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- EMDB-9765: Cryo-EM Structure of an Extracellular Contractile Injection Syste... -

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Basic information

Entry
Database: EMDB / ID: EMD-9765
TitleCryo-EM Structure of an Extracellular Contractile Injection System, baseplate in extended state, refined in C6 symmetry
Map data
Sample
  • Complex: baseplate in extended stateTripod (photography)
    • Protein or peptide: Pvc9
    • Protein or peptide: Pvc11
    • Protein or peptide: Pvc12
    • Protein or peptide: Pvc4
    • Protein or peptide: Pvc7
    • Protein or peptide: Pvc2
    • Protein or peptide: Pvc5
    • Protein or peptide: Pvc1
    • Protein or peptide: Pvc3
Keywordsassembly / Photorhabdus asymbiotica / PVC / contractile injection system / bacteriophage-like / PROTEIN TRANSPORT
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
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
Uncharacterized protein / Uncharacterized protein / Phage baseplate assembly protein / Uncharacterized protein / Uncharacterized protein / Phage_sheath_1C domain-containing protein / Uncharacterized protein / Phage tail sheath protein / Conserved hypothetical phage tail region protein
Similarity search - Component
Biological speciesPhotorhabdus asymbiotica (bacteria) / Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJiang F / Li N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System.
Authors: Feng Jiang / Ningning Li / Xia Wang / Jiaxuan Cheng / Yaoguang Huang / Yun Yang / Jianguo Yang / Bin Cai / Yi-Ping Wang / Qi Jin / Ning Gao /
Abstract: Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of ...Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea. Here, we report the cryo-EM structure of an intact PVC from P. asymbiotica. This over 10-MDa device resembles a simplified T4 phage tail, containing a hexagonal baseplate complex with six fibers and a capped 117-nanometer sheath-tube trunk. One distinct feature of the PVC is the presence of three variants for both tube and sheath proteins, indicating a functional specialization of them during evolution. The terminal hexameric cap docks onto the topmost layer of the inner tube and locks the outer sheath in pre-contraction state with six stretching arms. Our results on the PVC provide a framework for understanding the general mechanism of widespread CISs and pave the way for using them as delivery tools in biological or therapeutic applications.
History
DepositionDec 25, 2018-
Header (metadata) releaseApr 10, 2019-
Map releaseApr 10, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j0n
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6j0n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9765.png

Downloads & links

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Map

FileDownload / File: emd_9765.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.121 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.51128185 - 0.80977404
Average (Standard dev.)0.0033832553 (±0.032561515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 403.56003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1211.1211.121
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z403.560403.560403.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.5110.8100.003

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Supplemental data

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Sample components

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Entire : baseplate in extended state

EntireName: baseplate in extended stateTripod (photography)
Components
  • Complex: baseplate in extended stateTripod (photography)
    • Protein or peptide: Pvc9
    • Protein or peptide: Pvc11
    • Protein or peptide: Pvc12
    • Protein or peptide: Pvc4
    • Protein or peptide: Pvc7
    • Protein or peptide: Pvc2
    • Protein or peptide: Pvc5
    • Protein or peptide: Pvc1
    • Protein or peptide: Pvc3

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Supramolecule #1: baseplate in extended state

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

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Macromolecule #1: Pvc9

MacromoleculeName: Pvc9 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 15.990021 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MENQILTQLY GRGWAFPPVF SLEKGVEMAE GAEDVRQSLQ ILFSTEPGER LMRENYGCGL NDFMFENIRN ELIAEIESHI HDNVLRYEP RADMTDIQVR QSPGMGNTLQ VQVMYRLRGS DINQQIQGVL ALSEGRVTEV V

