomal protein L7Ae/L8/Nhp2 family / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Ribosomal protein S14/S29 / Ribosomal protein S19, bacterial-type / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
ATPase / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS14 ...ATPase / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS17 / RNA-binding protein / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS17 / LSU ribosomal protein L41E / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS19 / RNase L inhibitor
Similarity search - Component
Biological speciesThermococcus celer Vu 13 = JCM 8558 (archaea) / Saccharolobus solfataricus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKratzat H / Becker T
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: EMBO J / Year: 2020
Title: Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex.
Authors: Elina Nürenberg-Goloub / Hanna Kratzat / Holger Heinemann / André Heuer / Peter Kötter / Otto Berninghausen / Thomas Becker / Robert Tampé / Roland Beckmann /
Abstract: Ribosome recycling by the twin-ATPase ABCE1 is a key regulatory process in mRNA translation and surveillance and in ribosome-associated protein quality control in Eukarya and Archaea. Here, we ...Ribosome recycling by the twin-ATPase ABCE1 is a key regulatory process in mRNA translation and surveillance and in ribosome-associated protein quality control in Eukarya and Archaea. Here, we captured the archaeal 30S ribosome post-splitting complex at 2.8 Å resolution by cryo-electron microscopy. The structure reveals the dynamic behavior of structural motifs unique to ABCE1, which ultimately leads to ribosome splitting. More specifically, we provide molecular details on how conformational rearrangements of the iron-sulfur cluster domain and hinge regions of ABCE1 are linked to closure of its nucleotide-binding sites. The combination of mutational and functional analyses uncovers an intricate allosteric network between the ribosome, regulatory domains of ABCE1, and its two structurally and functionally asymmetric ATP-binding sites. Based on these data, we propose a refined model of how signals from the ribosome are integrated into the ATPase cycle of ABCE1 to orchestrate ribosome recycling.
History
DepositionDec 4, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tmf
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10519.png

Downloads & links

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Map

FileDownload / File: emd_10519.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map of post-processed maps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 360 pix.
= 390.24 Å		1.08 Å/pix.
x 360 pix.
= 390.24 Å		1.08 Å/pix.
x 360 pix.
= 390.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-24.47766 - 49.492874
Average (Standard dev.)0.0040332847 (±1.1207107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 390.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z390.240390.240390.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-24.47849.4930.004

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Supplemental data

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Additional map: post-processed map of ABCE1 after focused refinement

Fileemd_10519_additional_1.map
Annotationpost-processed map of ABCE1 after focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: post-processed map of the whole complex

Fileemd_10519_additional_2.map
Annotationpost-processed map of the whole complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: post-processed map of the 30S head after focused refinement

Fileemd_10519_additional_3.map
Annotationpost-processed map of the 30S head after focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 30S ABCE1 post-splitting complex

EntireName: 30S ABCE1 post-splitting complex
Components
  • Complex: 30S ABCE1 post-splitting complex
    • Complex: 30S small ribosomal subunit
      • RNA: 16S ribosomal RNA
      • Protein or peptide: 30S ribosomal protein S2
      • Protein or peptide: 30S ribosomal protein S3
      • Protein or peptide: 30S ribosomal protein S3Ae
      • Protein or peptide: 30S ribosomal protein S4
      • Protein or peptide: 30S ribosomal protein S4e
      • Protein or peptide: 30S ribosomal protein S5
      • Protein or peptide: 30S ribosomal protein S6e
      • Protein or peptide: 30S ribosomal protein S7
      • Protein or peptide: 30S ribosomal protein S8
      • Protein or peptide: 30S ribosomal protein S8e
      • Protein or peptide: 30S ribosomal protein S9
      • Protein or peptide: 30S ribosomal protein S10
      • Protein or peptide: 30S ribosomal protein S11
      • Protein or peptide: 30S ribosomal protein S12
      • Protein or peptide: 30S ribosomal protein S13
      • Protein or peptide: 30S ribosomal protein S14 type Z
      • Protein or peptide: 30S ribosomal protein S15
      • Protein or peptide: 30S ribosomal protein S17
      • Protein or peptide: 30S ribosomal protein S17e
      • Protein or peptide: 30S ribosomal protein S19P
      • Protein or peptide: 30S ribosomal protein S19e
      • Protein or peptide: RNA-binding protein
      • Protein or peptide: 30S ribosomal protein S24e
      • Protein or peptide: 30S ribosomal protein S27e
      • Protein or peptide: 30S ribosomal protein S27ae
      • Protein or peptide: 30S ribosomal protein S28e
      • Protein or peptide: 50S ribosomal protein L7Ae
      • Protein or peptide: LSU ribosomal protein L41E
    • Complex: ABCE1
      • Protein or peptide: ATPase
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: 30S ABCE1 post-splitting complex

