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- EMDB-53137: Cryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6... -

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Basic information

Entry
Database: EMDB / ID: EMD-53137
TitleCryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6), in extended state
Map dataCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in extended state
Sample
  • Complex: PlPVC baseplate (C6) in extended state
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Contractile injection system tube protein N-terminal domain-containing protein
    • Protein or peptide: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
    • Protein or peptide: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
    • Protein or peptide: Baseplate protein J-like domain-containing protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail sheath family protein
KeywordsContractile injection system / 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
Phage tail protein / Contractile injection system tube protein N-terminal domain-containing protein / Phage tail sheath family protein / Phage tail sheath family protein / Baseplate protein J-like domain-containing protein / Phage tail sheath family protein / Phage tail protein / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17 / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsMarin-Arraiza L / Taylor NMI
Funding support Denmark, Spain, 5 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF17OC0031006 Denmark
Novo Nordisk FoundationNNF23OC0081528 Denmark
LundbeckfondenR434-2023-289 Denmark
La Caixa FoundationLCF/BQ/EU21/11890147 Spain
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states
Authors: Marin-Arraiza L / Roa-Eguiara A / Pape T / Sofos N / Hendriks IA / Lund Nielsen M / Steiner-Rebrova EM / Taylor NMI
History
DepositionMar 14, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53137.png

Downloads & links

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Map

FileDownload / File: emd_53137.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in extended state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 700 pix.
= 840. Å		1.2 Å/pix.
x 700 pix.
= 840. Å		1.2 Å/pix.
x 700 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.8100571 - 1.6887823
Average (Standard dev.)-0.0002123651 (±0.043598384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 840.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized,...

Fileemd_53137_half_map_1.map
AnnotationCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in extended state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the PlPVC baseplate, 6-fold symmetrized,...

Fileemd_53137_half_map_2.map
AnnotationCryo-EM structure of the PlPVC baseplate, 6-fold symmetrized, in extended state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PlPVC baseplate (C6) in extended state

EntireName: PlPVC baseplate (C6) in extended state
Components
  • Complex: PlPVC baseplate (C6) in extended state
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Contractile injection system tube protein N-terminal domain-containing protein
    • Protein or peptide: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
    • Protein or peptide: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
    • Protein or peptide: Baseplate protein J-like domain-containing protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail sheath family protein

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Supramolecule #1: PlPVC baseplate (C6) in extended state

SupramoleculeName: PlPVC baseplate (C6) in extended state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Macromolecule #1: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 1 / Details: Pvc1 - tube protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 16.574574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAITPEQIAV EYPIPTYRFV VSVGDEQIPF NNVSGLDVHY DVIEYKDGIG NYYKMPGQRQ SINITLRKGV FPGDTKLFDW INSIQLNQV EKKDIAISLT NEAGTEILMT WNVANAFPTS FTSPSFDATS NEIAVQEIAL TADRVTIQAA

UniProtKB: Phage tail protein

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Macromolecule #2: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 2 / Details: Pvc2 - sheath protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 39.009828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTITTYPGV YIEEDASLSL SVSSSATAVP VFAVAGDNPL ISGKPYIRIS NWLEYLTLKN EQFDPANTLD ISLRAYFING GGYCYLVQT TDLEKQVPKL DDVTLLVAAG ENITTAVSTL CKPGKGLFAI FDGPTTELKS DGTSNSDYDP NPFAAVYYPW L TADWTTTI ...String:
MTTITTYPGV YIEEDASLSL SVSSSATAVP VFAVAGDNPL ISGKPYIRIS NWLEYLTLKN EQFDPANTLD ISLRAYFING GGYCYLVQT TDLEKQVPKL DDVTLLVAAG ENITTAVSTL CKPGKGLFAI FDGPTTELKS DGTSNSDYDP NPFAAVYYPW L TADWTTTI DIPPSAAIAG VYCSVDSTRG VWKAPANVPI QGGLQPKYPV TDDLQAQYNQ GKALNMIRTF PKSGTLVWGA RT LEDNDNW RYIPVRRLFN SAERDIKNAM SFAVFEPNSQ PTWERVRSAV NNYLYSLWQQ GGLAGNKPDD AYFVQIGKDI TMT DDDIKQ GKMIIKIGMA AVRPAEFIIL QFTQNTAQ

