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- EMDB-4782: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6... -

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Basic information

Entry
Database: EMDB / ID: EMD-4782
TitleCryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
Map dataCryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
Sample
  • Complex: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
    • Protein or peptide: Afp1
    • Protein or peptide: Afp2
    • Protein or peptide: Afp3
    • Protein or peptide: Afp5
    • Protein or peptide: Afp9
    • Protein or peptide: Afp4
    • Protein or peptide: Afp7
    • Protein or peptide: Afp11
    • Protein or peptide: Afp12
KeywordsAnti-feeding prophage / secretion system / AFP / contractile / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / : ...Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Afp12 / Afp11 / Afp9 / Afp7 / Afp5 / Afp4 / Afp3 / Afp2 / Afp1
Similarity search - Component
Biological speciesSerratia entomophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDesfosses A
CitationJournal: Nat Microbiol / Year: 2019
Title: Atomic structures of an entire contractile injection system in both the extended and contracted states.
Authors: Ambroise Desfosses / Hariprasad Venugopal / Tapan Joshi / Jan Felix / Matthew Jessop / Hyengseop Jeong / Jaekyung Hyun / J Bernard Heymann / Mark R H Hurst / Irina Gutsche / Alok K Mitra /
Abstract: Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, ...Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, bacterial type six secretion systems and R-pyocins is rapidly increasing, structural information on the contraction of bacterial phage-like protein-translocation structures directed towards eukaryotic hosts is scarce. Here, we characterize the antifeeding prophage AFP from Serratia entomophila by cryo-electron microscopy. We present the high-resolution structure of the entire AFP particle in the extended state, trace 11 protein chains de novo from the apical cap to the needle tip, describe localization variants and perform specific structural comparisons with related systems. We analyse inter-subunit interactions and highlight their universal conservation within contractile injection systems while revealing the specificities of AFP. Furthermore, we provide the structure of the AFP sheath-baseplate complex in a contracted state. This study reveals atomic details of interaction networks that accompany and define the contraction mechanism of toxin-delivery tailocins, offering a comprehensive framework for understanding their mode of action and for their possible adaptation as biocontrol agents.
History
DepositionApr 6, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseApr 17, 2019-
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: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rao
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rao
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4782.png

Downloads & links

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Map

FileDownload / File: emd_4782.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.36811557 - 0.52417195
Average (Standard dev.)0.0010271558 (±0.016190868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z486.000486.000486.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.3680.5240.001

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Supplemental data

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Half map: None

Fileemd_4782_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_4782_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6...

EntireName: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
Components
  • Complex: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
    • Protein or peptide: Afp1
    • Protein or peptide: Afp2
    • Protein or peptide: Afp3
    • Protein or peptide: Afp5
    • Protein or peptide: Afp9
    • Protein or peptide: Afp4
    • Protein or peptide: Afp7
    • Protein or peptide: Afp11
    • Protein or peptide: Afp12

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Supramolecule #1: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6...

SupramoleculeName: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Note that the needle is not resolved here because of 6-fold symmetry imposition
Source (natural)Organism: Serratia entomophila (bacteria)

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Macromolecule #1: Afp1

MacromoleculeName: Afp1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 16.449449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAITADDIAV QYPIPTYRFI VTLGDEQVPF TSASGLDINF DTIEYRDGTG NWFKMPGQRQ APNITLSKGV FPGKNAMYEW INAIQLNQV EKKDIMISLT NEAGTEVLVS WNVSNAFPTS LTSPSFDATS NEIAVQQITL MADRVTIQTA

UniProtKB: Afp1

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Macromolecule #2: Afp2

MacromoleculeName: Afp2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 38.784355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTVTTTYPGV YLSEDAVSSF SVNSAATAVP LFAYDSENTN TINKPIQVFR NWAEFTVEYP TPLEDAFYTS LSLWFMHGGG KCYLVNEAN IADAVAQYDD ITLIVAAGTD TTTYTAFTTV VGQGYRIFGL FDGPKEKIAG TAKPDEVMEE YPTSPFGAVF Y PWGTLASG ...String:
MTVTTTYPGV YLSEDAVSSF SVNSAATAVP LFAYDSENTN TINKPIQVFR NWAEFTVEYP TPLEDAFYTS LSLWFMHGGG KCYLVNEAN IADAVAQYDD ITLIVAAGTD TTTYTAFTTV VGQGYRIFGL FDGPKEKIAG TAKPDEVMEE YPTSPFGAVF Y PWGTLASG AAVPPSAIAA ASITQTDRTR GVWKAPANQA VNGVTPAFAV SDDFQGKYNQ GKALNMIRTF SGQGTVVWGA RT LEDSDNW RYIPVRRLFN AVERDIQKSL NKLVFEPNSQ PTWQRVKAAV DSYLHSLWQQ GALAGNTPAD AWFVQVGKDL TMT QEEINQ GKMIIKIGLA AVRPAEFIIL QFSQDIAQ