SupramoleculeName: 30S ABCE1 post-splitting complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30

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Supramolecule #2: 30S small ribosomal subunit

SupramoleculeName: 30S small ribosomal subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#29
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)

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Supramolecule #3: ABCE1

SupramoleculeName: ABCE1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #30
Source (natural)Organism: Saccharolobus solfataricus (archaea)

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Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 482.205531 KDa
SequenceString: AUUCCGGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC CGACUAAGCC AUGCGAGUCA UGGGGCGCCU UGCGCGCACC GGCGGACGG CUCAGUAACA CGUCGGUAAC CUACCCUCGG GAGGGGGAUA ACCCCGGGAA ACUGGGGCUA AUCCCCCAUA G GCCUGAGG ...String:
AUUCCGGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC CGACUAAGCC AUGCGAGUCA UGGGGCGCCU UGCGCGCACC GGCGGACGG CUCAGUAACA CGUCGGUAAC CUACCCUCGG GAGGGGGAUA ACCCCGGGAA ACUGGGGCUA AUCCCCCAUA G GCCUGAGG UACUGGAAGG UCCUCAGGCC GAAAGGGGCU CUGCCCGCCC GAGGAUGGGC CGGCGGCCGA UUAGGUAGUU GG UGGGGUA ACGGCCCACC AAGCCGAAGA UCGGUACGGG CCAUGAGAGU GGGAGCCCGG AGAUGGACAC UGAGACACGG GUC CAGGCC CUACGGGGCG CAGCAGGCGC GAAACCUCCG CAAUGCGGGC AACCGCGACG GGGGGACCCC CAGUGCCGUG GCAA CGCCA CGGCUUUUCC GGAGUGUAAA AAGCUCCGGG AAUAAGGGCU GGGCAAGGCC GGUGGCAGCC GCCGCGGUAA UACCG GCGG CCCGAGUGGU GGCCGCUAUU AUUGGGCCUA AAGCGUCCGU AGCCGGGCCC GUAAGUCCCU GGCGAAAUCC CACGGC UCA ACCGUGGGGC UUGCUGGGGA UACUGCGGGC CUUGGGACCG GGAGAGGCCG GGGGUACCCC UGGGGUAGGG GUGAAAU CC UAUAAUCCCA GGGGGACCGC CAGUGGCGAA GGCGCCCGGC UGGAACGGGU CCGACGGUGA GGGACGAAGG CCAGGGGA G CGAACCGGAU UAGAUACCCG GGUAGUCCUG GCUGUAAAGG AUGCGGGCUA GGUGUCGGGC GAGCUUCGAG CUCGCCCGG UGCCGAAGGG AAGCCGUUAA GCCCGCCGCC UGGGGAGUAC GGCCGCAAGG CUGAAACUUA AAGGAAUUGG CGGGGGAGCA CUACAAGGG GUGGAGCGUG CGGUUUAAUU GGAUUCAACG CCGGGAACCU CACCGGGGGC GACGGCAGGA UGAAGGCCAG G CUGAAGGU CUUGCCGGAC ACGCCGAGAG GAGGUGCAUG GCCGCCGUCA GCUCGUACCG UGAGGCGUCC ACUUAAGUGU GG UAACGAG CGAGACCCGC GCCCCCAGUU GCCAGUCCUU CCCGCUGGGG AGGAGGCACU CUGGGGGGAC CGCCGGCGAU AAG CCGGAG GAAGGAGCGG GCGACGGUAG GUCAGUAUGC CCCGAAACCC CCGGGCUACA CGCGCGCUAC AAUGGGCGGG ACAA UGGGA UCCGACCCCG AAAGGGGAAG GGAAUCCCCU AAACCCGCCC CCAGUUCGGA UCGCGGGCUG CAACUCGCCC GCGUG AAGC UGGAAUCCCU AGUACCCGCG UGUCAUCAUC GCGCGGCGAA UACGUCCCUG CUCCUUGCAC ACACCGCCCG UCACUC CAC CCGAGCGGGG UCCGGAUGAG GCCUGAUCUC CCUUCGGGGA GGUCGGGUCG AGUCUGGGCU CCGUGAGGGG GGAGAAG UC GUAACAAGGU AGCCGUAGGG GAACCUACGG CUCGAUCACC UCC