UniProtKB: Phage tail sheath family protein

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Macromolecule #3: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 3 / Details: Pvc5 - tube protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 17.178578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHNLYTPSVS HRFIASFLFN NIPSPLDIAF QRISGLSREL QTTQYSQGGE NARNVWLAEK IQHGSLHLER GVMTVTPLTL MFDRVLRGE KAVYADVVIM LLNENSVPVA SWTLSNALPV RWSTGDFDAN SNAVLVNSLE LRYQDMRWLG VKV

UniProtKB: Phage tail protein

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Macromolecule #4: Contractile injection system tube protein N-terminal domain-conta...

MacromoleculeName: Contractile injection system tube protein N-terminal domain-containing protein
type: protein_or_peptide / ID: 4 / Details: Pvc7 - tube initiator protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 24.84008 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLIERGLSK LTLTAFKDRE GKISVGSLQA MYNPDAIQLD YQTHYQQDES VNHTRKSSHY VSSPPAGLSL VLLFDASMPG NNIPVETQL TTLKALCAVD PSTHVPHFLK IKWGKMRWEN KSYFAGRASG LTINYTLFDR DATPLRASAT LSLVADESFV I QATEQQLK ...String:
MSLIERGLSK LTLTAFKDRE GKISVGSLQA MYNPDAIQLD YQTHYQQDES VNHTRKSSHY VSSPPAGLSL VLLFDASMPG NNIPVETQL TTLKALCAVD PSTHVPHFLK IKWGKMRWEN KSYFAGRASG LTINYTLFDR DATPLRASAT LSLVADESFV I QATEQQLK SPPVTTVSVT DMLTLPLIAL GAGASLASGI DYLSLAWQND LDNLDDFTPG QTLQAQEKA

UniProtKB: Contractile injection system tube protein N-terminal domain-containing protein

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Macromolecule #5: Photorhabdus luminescens subsp. laumondii TTO1 complete genome se...

MacromoleculeName: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
type: protein_or_peptide / ID: 5 / Details: Pvc9 - sheath adaptor protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 27.145588 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTNKILADIY GRGWAFPPQF FIGERIPYED YSSDLNKYLS EKKIEAEQIV KIQACIKESV MCYDFHAKIT STQVSKQTNL PNPLNILVT YTLGDSEISQ KIQGVLRVSQ DDPPQFSIKD NSRTGIAIAE GTQNVLQSIN ILFLTEPGER IMREDYGCGL N DYLFANIS ...String:
MTNKILADIY GRGWAFPPQF FIGERIPYED YSSDLNKYLS EKKIEAEQIV KIQACIKESV MCYDFHAKIT STQVSKQTNL PNPLNILVT YTLGDSEISQ KIQGVLRVSQ DDPPQFSIKD NSRTGIAIAE GTQNVLQSIN ILFLTEPGER IMREDYGCGL N DYLFANIS DELMTDIQTH IEERVLRYEP RAEITSIQVN QRTNLPSTLH VQVTYALRGS DINQQIEGVL EVNEGRVQVS L

UniProtKB: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17

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Macromolecule #6: Photorhabdus luminescens subsp. laumondii TTO1 complete genome se...