UniProtKB: Phage baseplate assembly protein

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Macromolecule #2: Pvc11

MacromoleculeName: Pvc11 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 82.807523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELNELTNKL SNLVPMTDFK LDNRASLQLL KYIEAYTKII PFNSGDKYWN DFFFMSGNTP EKLAKLYQKE IEPNGELLPQ QAFLLAVLR LLETPISLLN VLPAAHRELY YRELLGLSSH AAQPDQVALS MELNSTVMEQ LLPEGTLFEA GQDEQGNALQ Y ALDASLLA ...String:
MELNELTNKL SNLVPMTDFK LDNRASLQLL KYIEAYTKII PFNSGDKYWN DFFFMSGNTP EKLAKLYQKE IEPNGELLPQ QAFLLAVLR LLETPISLLN VLPAAHRELY YRELLGLSSH AAQPDQVALS MELNSTVMEQ LLPEGTLFEA GQDEQGNALQ Y ALDASLLA NRGYISDLRW LRNDGEKQWV TSAPWDLQAQ VSLPSDGIRL FGKTNSDQQV FGGVLITSSL LAMEAGIRKI IV TFEQEMN TQELVAQVSS GNQWLTLTSE VNKKEVTLTL SDKEPAISAP EDLDNLFFTQ PVLRLQGKDS QALPEVTGIS VSE KDDTKD TSFEMYHLTP FGYSSDIEPL EENPALYLGF TDVKPGQTLA LYWKLKSPQQ PTVSWYYLDQ HNQWAELDSW VSDG TQNLY QDGTWHVELP VDASNQAEQM PVGRYWLRAV VEVPAHEGAL GKAPWLYGLI YNAMTATLVN VDSISDSHFL TPLPA SSIQ RPVEPIIVLA SVNQPWASWG GRIPESYSAF FERIAQNLSH RNRSLTWGNM VTLLKERYVS IFDVKYPGND ELTRVP ALE QQQLTVIPAN RYNDSDDSLR PVLNPARLQE MADWLQQKDS PWASIEVRNP EYLDVKIHYE VIFKPDVNED FGYRQLQ QQ LCEVYMPWSI DEQRPVVLNN SINYFQLLAT IQQQPLVERV TRLTLHRADS SDESDGTASV EAKDNEVLIL VWEEDDNL Q YRGNDYE

UniProtKB: Uncharacterized protein

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Macromolecule #3: Pvc12

MacromoleculeName: Pvc12 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 107.761789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNQDALFHS VKDDIHFDTL LEQAHQVIEK QAEKLWSDTA EHDPGITFLQ GISYGVSDLA YRHTLPLKDL LTPAPDEQQQ EGIFPAEFG PHNTLTCGPV TADDYRKALL DLHSSDSLDG TQQDEGDFLF RSVQLVREPE KQRYTYWYDA TKREYSFVNS E GAKEFTLR ...String:
MSNQDALFHS VKDDIHFDTL LEQAHQVIEK QAEKLWSDTA EHDPGITFLQ GISYGVSDLA YRHTLPLKDL LTPAPDEQQQ EGIFPAEFG PHNTLTCGPV TADDYRKALL DLHSSDSLDG TQQDEGDFLF RSVQLVREPE KQRYTYWYDA TKREYSFVNS E GAKEFTLR GNYWLYLEPT RWTQGNIAAA TRQLTEFLTK NRNIGESVSN IIWLQPVDLP LLLDVELDDD VGAQDVPGIF AA VYSTAEQ YLMPGAQRYR TEVLQNAGMS NDQIFEGPLL EHGWIPELPA ARDYTQRLTL NLSRLVNSLL EIEGIKHVNR LRL DDSFDK TAIEPVKGDT WSWSIKEGYY PRLWGEDPLN QLAQQNGPLR VIAKGGISVS VSKEQIQASL PSQSLIQNEP VILA YGQHR DVGSYYPVSD TLPPCYGLQH SLSESEHLLP LHQFMLPFEQ LLACGCQQIA MLPRLLAFQR EGYEVWGDQW PFKSG SVND DAHQDYAPAL KDLLGQIALD SDHELDIINY LLGYFGTQRA PRTFTTQLDD FRAVQQGYLA QQPTLTYHRS NIRIDQ VSS LQKRIAARMG LGGELFKPQP DLSQLPFYLI EHRALLPVKP NSQFDKEQKP ASVTEEGGSQ TGQHYVVIEQ KGIDGKL TQ GQVINLILYE GEQGETQFTI RGQMVFKTEG DKFWLDVNNS AQLEYNLARV MTAAKASKLF WQNSPVWMED MGYRLAYA S DQSSLPVNQR RLTRTVQTPF PPMVVVGSEI TLLKQVGIVN LKKAESEKLY AKVVSFDRIE GTLIIERLGN STLAFPTSE EAWRYSWYFS GEKYERTDRF SFVISVVVNS DLIKLPGVDP YKLEEWVKET ILTEFPAHIS MIIHWMDREA FLNFANTYQR WQNNGTPLG DAAYSILESL TLGKLPSALK GVGTMRIATS SQREEVVGSN GDQWNTDGIT QNELFYVPKE S

