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- EMDB-34955: Baseplate of DT57C bacteriophage in the full state -

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Basic information

Entry
Database: EMDB / ID: EMD-34955
TitleBaseplate of DT57C bacteriophage in the full state
Map dataComposite map for the baseplate
Sample
  • Virus: Escherichia phage DT57C (virus)
    • Protein or peptide: Baseplate hub protein
    • Protein or peptide: Distal tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: L-shaped tail fiber assembly
    • Protein or peptide: L-shaped tail fiber assembly
    • Protein or peptide: Tape measure protein
    • Protein or peptide: Tail tube protein
KeywordsBaseplate / T5 / VIRUS / VIRAL PROTEIN
Function / homology
Function and homology information


: / : / : / Distal tail protein pb9, A domain C-terminal / Distal tail protein pb9, A domain, N-terminal / Distal tail protein pb9, B domain / Intramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / Tip attachment protein J ...: / : / : / Distal tail protein pb9, A domain C-terminal / Distal tail protein pb9, A domain, N-terminal / Distal tail protein pb9, B domain / Intramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / Tip attachment protein J / Putative phage tail protein / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Distal tail protein / Tail tube protein / Baseplate hub protein / Minor tail protein / L-shaped tail fiber assembly / L-shaped tail fiber assembly / Tape measure protein
Similarity search - Component
Biological speciesEscherichia phage DT57C (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAyala R / Moiseenko AV / Chen TH / Kulikov EE / Golomidova AK / Orekhov PS / Street MA / Sokolova OS / Letarov AV / Wolf M
Funding support Russian Federation, Japan, 4 items
OrganizationGrant numberCountry
Russian Science Foundation21-44-07002 Russian Federation
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
Japan Society for the Promotion of Science (JSPS)20K06581 Japan
Ministry of Agriculture, Forestry and Fisheries (MAFF)20320378 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Nearly complete structure of bacteriophage DT57C reveals architecture of head-to-tail interface and lateral tail fibers.
Authors: Rafael Ayala / Andrey V Moiseenko / Ting-Hua Chen / Eugene E Kulikov / Alla K Golomidova / Philipp S Orekhov / Maya A Street / Olga S Sokolova / Andrey V Letarov / Matthias Wolf /
Abstract: The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a ...The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a different receptor (BtuB) and features highly divergent lateral tail fibers (LTF). Considerable portions of T5-like phages remain structurally uncharacterized. Here, we present the structure of DT57C determined by cryo-EM, and an atomic model of the virus, which was further explored using all-atom molecular dynamics simulations. The structure revealed a unique way of LTF attachment assisted by a dodecameric collar protein LtfC, and an unusual composition of the phage neck constructed of three protein rings. The tape measure protein (TMP) is organized within the tail tube in a three-stranded parallel α-helical coiled coil which makes direct contact with the genomic DNA. The presence of the C-terminal fragment of the TMP that remains within the tail tip suggests that the tail tip complex returns to its original state after DNA ejection. Our results provide a complete atomic structure of a T5-like phage, provide insights into the process of DNA ejection as well as a structural basis for the design of engineered phages and future mechanistic studies.
History
DepositionDec 14, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34955.png

Downloads & links

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Map

FileDownload / File: emd_34955.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map for the baseplate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.4 Å/pix.
x 400 pix.
= 560. Å		1.4 Å/pix.
x 400 pix.
= 560. Å		1.4 Å/pix.
x 400 pix.
= 560. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-11.233155 - 29.177932999999999
Average (Standard dev.)0.0007087032 (±1.0121529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 560.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34955_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_34955_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_34955_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage DT57C

EntireName: Escherichia phage DT57C (virus)
Components
  • Virus: Escherichia phage DT57C (virus)
    • Protein or peptide: Baseplate hub protein
    • Protein or peptide: Distal tail protein
    • Protein or peptide: Minor tail protein
    • Protein or peptide: L-shaped tail fiber assembly
    • Protein or peptide: L-shaped tail fiber assembly
    • Protein or peptide: Tape measure protein
    • Protein or peptide: Tail tube protein

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Supramolecule #1: Escherichia phage DT57C

SupramoleculeName: Escherichia phage DT57C / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2681606 / Sci species name: Escherichia phage DT57C / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Baseplate hub protein