GENBANK: GENBANK: CP014854.1

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Macromolecule #2: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 22.297914 KDa
SequenceString: YLVPLDQYLA AGVHIGTQQK TQDMKKFIYR VRQDGLYVLD VRKTDERLRT AGKFLAKFDP TSILAVSVRL YGQKPVKKFG EVTGARAIP GRFLPGTMTN PQVKNFIEPD VLIVTDPRAD HQAMKEAIEI GIPIVALVDT ENFLSYVDLA IPTNNKGRKA L ALIYWILA ...String:
YLVPLDQYLA AGVHIGTQQK TQDMKKFIYR VRQDGLYVLD VRKTDERLRT AGKFLAKFDP TSILAVSVRL YGQKPVKKFG EVTGARAIP GRFLPGTMTN PQVKNFIEPD VLIVTDPRAD HQAMKEAIEI GIPIVALVDT ENFLSYVDLA IPTNNKGRKA L ALIYWILA REILYNRKEI ESREDFKVPV EEFEMRI

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #3: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 21.707383 KDa
SequenceString: MAIERYFIEE GVREMLIDEY LEKELRRAGY SGIDIKKTPL GTKVVIFAAS PGYVIGRGGR RIRELTRILE RQFGLENPQI EVEEIKNPY LNAKVQAIRL ARALERGIHF RRAAYSAIRA IMRNGARGVE IRLSGKLTGE RAKSVRFYQG YLAKVGNPAE T LVSRGYAQ ...String:
MAIERYFIEE GVREMLIDEY LEKELRRAGY SGIDIKKTPL GTKVVIFAAS PGYVIGRGGR RIRELTRILE RQFGLENPQI EVEEIKNPY LNAKVQAIRL ARALERGIHF RRAAYSAIRA IMRNGARGVE IRLSGKLTGE RAKSVRFYQG YLAKVGNPAE T LVSRGYAQ AKLKLGVIGV KVSIMPPDAK LPDEI

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #4: 30S ribosomal protein S3Ae

MacromoleculeName: 30S ribosomal protein S3Ae / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 21.588188 KDa
SequenceString:
DKWKMKEWYV VYAPDFFGSK EIGLTPADEP EKVIGRVIET TLRDLTGDFT KGQVKLYFQI YDVKGQNAYT KFKGHTLARS YIRSLVRRR TTRIDGIFNV TTKDGYKLRV MGMVIAYRRI QTSQERAIRE IIRDIIYKKA EELNYRDFVL EAVSGKMAAE I AKEARRIY PIKRAEIRKI KVLAEP

UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #5: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 20.975336 KDa
SequenceString:
DPKRQRKKYE TPSHPWIKER LDRERVIMRK YALKNKKELW RHETQLKEFR RRARRLLAAR GKQAEVERVQ LLQRLNRLGL LPADAVLDD VLSLTVEDVL DRRLQTIVYK KGLARTPRQA RQLIVHGHIE VNGQIIRSPG YLVLKAEEDT ITYSKTSPFA R ESHPERMV IEQAKQGGEA

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #6: 30S ribosomal protein S4e

MacromoleculeName: 30S ribosomal protein S4e / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 27.849559 KDa
SequenceString: RKGAKRHLKR LAAPDQWYIS RKRYKWAVRP RPGPHSMKTS IPLLYIVRDY LGYAKTAREA RKILNEGRIL VDGRVRRDYK FPVGIMDVV SIPETGEHYR VLPNRIGKLV LHPISEKEAN IKPLRISNKR MVKGAKVQLN LHDGSNHLVT VDDKDNYRTA Y TVLMKVPD ...String:
RKGAKRHLKR LAAPDQWYIS RKRYKWAVRP RPGPHSMKTS IPLLYIVRDY LGYAKTAREA RKILNEGRIL VDGRVRRDYK FPVGIMDVV SIPETGEHYR VLPNRIGKLV LHPISEKEAN IKPLRISNKR MVKGAKVQLN LHDGSNHLVT VDDKDNYRTA Y TVLMKVPD REVIEILPFD VGAYVFVTRG KNVARKGKIV EVRRFPMGWP DVVTIEDENG ELFDTLKEYA FVVGKEKPEI SL P