MacromoleculeName: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
type: protein_or_peptide / ID: 6 / Details: Pvc11 - baseplate protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 101.454625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGQAELDNKL SAIVPDTVFK LDERSTLDIL NWLKAYAEKI PFDQDKNQFW DSFYFIQENT PEELEDIYQH ANKADGLLPP HQAFVFAFL KLLETSNRLL NTFPARHRDL YYRELLGLSP RKAQADSVAL GITLNTDNAE YLIPKGTLFD AGQDSVGNPL Q YTSETDLL ...String:
MGQAELDNKL SAIVPDTVFK LDERSTLDIL NWLKAYAEKI PFDQDKNQFW DSFYFIQENT PEELEDIYQH ANKADGLLPP HQAFVFAFL KLLETSNRLL NTFPARHRDL YYRELLGLSP RKAQADSVAL GITLNTDNAE YLIPKGTLFD AGQDSVGNPL Q YTSETDLL ANQGELTDLR WYRKDKDSWQ STIPLSLSDN IALPENGIQL FSPTANDVAV LSGYLIKSSL FSMPEGERHI TL TLENDWE GQAEHLTAKI STGDHWLSLS VNPNRTNKNT IELELSSTDD PISPPDNLDG MTFDIPVLKL GTTQKPMLPK ITG IEININ GNRSVRYASD GGIEQTDTTS SPFGQSPSLG SGFNLVAPEW YGTENATLTM TPQWVGLPTS SFSTWYDKYN PKPA SNGVF KVQGYLVTSQ KRDVLNDAKS QPLFDGTGAP QGQSLTFILP AMHYPLTDSP SPNEWPASVR IELAEQDFMH AQYWQ NPTD KNVPYTPQIS ALQIQFSTTA KPEQFTVYPL TPFGWANTNE DPPSFTNDAL YLGFTNVLPG QTLSLYWQLE GFKALN LSW FYLNQSNTWG SLDQLVDDQT HNLFDQGTWR TLLPQDASNQ ATLMPTGRYW LKAEITHQAE SQDYPKIKGI LYNAATA TL INAELVETDH FINGLPADSI TQPVNALVAI DSINQPWVSW NGRPEETEQA FLTRVSARLS HRNRVLSWDN IVTLLKEQ F VSLFDVKYPS ASELTKIPAQ KEQQLIAIPD SRYKDNDDAL RPILNPARLA EMVDWISQLS SPWTTLKINN PTYVDVLIS YQLVFVTGIN PDYGRHQLQQ ELSRKYMPWA EDSAIGVTTG NRIDYYPLLA TIQQSPLVER VTNLTLKKSS QTAGAVGDSV EAADNEVLI LVWSENSSTN KGADSE

UniProtKB: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17

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Macromolecule #7: Baseplate protein J-like domain-containing protein

MacromoleculeName: Baseplate protein J-like domain-containing protein / type: protein_or_peptide / ID: 7 / Details: Pvc12 - baseplate protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 110.905555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNQDALFPI VKDDIAFETL LTQAKTVIEQ QSGQLWSNTE ENDPGITLLE ACCYGASDLA YRHSLPLRDL LTPEKQEQTL GDGIFPQEF GPQQMLTCGP ITAEDYRRAL LDLHSSDTDN ETSEDYFFFN DVRLICEPES ERYKYWYNKE SREYSFIQEQ E QEQEQLQL ...String:
MNNQDALFPI VKDDIAFETL LTQAKTVIEQ QSGQLWSNTE ENDPGITLLE ACCYGASDLA YRHSLPLRDL LTPEKQEQTL GDGIFPQEF GPQQMLTCGP ITAEDYRRAL LDLHSSDTDN ETSEDYFFFN DVRLICEPES ERYKYWYNKE SREYSFIQEQ E QEQEQLQL TLRGNYWLYL LPNRETEDDK TLTQKRLNDF LKDNRNLGES VSKIIWLQPV DFLLQLDIEL DDDVSDLADI FA QVYMTTE QMVLTSPLRY STQAMIEQGY SNEEIFEGPY LHHGWIPELS AAKDYTKPTE LKLSHLANRL LAIPGVQNIT RLA LGKHDE NISPLADDSW SWTIAQGYYP RLWGNDPLDL ISSSASPLTI TAKGGVKITV SKQDIENKII AEPLIETQPE LLNW GKHRK VLDYYPVSNK LPACYGLQTY AETQQQVHLH QFMLPFEQML ANGCAELALL PKLLAFKQRG NTVYGTQWPF KANTV GQQV HQEIMPDLIK QLNNDSQINS DDGIHSQNYT KELSILNYLL EYFGTHRAAR PLTLDSLDFL STQRGYLAQQ PELTYQ RNN IRIDKVSALQ KRIAARLGLG GKCFEETSKL DELPFYLIEH RQLLPVKPDT KFDKEQKPDK LKIKSVPNSK NQQLIIT QN GTTGQLLYGQ VINLIIKEKE NQDIRVKFIL RGQMITDITG ESFILDTRNS TALARSLIDV QNAYNDGNLY WCNSPVWM E DMDYQLVYAS EIYQTGTENE RWITSSPQSP FPAMIEENDE ITLKYVITPS GPKKSDHELK ANVIKFDRIQ GKILIKLTQ DSQDNFPLAA DAWRYRWYFS SEKYALADRF SFVVSMVINS QLVKNDDVDP YKLESWAKTE ILAEFPAHLS MIIHWLSPED FKDFVSTYQ RWQNNGAPLG DEAYHVLETL TLGRLPSAAT GIGNMRIATA QQRIGVVGES GKEWNTEVII SNQLVYVPYT G ENLNKR