MacromoleculeName: Baseplate hub protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 107.114055 KDa
SequenceString: MKQILDSARN YLKNNSRIKT ASLISLELPG STGTSTAFIY LTDYFRDVIY NGILYQAGKV KSISPHKQNR DLSIGSLSFT ITGTAQDEV LKLVQNGVSF LDRTVSIHQA IITEDGSILP VDPDTNGPLL YFRGRITGGG IKDNISTSGV GTSTITWNCS N QFYDFDRV ...String:
MKQILDSARN YLKNNSRIKT ASLISLELPG STGTSTAFIY LTDYFRDVIY NGILYQAGKV KSISPHKQNR DLSIGSLSFT ITGTAQDEV LKLVQNGVSF LDRTVSIHQA IITEDGSILP VDPDTNGPLL YFRGRITGGG IKDNISTSGV GTSTITWNCS N QFYDFDRV NGRYTDDASH RGLEVVAGQL LPSNGAKRLE YQEDYGFFHA NKSISILAKY QVQEERYKLK SKKKLFGLSR SY SLKKYYE TVTKEVDIDF NLAAKYIPVV YGVQKIPGIP IFADTELHNP NIVYVVYAFA EGEIDGFLDF SFGDNPMICV DAN DSSART CFGTKKIVGD TMQRIASGIS SSSPSVHGQE YRYNDGNGDI RIWTYHGKSN QTASDVLVNI ARNRGFYLQN MNGN GPEYW DARYKLLDTA YAVVRFTINE NRTEIPEVSA EIQGKKVKVY HSDGRVTANS TSLNGIWQTL DYLTSDRYGA NITID QFPL QQLIQEAAIL DIIDESYQVS WQPYWRYVGW TNPLAENRQI VQMNTILDTS ESVFKNVQGL LESYGGAINN LSGQYR VTV EKYSNTPLEI NFLDTYGDLE LSDTTGRNKF NSVQASIVDP ALSWKTNSIT FYNSNYKEQD KNLDKKLQLS FANITNY YT ARSFADRELK KSRYSRTLSF SLPYQFIGIE PNDAIAFTYD RYGWDRKYFL VDEVENSREG KINVTLQEYG EDVFINSG Q VDNSGNDIPD ISNNVLPPRD FKYTPTPGGL VGSIGKNGEL SWLPSLTNNV VYYSIVHSGH AEPYIVQQLE TNPNERMIQ EIIGEPAGLA IFEIRAVDIN GRRSSPVTLS IELNSAKNLS VVSNFRVTNT ASGDVTEFVG PDVKLAWDRI PEEDIIESIF YTLEIHDPQ NRMLRSVRIE NQYTYDYLLT YNKADFALQN SDALGINRKL YFRIRAEGDD GEQSVEWASI

UniProtKB: Baseplate hub protein

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Macromolecule #2: Distal tail protein

MacromoleculeName: Distal tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 22.666484 KDa
SequenceString: MRLPDPYTNP ELSGLGFESV NLIDNDPVIR DELPNGKVNE VKVSAQYWGI NISYPELFPD EYSVLDAFIL EYKRTGGYID VILPQYEAF RVRGNTNLVN IPAGQKGSNI TMDTQGVLTG IPKPGDLFKL SNHPKVYKIT SFNRSGNSWS INVYPDLFIT T TGAEKPVF ...String:
MRLPDPYTNP ELSGLGFESV NLIDNDPVIR DELPNGKVNE VKVSAQYWGI NISYPELFPD EYSVLDAFIL EYKRTGGYID VILPQYEAF RVRGNTNLVN IPAGQKGSNI TMDTQGVLTG IPKPGDLFKL SNHPKVYKIT SFNRSGNSWS INVYPDLFIT T TGAEKPVF NGILFRTKLM NGDAFGSTLN NNGTYSGISL NLRESL

UniProtKB: Distal tail protein

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Macromolecule #3: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 34.513672 KDa
SequenceString: MYYSLMRESK VIVEYDGRAF HFDALSNYDV QTSYEEFKTL RRTIHRRTNY ADSVINAQTP SSISLAINFS NTLTEANFFE WLGFDRKGN TFLLPLYSNN IEPIMFNIYI VNKDNNCVYF ENCYVSTVDF SLDKNIPILN VGIESGKFSE VSTYREAASI I QGEAMSYS ...String:
MYYSLMRESK VIVEYDGRAF HFDALSNYDV QTSYEEFKTL RRTIHRRTNY ADSVINAQTP SSISLAINFS NTLTEANFFE WLGFDRKGN TFLLPLYSNN IEPIMFNIYI VNKDNNCVYF ENCYVSTVDF SLDKNIPILN VGIESGKFSE VSTYREAASI I QGEAMSYS PVIVSTNGNI LPGLISASLS FQQQCSWRED KSVFDINKIY NNKRAYVNEM NASATISLYY LKRFAGDMVY NI EPETDVP LNIRNNNISI DFPLARISKR LNFSDVYKVE WDIIPTASSD PVRIDFFGEI KND