UniProtKB: Small ribosomal subunit protein eS4

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Macromolecule #7: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 24.543494 KDa
SequenceString: SQRVLEEWEP RTKLGQLVKA GQITDIHEIF RKGYQIKEPE IVDVLLPEVN MRENQEVLDI ALTVRMTDSG RRIRFRVLAA VGNRDGYVG LGIGHGREVG IAIRKAINYA KMNIIEIKRG CGSWECRCRR PHSIPFAVEG KEGSVRVKLM PGPRGLGLVI G DVGKKILS ...String:
SQRVLEEWEP RTKLGQLVKA GQITDIHEIF RKGYQIKEPE IVDVLLPEVN MRENQEVLDI ALTVRMTDSG RRIRFRVLAA VGNRDGYVG LGIGHGREVG IAIRKAINYA KMNIIEIKRG CGSWECRCRR PHSIPFAVEG KEGSVRVKLM PGPRGLGLVI G DVGKKILS LAGVQDVWSQ SLGETRTTVN FAKAVFNALY NTNRVAIQPG MEEKYGIVVG RE

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #8: 30S ribosomal protein S6e

MacromoleculeName: 30S ribosomal protein S6e / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 13.829025 KDa
SequenceString:
MATFKLVISN PRNGIARQVE ISGESAEKLV GKRIGDEIPA SELGLNLTEI FGEEIPGDVK LRITGGTDRD GFAMRPDVHG PRRVKILVS RGPGFRPKER GERRKKTVRG NTISPEIVQV NMKLVF

UniProtKB: Small ribosomal subunit protein eS6

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Macromolecule #9: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 24.287164 KDa
SequenceString: AKALTERFYQ PKELKVMGRW SVEDVTVNDP SLRPYINLEA RLLPHSHGRH AKKAFGKANV HIVERLINKV MRSGASSHKA GGHFMRREH RSLMSKKMKA YEVVKEAFMI IERRTKQNPI QVLVRAIENS APREDTTTIA FGGIRYHMAV DVSPLRRLDI A LKNIALGA ...String:
AKALTERFYQ PKELKVMGRW SVEDVTVNDP SLRPYINLEA RLLPHSHGRH AKKAFGKANV HIVERLINKV MRSGASSHKA GGHFMRREH RSLMSKKMKA YEVVKEAFMI IERRTKQNPI QVLVRAIENS APREDTTTIA FGGIRYHMAV DVSPLRRLDI A LKNIALGA SAKCYRNKTS YAQALAEEII AAANADPKSF AYSRKEEIER IAQSSR

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #10: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 14.493863 KDa
SequenceString:
TLLDPLANAL SHITNSERVG KKEVYLKPAS KLMGEVLRVM QENGYIGEFE FIDDGRAGIY RVQLIGKINK AGAIKPRFPV KAREYEAWE KRFLPAFEFG ILIVSTSQGV MTHKEAIEKG IGGRLIAYVY

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #11: 30S ribosomal protein S8e

MacromoleculeName: 30S ribosomal protein S8e / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 14.164609 KDa
SequenceString:
AIWQGRSLKK PSGGRIILAR KKRKRELGRE PAFTRVGEEK EKKKIIRTYG GNRKVRLIEA IYANVFENGK GRKVKVLGVV ENPANRQYV RRDIITKGAI IETEAGRAIV TSRPGQDGVV NAVLIKE

UniProtKB: Small ribosomal subunit protein eS8

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Macromolecule #12: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 14.893458 KDa
SequenceString:
MKVIQTAGKR KTAIARATIR EGKGRVRINH RPVEIIEPEI ARFTIMEPLV LAGEEIVKGV DIDVKVEGGG FMGQAEAARV AIARALVEW TNDMNLKEKF MKYDRTMLVG DSRRTEPHKP NRSTKGPRAK RQK