UniProtKB: Uncharacterized protein

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Macromolecule #4: Pvc4

MacromoleculeName: Pvc4 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 45.866652 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MERLQPGVTL TESIITMGQQ EIPSAVPVFI GYTVRYPEQS EASVRIDSLA EYTSLFGDDH VMMFAVRHYF DNGGQQAFVL PLKDNMPSV EMTTAEAENL IAALRSATVS EAIGGHSQIT LILVPDMARL NDSDIDDSST QVSLWSQGWE ALLQLSQVRP N LFVLLDAP ...String:
MERLQPGVTL TESIITMGQQ EIPSAVPVFI GYTVRYPEQS EASVRIDSLA EYTSLFGDDH VMMFAVRHYF DNGGQQAFVL PLKDNMPSV EMTTAEAENL IAALRSATVS EAIGGHSQIT LILVPDMARL NDSDIDDSST QVSLWSQGWE ALLQLSQVRP N LFVLLDAP DNVEQAQKCM TTLSSDYRQW GAAYWPRLET TYQKEISGKD NESQGIFQGT VLSPTAAVAA VIQRTDNDAG VW KAPANIA LSQVIRPVKS YLQGSVLFNS SGTSLNVIRS FPGKGIRVWG CRTLENTDNT QWRYLQTRRL VSYVTAHLTQ LAR MYVFEP NNELTWMKLK GQSYNWLRQL WLQGGLYGSQ EDEAFNILLG VNETMTEDDV RAGKMIMKVE LAVLFPAEFI EISL VFNTQ TEALS

UniProtKB: Phage_sheath_1C domain-containing protein

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Macromolecule #5: Pvc7

MacromoleculeName: Pvc7 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 25.336664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLIERGLAK LTINAYKDRE GKIRAGTLQA MYNPDSLQLD YQTDYQQSQA INSEKQSSIY VQAKPAGLSL ELIFDATMPG NKTPIEEQL MQLKQLCSVD ATSNETRFLQ VKWGKMRWES RGYFAGRAKS LSVNYTLFDR DATPLRVRVI LALVADESLV L QETEQNLQ ...String:
MSLIERGLAK LTINAYKDRE GKIRAGTLQA MYNPDSLQLD YQTDYQQSQA INSEKQSSIY VQAKPAGLSL ELIFDATMPG NKTPIEEQL MQLKQLCSVD ATSNETRFLQ VKWGKMRWES RGYFAGRAKS LSVNYTLFDR DATPLRVRVI LALVADESLV L QETEQNLQ SPAKIALRIQ DGVSLALMAA STASTLSGGV DYLTLAWQNG LDNLNGFVPG EILQATRGDE S