UniProtKB: Minor tail protein

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Macromolecule #4: L-shaped tail fiber assembly

MacromoleculeName: L-shaped tail fiber assembly / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 15.384226 KDa
SequenceString:
MSTENRVIDI VVDEKVPYGL IMQFMDVDDS VYPPSEIPVN LTGYSLRGTI KSSLDENAET LASFTTSIID AAQGAAAISL SVADVTNIG EKASKERDKY NPRQRFAGYY DILMTRDVIG SEVSSFRIME GKVYISDGVT Q

UniProtKB: L-shaped tail fiber assembly

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Macromolecule #5: L-shaped tail fiber assembly

MacromoleculeName: L-shaped tail fiber assembly / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 113.712461 KDa
SequenceString: MALKTKIIVQ QILNIDDTTT TASKYPKYTV VLGNSISSIT AGELTAAVEA SAGSAAAAKG SEIAAKESEL NAKDSENEAA ISAGASEES ASQSAASAAE SERQAGLSKG SADNSAASAQ ESEGFRDSAE LAAQNAEQSR LLAEQAKTAA QQAQTAAEAA K TGAETAKD ...String:
MALKTKIIVQ QILNIDDTTT TASKYPKYTV VLGNSISSIT AGELTAAVEA SAGSAAAAKG SEIAAKESEL NAKDSENEAA ISAGASEES ASQSAASAAE SERQAGLSKG SADNSAASAQ ESEGFRDSAE LAAQNAEQSR LLAEQAKTAA QQAQTAAEAA K TGAETAKD GADAAATTAG EHAAAARQSE LNAKISETNA AGSATEAGDK AIDATTEADR AKAEADRATQ IVDSKLDKVD IS GFIKVYK TKAEADADVV NRVLDEKVLV WNQTNSKYGW YKVAGTAETP VLELVETEQK LTSVNNVRAD DAGNVQITLP GGN PSLWLG EVTWFPYDKD SGVGYPGVLP ADGREVLRVD YPDTWEAIEA GLIPSVSEAE WQAGASLYFS TGDGSTTFRL PDMM QGQAF RAPTKGEEDA GVIKDQIPYV VTVNGISPDA ITGNVEIDTS LQGTVSINQG GTGATTKEDA RIALELYSTT EVDSA LADK ADIATTYTKT EVDSALADKA DIATTYTKVE VDSALADAKT QSDTDYLLKA NNLSDLADRA AAWLNVRPIG STPLAG DPV GDYDAVTKRW VENKINTGTV GPTMNGVMNY GVGDFHLRDS RAYIQPYEVV SDGQLLNRAD WPELWAYAQM LSPISDA DW LADPTKRGQY SLGDGSTTFR VPDRNGVQTG SISALFGRGD GGASSTGGTI LDSAAPNITG SFGRLVYAST GTIYEANT G TGAFSAVLSQ AKYKRLSEIS AADGTAATYP SGFEFFASNS SPVYGRGSTE VRPKAFTGVW VIRASGGFVA ANTSWSVIN GDATRPADGT TADGGEIISR YNVNGVREAQ MSWRIRAQIG AEHYARLNVY NATANRTAVY DFNDLGTFSA ENLHSKGAIY SDGNLTIQN QGWPGINFKS NRYNTPATQI GGSTIIEVSG TDGNVSGVNL IRRRGDGNQA GQIIVSFPTT GGAIALQGTS G IEYKKDVT DADAQEAMDR INGQRLVNFV YKDDEQERVR FGVIAEEAEL IAPQYIKHNQ VSYEDILDEE GNKIGEKTRD RP SVDVNPI VMDLMGCVQA LNAKIAALEA RIAELESKE

UniProtKB: L-shaped tail fiber assembly

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Macromolecule #6: Tape measure protein