UniProtKB: Baseplate protein J-like domain-containing protein

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Macromolecule #8: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 8 / Details: Pvc3 - sheath protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 51.330875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPTIPTYPGV YIEEDASLNL SVNQGNTAIP VFIGLFSPKN TNLKSQVTRV NSWLDFTNLF NAGCIAPITI KSTKRASMPA PTLLENVKG DTAVVATPGI SVDADNKDPT YTYKVIVNYT TSSDALKLYF QNGGGPCYIL PQLDRLTQGF LDSIPELIKQ A LEITLIVC ...String:
MPTIPTYPGV YIEEDASLNL SVNQGNTAIP VFIGLFSPKN TNLKSQVTRV NSWLDFTNLF NAGCIAPITI KSTKRASMPA PTLLENVKG DTAVVATPGI SVDADNKDPT YTYKVIVNYT TSSDALKLYF QNGGGPCYIL PQLDRLTQGF LDSIPELIKQ A LEITLIVC PEWDSGYQSK IYNSLTSSLL NAGYFLIADN QDKNTALITE VASQTATYYP AVKVSQLIQA EDSQIAVSGY ED AKTKSDE VKNLAQLKEK NPTVYQQAVQ KIQAIQDEIA ANGNIIPVSA VMAGIYCATD ASRGVWKAPA NIVLSGISDV AER LTDDEQ GEMNSKGINA IRYFSHKGFV VWGARTLQND DNWRYIPVRR LFNAAERDIK QAMQSVVFEP NSQPTWERVK SAID NYLYS LWQQGALAGN KPQEAYFVQI GKDVTMSDDD IKQGKMIVKV GMAAVRPAEF IILQFSQQVA Q

UniProtKB: Phage tail sheath family protein

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Macromolecule #9: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 9 / Details: Pvc4 - sheath initiator protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 44.076059 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEITQPSVTI TENLIFPKQN DSFIGIPVFI GYTSSPVDKT AIKLHSLADF ARSFPESGLM YYSVRHFFEN GGQQAYVLSL GTEQQLSDF SSLITALQQA WLAQTIAAEN DITLIITPDV IRFDQTEISD TQRDLWLQLW QSVLNLCKSR RGIMGLLDAP D DPTLAAKC ...String:
MEITQPSVTI TENLIFPKQN DSFIGIPVFI GYTSSPVDKT AIKLHSLADF ARSFPESGLM YYSVRHFFEN GGQQAYVLSL GTEQQLSDF SSLITALQQA WLAQTIAAEN DITLIITPDV IRFDQTEISD TQRDLWLQLW QSVLNLCKSR RGIMGLLDAP D DPTLAAKC LQQFSSADRQ WGVVYWPLLK SAYQDNTQNP IVLSPTAAVA AVIQRNDNQQ GVWTAPANIA LSKVISPVRA YI EANALFN PDGTSLNLVR SFPGKGIRIW GCRTLENTHD SPWSYIQTRR LVSYIEAYMT QLGRAFVFEP NNAITWMKFK GQA HNWLRQ LWLKGGLRGT QEDQAFEVLL GVDESMREAD LRAGKMIIKI RLAVLIPAEF IELNLTFDTR TGTIPS

UniProtKB: Phage tail sheath family 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Patch CTF Estimation in cryoSPARC, fit local CTF to micrograph, including tilted, bent, deformed samples
Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio model was generated in cryoSPARC
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53537
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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