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #13: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 11.731678 KDa
SequenceString:
MQKARIKLAS TDIKALNEVT DQIRQIAERT GVRMSGPIPL PTKRIRITTR KSPDGEGTAT FDKFELRVHK RLVDIEADER AMRQIMRIR VPEDVTIEIE LIS

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #14: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 14.308396 KDa
SequenceString:
QVNLKKKEKW GVAHIYSSYN NTIIHITDLT GAETVSRWSG GMVVKADRDE PSPYAAMIAA RRAAEEAMEK GFTGVHIKVR APGGSKSKS PGPGAQAAIR ALARAGLRIG RVEDVTPIPH DGTRPKGGRR GRRV

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #15: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 16.101055 KDa
SequenceString:
GKKAPYGEFA GRKLKLKRKK FRWSDIRYKR RVLRLKEKSD PLEGAPQAKG IVLEKIAVEA KQPNSAMRKA VRVQLIKNGK VVTAFTPGD GAINHIDEHD EVIIEGIGGP KGGSMGDIPG IRYKVVKVNR VSLKELVKGR KEKPR

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #16: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 15.768306 KDa
SequenceString:
DEFRHIVRIA GVDLNGNKQL RWALTGIRGI GINFATMVLR VAGIDPYMKT GYLTNEQIKK IEEILEDPVA HGIPAWAVNR PKDYETGKD MHLITAKLVM AWREDVNRLR RVRAYRGIRH ELGLPLRGQR TRSNFRH

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #17: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 6.587996 KDa
SequenceString:
MAKADYNKRK PRKFGKGARR CVRCGQYGPV IRVHGLMLCR HCFREIAPKL GFKKYE

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #18: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 17.47573 KDa
SequenceString:
MARMHARKRG KSGSKRPPRT APPTWVEYTA EEVEGLVVKL RKEGYSAAMI GTILRDQYGI PSVKLITGKK ITKILEENGL APQIPEDLM ALIRKAVNLR KHLEMHPKDR HSMRGLQLTE SKIRRLVKYY RRTGKLPAKW RYDPEQAKLL VR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #19: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 12.99611 KDa
SequenceString:
MREIGLKVQP PAEKCDDPHC PWHGHLRIHG RYFEGIVVSD KGKKTVVVER RHYHYLKKYE RYELRRSKVH AHNPECIDAK VGDRVLVAE TRPISKTKSW VVVAVTKRAG ER

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #20: 30S ribosomal protein S17e

MacromoleculeName: 30S ribosomal protein S17e / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 7.723957 KDa
SequenceString:
MGNIKQMFIK RTARELFDRY PNEFSRDFEH NKKKVEELTN VTSKTIRNRI AGYITKLVRM KEEG

UniProtKB: Small ribosomal subunit protein eS17

+
Macromolecule #21: 30S ribosomal protein S19P

MacromoleculeName: 30S ribosomal protein S19P / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 13.511957 KDa
SequenceString:
EFKYRGYTFE ELLNMSLEDF AKLLPSRQRR SLKRGLSPEQ KKLLRKIRLA RKGKYKKPIR THSRDMVILP EMVGITIHVY NGKEFVPVE IKEEMIGHYL GEFALTRKVV QHGSPG

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #22: 30S ribosomal protein S19e

MacromoleculeName: 30S ribosomal protein S19e / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 17.203732 KDa
SequenceString:
ATVYDVPGDL LVERTAKALK EVEAIKPPEW APFVKTGRHK ERIPEQEDWW YYRVASIFRK IYIDGPVGIE RLRTWYGGRK NRGHAPEHF YKAGGSIIRK ALQQLEAAGF VQKVPGEGRI VTPQGQSFLD RIATELKKEL EEQLPELKKY

UniProtKB: Small ribosomal subunit protein eS19

+
Macromolecule #23: RNA-binding protein

MacromoleculeName: RNA-binding protein / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 6.292359 KDa
SequenceString:
KFEVPVCTSC GKEITPREHA THFVCPNCGE AIIWRCESCR VLSVPYKCPK CGWEGP

UniProtKB: RNA-binding protein

+
Macromolecule #24: 30S ribosomal protein S24e

MacromoleculeName: 30S ribosomal protein S24e / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 11.406222 KDa
SequenceString:
MEIKVREMKE NRLLGRKEIY FDVIHEGEAT PSRADVKGKL VAMLDLNPET VVIQYIRSYF GSRVSRGYAK AYESKERMLY IEPEYVLVR DGIIKKEE