UniProtKB: Afp2

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Macromolecule #3: Afp3

MacromoleculeName: Afp3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 48.777566 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATVTSVPGV YIEEDASPAM SVSASATAVP LFVARFTPLK PELAGVITRI GSWLDYTILF DSNVPSSARV TVSSTAVEPS PEFDALETA SSKATTTYTY QIDDTEVVDP TASVALRLYF QNGGGPCYLY PLEKADDNGP LAALPDLIDE VGEITLLASP D PDETYRTA ...String:
MATVTSVPGV YIEEDASPAM SVSASATAVP LFVARFTPLK PELAGVITRI GSWLDYTILF DSNVPSSARV TVSSTAVEPS PEFDALETA SSKATTTYTY QIDDTEVVDP TASVALRLYF QNGGGPCYLY PLEKADDNGP LAALPDLIDE VGEITLLASP D PDETYRTA VYGALAASLD QHKGYFLLAD SVNGDAPSAV GGSAQVAVYY PNVEVPHTRK LDDAEVAIDG YLDDEGKAVT TL AALRVVN TEFAGEIAQS LSGDLSAPLS LPPSALIAGV YGKTDGERGV WKAPANVVLN GVSDVSVRVT NEQQAELNPK GIN VIRHFS DRGLVVWGSR TQKDDDDWRY IPVRRLFDAA ERDIKKALQP MVFEPNSQLT WKRVQTAIDN YLYRLWQQGA LAGN KAEEA YFVRVGKGIT MTQDEINQGK MIIQVGMAAV RPAEFIILKF TQDMSQ

UniProtKB: Afp3

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Macromolecule #4: Afp5

MacromoleculeName: Afp5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 17.026539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTPAVSHRF LVNFLFNNIP NPFDIAFQRI SGLSRTLEVS QHREGGENVR NLWLAEQVNH GSLVLERGVM NASPLTLQFD RVLRRESTQ WANVVIMLLN ELSLPVTTWT LSHALPVRWQ MGDLDAGSNQ VLINTLELRY QDMRMLGVKL

UniProtKB: Afp5

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Macromolecule #5: Afp9

MacromoleculeName: Afp9 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 15.693884 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSNDILKATL GQCWAFPPRF SPDTGVSLTA GVEAVMQSLR VLFMTEPGER IMRESYGGGM HDFIFENITD ELLANIHNRI EESILRHEP RALLKDVIIQ PDKQEASRLR AQITVYLAGS DLVETVDGTL NIHDGQTLRL L

UniProtKB: Afp9

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Macromolecule #6: Afp4

MacromoleculeName: Afp4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 45.565633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTMVLPGVSY NETLLTQASN DDPVTMPLFI GYTPPDTAIP VTVMQPVSVG SLTQANSLFG QRGTLAYSLR HFFENGGLQC YVLPLGPGK GEPAARLQEL IAALQTPQML ETLLADDKTG LVLVPELSEL NEVSSTSLSA EGVDAAEVDA DALWYQGWQV L LTLCRQAP ...String:
MTMVLPGVSY NETLLTQASN DDPVTMPLFI GYTPPDTAIP VTVMQPVSVG SLTQANSLFG QRGTLAYSLR HFFENGGLQC YVLPLGPGK GEPAARLQEL IAALQTPQML ETLLADDKTG LVLVPELSEL NEVSSTSLSA EGVDAAEVDA DALWYQGWQV L LTLCRQAP QRFALLELPE DPASAVTLTQ QSFSADQCQR GAAWWPRLET SYQDESSAPV VLSPLPAVAA AIQRSAHDNG VW KAPANIA LAKTRRPTQS ILTSQALLDN QGVSCNLIRS FVGKGVRLWG CRTLLNEENT AWRYIQIRLL VSSVEHYLSK LAR AYLFEP NTAPTWMKLK GQVWTWLRQQ WLAGAFFGTV EDEAFSLSIG LDETMTEDDI RHGKMILQVR LALLAPAEFI AISL TLDLR DGTASAQTGG QS

UniProtKB: Afp4

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Macromolecule #7: Afp7

MacromoleculeName: Afp7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 25.259434 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLLERGLSK LTLNAWKDRE GKIPAGSMSA MYNPETIQLD YQTRFDTEDT INTASQSNRY VISEPVGLNL TLLFDSQMPG NTTPIETQL AMLKSLCAVD AATGSPYFLR ITWGKMRWEN KGWFAGRARD LSVTYTLFDR DATPLRATVQ LSLVADESFV I QQSLKTQS ...String:
MSLLERGLSK LTLNAWKDRE GKIPAGSMSA MYNPETIQLD YQTRFDTEDT INTASQSNRY VISEPVGLNL TLLFDSQMPG NTTPIETQL AMLKSLCAVD AATGSPYFLR ITWGKMRWEN KGWFAGRARD LSVTYTLFDR DATPLRATVQ LSLVADESFV I QQSLKTQS APDRALVSVP DLASLPLLAL SAGGVLASSV DYLSLAWDND LDNLDDFQTG DFLRATKGEE V