MacromoleculeName: Tape measure protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 132.626406 KDa
SequenceString: MTDKLIRELL IDVKQKGATR TAKSIENVSD ALENAAAASE LTNEQLGKMP KTLYSIERAA DRAAKSLTKM QASRGMAGIT KSIDSIGAK LDDLSIAMIE VADKLEAGFD GVSRSVKVMG NDVAAATEKV QDRLYDTNRV LGGTARGFND TAGAAGRASR A IGNTSGSA ...String:
MTDKLIRELL IDVKQKGATR TAKSIENVSD ALENAAAASE LTNEQLGKMP KTLYSIERAA DRAAKSLTKM QASRGMAGIT KSIDSIGAK LDDLSIAMIE VADKLEAGFD GVSRSVKVMG NDVAAATEKV QDRLYDTNRV LGGTARGFND TAGAAGRASR A IGNTSGSA RGATRDFAAM AKVGGGLPLL YAAIASNIFV LQSAFEQLKL GDQLNRLEEF GVIVGTQTGT PVQSLARSLQ EA AGYAISF EEAMRQASSA SAYGFDAEQL NKFGLVARRA AAVLGVDMTD ALNRVIKGVS KQEIELLDEL GVTIRLNDAY ADY VKQLNA ANTGITYNIN SLTTFQKQQA YANAVIAEST KRFGYLDEVL RATPWEQFAA NADAALRTIQ QAAAKYLGPV IDAI NTVFY TSQASISAEA ARAQEQTNKQ IDPTNVGAVA LSLSASEEGY NKALDMYKES LDKRNKLKSE FDKRMEQADF YTKLA IRQV GEGIPAGLAT AGASEANKKF VEETAAMGLQ VARLDKEVTD STENLNAWKS AYQAAGAAAA KANPEFQKQI NLQRDT TDP GAVYDFNSTV LKGLTEQQKA YNQTKKTASD LANDIQNVAQ NTDTAAKTSA TLADAIKNIE SLSLGTGKSA DEYVKNL NL GYNTLSEMKT ASQALSEYVK LTGNETKNQL AVQQKIADVY NQTKDKEKAQ EAGRRLELQQ LEEQEAALRR VLQTNQGN K AVEREIEKIQ LEKIKLTNQG MEAQKKVKDY TDKILGVDRE IALLNNRTMT DTQYRLAQLN LELTIEKEKY EWYTKQADK QKEAEQSRRA QAQIEREIWK FHQDQQAEMT SKRQEAFENT LTSMFPLAGE MQKMEMQLDF YTQMKELTKD NANEQMRWNA EIAKTRAQM SALTAQRNAQ MQSSVGSSLG AVYTPTTGLS GEDKKFADMG NQLASYDQAI SKLSELNSEA TAVAQSMGNL A NAMIQFSQ GSLDTTSTIA VGMQTVASMI QYSTSQQVSA IDQAIAAEQK RDGKSEASKA KLKKLEAEKL KIQQDAAKKQ II IQTAVAV MQAATAVPYP FSIPLMIAAG LAGALALAQA SSASGMSSIG DSGADTASYL TLGERQKNID VSMSANAGEL SYV RGDKGI GNANSFVPRA EGGNMYPGVS YQMGEHGTEV VTPMVPMKAT PNDELKNSSN STAGRPIILN ISAMDAASFR EFAS SNSGA LRDAVELALN ENGASLKTLG NS

UniProtKB: Tape measure protein

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Macromolecule #7: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 50.759051 KDa
SequenceString: MSLQLLRNTR IFVSTVKTGH DTTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAEW SFSTYILPYE DTTTGKQIV PDYMLWHALS SGKAIDLDGD TGAHNNATNF MVNFKDNAYH ELAMLHIYIL TDNAWSYIDS CQINQAEVNV D IEDIGRVT ...String:
MSLQLLRNTR IFVSTVKTGH DTTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAEW SFSTYILPYE DTTTGKQIV PDYMLWHALS SGKAIDLDGD TGAHNNATNF MVNFKDNAYH ELAMLHIYIL TDNAWSYIDS CQINQAEVNV D IEDIGRVT WSGNGNQLIP LDEQPFDPDA LGIDDETYMT IQSSYIKNKL TILKIKDMDS DKEYDIPITG GTFTINNNIT YL TPNIMSR VNIPIGSFTG AFELTGSLTA YLNDKSLGSM ELYKDLVRTL KVVNRFEIAL ILGGEYDDER PAAVLVAKQA HVN IPTIET DDVLGTSVEF KAIPTDLDTG DEGYLGFSNK YTKTTVANLI ATGDGAETPP ILVESITVKS AADATSVTNS DTLQ MSVEV TPPEATNTAV TWSISSGDAA TIDAESGLLT ADVSKTGEVI VKAVAKDGSG VEGTKTITVS AGE

UniProtKB: Tail tube protein

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model generated in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 42697
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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