UniProtKB: Small ribosomal subunit protein eS24

+
Macromolecule #25: 30S ribosomal protein S27e

MacromoleculeName: 30S ribosomal protein S27e / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 6.835214 KDa
SequenceString:
LPKNLIPMPK SRFLRVKCID CGNEQIVFSN PSTTVRCLVC GATLVEPTGG KGILKAKVLE VLE

UniProtKB: Small ribosomal subunit protein eS27

+
Macromolecule #26: 30S ribosomal protein S27ae

MacromoleculeName: 30S ribosomal protein S27ae / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 5.995112 KDa
SequenceString:
MGQKWKLYEV KGGKVRRKNK FCPRCGPGVF MAEHKDRWSC GRCGYTEWKR

UniProtKB: Small ribosomal subunit protein eS31

+
Macromolecule #27: 30S ribosomal protein S28e

MacromoleculeName: 30S ribosomal protein S28e / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 7.356496 KDa
SequenceString:
MSDEGYPAEV IEIVARTGVT GGVTQVKVRI LEGRDKGRVI RRNVKGPVRV GDIVILRETE REAREI

UniProtKB: Small ribosomal subunit protein eS28

+
Macromolecule #28: 50S ribosomal protein L7Ae

MacromoleculeName: 50S ribosomal protein L7Ae / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 13.351441 KDa
SequenceString:
MAKPSYVKFE VPAELAEKAL EAVELARDTG RIRKGTNETT KAVERGQAKL VVIAEDVDPE EIVAHLPPLC EEKEIPYIYV PSKKELGAA AGIEVPAASV AILEPGKGRE LVEDIAAKVR ELMK

UniProtKB: Large ribosomal subunit protein eL8

+
Macromolecule #29: LSU ribosomal protein L41E

MacromoleculeName: LSU ribosomal protein L41E / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus celer Vu 13 = JCM 8558 (archaea)
Molecular weightTheoretical: 5.023395 KDa
SequenceString:
MKRRPRKWKK KGRMRWKWIK KRIRRLKKQR RKERGLI

UniProtKB: LSU ribosomal protein L41E

+
Macromolecule #30: ATPase

MacromoleculeName: ATPase / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 67.201469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRVAVINYDF CKPDKCNLEC INFCPVDRSG GKAIELSEIV KGKPVIYEET CIGCGICVKK CPYEAISIVN LPDELEGEVI HRYKVNGFK LFGLPTPKNN TILGVLGKNG VGKTTVLKIL AGEIIPNFGD PNSKVGKDEV LKRFRGKEIY NYFKELYSNE L KIVHKIQY ...String:
MRVAVINYDF CKPDKCNLEC INFCPVDRSG GKAIELSEIV KGKPVIYEET CIGCGICVKK CPYEAISIVN LPDELEGEVI HRYKVNGFK LFGLPTPKNN TILGVLGKNG VGKTTVLKIL AGEIIPNFGD PNSKVGKDEV LKRFRGKEIY NYFKELYSNE L KIVHKIQY VEYASKFLKG TVNEILTKID ERGKKDEVKE LLNMTNLWNK DANILSGGGL QRLLVAASLL READVYIFDA PS SYLDVRE RMNMAKAIRE LLKNKYVIVV DHDLIVLDYL TDLIHIIYGE SSVYGRVSKS YAARVGINNF LKGYLPAENM KIR PDEIKF MLKEVSDLDL SKDLKTKMKW TKIIKKLGDF QLVVDNGEAK EGEIIGILGP NGIGKTTFAR ILVGEITADE GSVT PEKQI LSYKPQRIFP NYDGTVQQYL ENASKDALST SSWFFEEVTK RLNLHRLLES NVNDLSGGEL QKLYIAATLA KEADL YVLD APSSYLDVEE RYIVAKAIKR VTRERKAVTF IIDHDLSIHD YIADRIIVFK GEPEKAGLAT SPVTLKTGMN EFLREL EVT FRRDAETGRP RVNKIGSYLD RVQKERGDYY S

UniProtKB: ATPase

+
Macromolecule #31: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 31 / Number of copies: 29 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #33: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 33 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #34: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 34 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 293010
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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