UniProtKB: Afp7

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Macromolecule #8: Afp11

MacromoleculeName: Afp11 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 67.327516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDLEQLKQI LGNGLTDQTF LLEPRTGKGL LNLMAKYTEA VPFAGHTDAD WKDFWMAGCT LEALSDIYQY PGLAEKKLPV QQAFLLALL HLLETPRAML NTVPARHRSL YYRDLLGFAP RAPQPDSVAV SFTLQRNSSP YALPAGSLLD GGQDSAGNSI T YQTDDSLL ...String:
MSDLEQLKQI LGNGLTDQTF LLEPRTGKGL LNLMAKYTEA VPFAGHTDAD WKDFWMAGCT LEALSDIYQY PGLAEKKLPV QQAFLLALL HLLETPRAML NTVPARHRSL YYRDLLGFAP RAPQPDSVAV SFTLQRNSSP YALPAGSLLD GGQDSAGNSI T YQTDDSLL ITGQQLEQLC WTAQVGETWK RYTAIDSATG VTLPAEGLRL FTATGQGTDT KEKAPELYLG FSGTSAQDTL SL YWSVRAS SALDVTWWYY QGTKWASLDA ELQDNTASLS VSNLWRARLP ADSQPGSGLP QDDEPLEAGY YWIKGTLKEN KEA KDENSP AEAMPQLQAV LANAMTATLN VAQAIDDSHF SQPLPANTIN QLVTPVAAIS DVRQPLPSVG GQPRETEMAM LQRA APRIA HRQRAITWNN MRSLLMEHYP EIFDVRFPDV DKLSRLPALE VQSLMVIPDG RYGDNDDALR PALSNGRLSR MAQWL SQYT SLWAAPTLKN PKYIDVTARY RVTFVVGIRP DYGYRQLAAQ LQHDYMPWAT DRRQAVTPGN QVDYYQLLAT LQQSPL VQS VNALVLSHDV IDETGKPTSM ETQSTVTARD DEVLILCPEG ETHV

UniProtKB: Afp11

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Macromolecule #9: Afp12

MacromoleculeName: Afp12 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 106.905594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKENALFPA VKDAIVFDAL WQQAHEKVTA LSGEIWTDTG DHDPGVTLLQ SATWNCSDLS YRASLSLNDL LTHQDQSTLF PEEFGPEQV LTCNTVTAED YRRALLDVHS SDIQALDTPE QDFLFSDVSL TQEPKEHRFH WWYNAEKREY SFRKPTDSGE V NELKLRGN ...String:
MSKENALFPA VKDAIVFDAL WQQAHEKVTA LSGEIWTDTG DHDPGVTLLQ SATWNCSDLS YRASLSLNDL LTHQDQSTLF PEEFGPEQV LTCNTVTAED YRRALLDVHS SDIQALDTPE QDFLFSDVSL TQEPKEHRFH WWYNAEKREY SFRKPTDSGE V NELKLRGN LWLSLVPTRY TQSLSPENLA AVEQCLAEFL AAHRNLGEVV SRITWLQPAT FSPRMTIELA DNIGDINQVA AQ IYQVTDA FLRPAVARYT TEQRRALGDA DDAIFEGPRL KHGWQQTAPS QITSGGYVLN LGPLVNLLLA IPGVASLSTL SVD KGDGHI TAVTGDNLRW QVADGYYPLL WGAPPLSLLA GDDSPLTLVS KGGIRNTLES EAMAGYLTQA DLIVTTPTVL PAGR FRDQT LYIPIGQRQP ECYALQQPDT VIDDQTRAVH QFLLPVDQLL ADGTAELAQL PTLLAFKNRG DAIRGTRWPY TNAMV QQAI HQPYAKTLEA IAQQDAAIFT QDKQPVGGNY ARELDFLQYL LGYFGTQRAA LPLTLDLPDF LATQRAYLAQ QPALGY DRI NIRIDQVSAL QKRIAARIGL DSICFADNPD LGQLPFYLIE HRQLLPQTPD STFDSEQTPS GFAVAEPDIT LTQAGSV GK VVQGQLIDLI AIEGGSRLHV SRLLVIKAEG DSFTVSTENS QQLHNTLSRL ETAWASHNLR WQNSNVWLQD MDYRLNYA E AKLQPANPQQ RLLASNAQSP YPAMVSVGDG IVLRPAGLQF YMPGANATRA ATLDADWQLA ATVKAVDPIA GTLLIEKAA GSTEDFPSAE SSFRYQWAFS QANYATTDRF SFVVSAVLNR RLIENPNIVP EQLVAWIQET IMAEFPAHVS LINHWLDDAT FNNFGVTYS RWQNSGMPLG DDAFALMQIL TLGHLPVTQL DIGLMRIATE EQRTEVIGDG SQWHEDVILR EELFYVPKDV Q TTL

UniProtKB: Afp12

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 20.0 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

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46991
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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