UniProtKB: Uncharacterized protein

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Macromolecule #6: Pvc2

MacromoleculeName: Pvc2 / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 39.374281 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTVTSYPGV YIEELNSLAL SVSNSATAVP VFAVDEQNQY ISEDNAIRIN SWMDYLNLIG NFNNEDKLDV SVRAYFANGG GYCYLVKTT SLEKIIPTLD DVTLLVAAGE DIKTTVDVLC QPGKGLFAVF DGPETELTIN GAEEAKQAYT ATPFAAVYYP W LKADWANI ...String:
MTTVTSYPGV YIEELNSLAL SVSNSATAVP VFAVDEQNQY ISEDNAIRIN SWMDYLNLIG NFNNEDKLDV SVRAYFANGG GYCYLVKTT SLEKIIPTLD DVTLLVAAGE DIKTTVDVLC QPGKGLFAVF DGPETELTIN GAEEAKQAYT ATPFAAVYYP W LKADWANI DIPPSAVMAG VYASVDLSRG VWKAPANVAL KGGLEPKFLV TDELQGEYNT GRAINMIRNF SNTGTTVWGA RT LEDKDNW RYVPVRRLFN SVERDIKRAM SFAMFEPNNQ PTWERVRAAI SNYLYSLWQQ GGLAGSKEED AYFVQIGKGI TMT QEQIDA GQMIVKVGLA AVRPAEFIIL QFTQDVEQR

UniProtKB: Phage tail sheath protein

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Macromolecule #7: Pvc5

MacromoleculeName: Pvc5 / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 17.506895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNDYYTPVVS HRFMASFIFN RIPDPLDIRF QRISGLSREL QVTQYSEGGE NARNNYLAEK IQHGTLTLER GVMTVSPLTW MFDRVLSGE KIAYADVVVM LLNENSLPLS SWTLSNALPV RWQTSDFDAN SNAILVNTLE LRYQDMRWLG VKI

UniProtKB: Uncharacterized protein

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Macromolecule #8: Pvc1

MacromoleculeName: Pvc1 / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 16.532557 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTSTSQIAV EYPIPVYRFI VSVGDEKIPF NSVSGLDISY DTIEYRDGVG NWFKMPGQSQ STNITLRKGV FPGKTELFDW INSIQLNQV EKKDITISLT NDAGTELLMT WNVSNAFPTS LTSPSFDATS NDIAVQEITL MADRVIMQAV

UniProtKB: Conserved hypothetical phage tail region protein

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Macromolecule #9: Pvc3

MacromoleculeName: Pvc3 / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 48.794949 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSAILKAPGV YIEEDASLAL SVSNSATAVP VFIGKFTPTV VDSIQVCTRI SNWLEFTSSF SLAPTVEIVV QSNTESESES ETYHYIETI NLSPAVEALR LYFQNGGGAC YIYPLNDAED ELVLAAIPEV IEQKGDITLL VCPELDLDYK TKIYGAVSSL L NDNKVGYF ...String:
MSAILKAPGV YIEEDASLAL SVSNSATAVP VFIGKFTPTV VDSIQVCTRI SNWLEFTSSF SLAPTVEIVV QSNTESESES ETYHYIETI NLSPAVEALR LYFQNGGGAC YIYPLNDAED ELVLAAIPEV IEQKGDITLL VCPELDLDYK TKIYGAVSSL L NDNKVGYF LIADSNDGES VSGVWNSAKA AAYYPQLETN LKFSTLPGDK DIRISGYQDD DETHKPKNLD ELRTINEALA QD IDARLLE EKQRAVIIPP SAAIAGIYCQ TDNRRGVWKA PANVALTGIG SLLDKVDDER QGEMNDKGIN VIRSFTDRGF MVW GARTCV DAANISWRYI PVRRLFNSVE RDIRQALRAV LFETNSQPTW VRAKAAVDQY LYTLWQKNAL MGARPEEAYF VQIG QDITM SEADIKQGKM IMTVGLAAVR PAEFIILQFT QDVVQ

UniProtKB: Uncharacterized 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 / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 46.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63000

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