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- EMDB-11745: Cryo-EM structure of an extracellular contractile injection syste... -

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Basic information

Entry
Database: EMDB / ID: EMD-11745
TitleCryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the baseplate complex in extended state applied 3-fold symmetry.
Map data
Sample
  • Complex: The baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 3-fold symmetry.
    • Protein or peptide: baseplate protein (Algo12)
    • Protein or peptide: Baseplate_J domain-containing protein
    • Protein or peptide: LysM domain-containing protein
    • Protein or peptide: Putative tail lysozyme
    • Protein or peptide: Phospholipid/glycerol acyltransferase
    • Protein or peptide: Putative phage tail sheath protein FI
    • Protein or peptide: Phage tail protein
    • Protein or peptide: inner protein (Algo6)
    • Protein or peptide: Phosphoserine phosphatase SerB
Keywordsextracellular contractile injection system / STRUCTURAL PROTEIN
Function / homology
Function and homology information


acyltransferase activity / structural molecule activity
Similarity search - Function
Protein of unknown function DUF5908 / Family of unknown function (DUF5908) / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Baseplate protein J-like / Baseplate J-like protein / Type VI secretion system, RhsGE-associated Vgr protein / Conserved hypothetical protein CHP02241 ...Protein of unknown function DUF5908 / Family of unknown function (DUF5908) / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Baseplate protein J-like / Baseplate J-like protein / Type VI secretion system, RhsGE-associated Vgr protein / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Uncharacterized protein / Baseplate protein J-like domain-containing protein / Putative tail lysozyme / Phosphoserine phosphatase SerB / LysM domain-containing protein / Uncharacterized protein / Phospholipid/glycerol acyltransferase / Phage tail protein / Putative phage tail sheath protein FI
Similarity search - Component
Biological speciesAlgoriphagus machipongonensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsXu J / Ericson C
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
European Research Council (ERC) Switzerland
Swiss National Science Foundation Switzerland
Other private Switzerland
CitationJournal: Nat Microbiol / Year: 2022
Title: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis.
Authors: Jingwei Xu / Charles F Ericson / Yun-Wei Lien / Florentine U N Rutaganira / Fabian Eisenstein / Miki Feldmüller / Nicole King / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). ...Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a 'cap adaptor' located at the distal end, a 'plug' exposed to the tube lumen, and a 'cage' formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re-engineering CISs.
History
DepositionSep 17, 2020-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7aef
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7aef
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11745.png

Downloads & links

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Map

FileDownload / File: emd_11745.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.15492803 - 0.21912512
Average (Standard dev.)0.0005473138 (±0.0070736934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1550.2190.001

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Supplemental data

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Sample components

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Entire : The baseplate complex of an extracellular contractile injection s...

EntireName: The baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 3-fold symmetry.
Components
  • Complex: The baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 3-fold symmetry.
    • Protein or peptide: baseplate protein (Algo12)
    • Protein or peptide: Baseplate_J domain-containing protein
    • Protein or peptide: LysM domain-containing protein
    • Protein or peptide: Putative tail lysozyme
    • Protein or peptide: Phospholipid/glycerol acyltransferase
    • Protein or peptide: Putative phage tail sheath protein FI
    • Protein or peptide: Phage tail protein
    • Protein or peptide: inner protein (Algo6)
    • Protein or peptide: Phosphoserine phosphatase SerB

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Supramolecule #1: The baseplate complex of an extracellular contractile injection s...

SupramoleculeName: The baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 3-fold symmetry.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)

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Macromolecule #1: baseplate protein (Algo12)

MacromoleculeName: baseplate protein (Algo12) / type: protein_or_peptide / ID: 1
Details: the residues (552-end) are not built up in the model due to the poor map density.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 107.770953 KDa
SequenceString: MSTLNKHISI PKDMSSKDDL DFHFLREEGI RYIKELGSNF WTDYNTHDPG ITMLEVLCYA ISDLGNRINI PIEDLIANEE GGVKGQFYK VQEILPSAPT SELDLRKLFI DIEGIKNCWI KRERVTVFAD LKNQKLSYEK TIWEDLKENQ KAQFDLKGLY R ILVETEDA ...String:
MSTLNKHISI PKDMSSKDDL DFHFLREEGI RYIKELGSNF WTDYNTHDPG ITMLEVLCYA ISDLGNRINI PIEDLIANEE GGVKGQFYK VQEILPSAPT SELDLRKLFI DIEGIKNCWI KRERVTVFAD LKNQKLSYEK TIWEDLKENQ KAQFDLKGLY R ILVETEDA DKVLSESLEK AVFTKFHANR NLCEDLIKVE KVATEPISVC ANVEVAPEAD EELIHAQILI AIEDYLAPSP RH YSLKQMV DKGYTMDEIF EGPFLENGFI DTVELKASEL RKEVRLSDII NIIMSIDGVK IVKEITLGNC DENDGIENNQ WVI CIPENK KPKLCKKTTI NYFKGILPIN LNPVRVDNHK SKILASRLEN DLKAKDDLEP AIPQGTFADW GEYSSIQHEF PETY GISDI GLPPKLGVKR AVLARQLKGY LLFFDQILAS YFEHLSKIKS LLSLDQGPSF TYFTQAIKDI KDVEELFKDP TLLEN DEEL TKSLIGKLDD TIERRNQLMD HLIARFAENF SSYAFLMKFL YGESTDEIVL QDKQSFLREY KEISRERGEG FNFYEQ SND NLWDTLNVSG AQKRISKLVG VKDYSRRNLS DTAVEIYRYE HVDGNWVYRW RIRDENGKVL LSATTSYPTY NSAGNEM YF AILKILETPL SDLEKLLEVN FRNENEAGSF HFHKAATSNK FSFDIINPVI DSESSSDFIV AKQYTYYPDR TQAVLGAI S LLNFIKYTFT EEGIYLVEHI LLRPSPLDPE YLAMQTDAGK EYIEGNFLPF CSDDYENCKM IDPYSFRVSI VLPGFTYRF ANKDFRDYLE NLIREELPAH IVAKICWIGY RKGEEPELFQ EDVENPETPI FKENQLEIFE KAYKNYLFEL TDIHKRKGFI ASMNKYNQV LNEMTSSLTG LHTIYPTGRL YDCEDEEEEL DGKLILGKTN LGTL

UniProtKB: Uncharacterized protein

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Macromolecule #2: Baseplate_J domain-containing protein

MacromoleculeName: Baseplate_J domain-containing protein / type: protein_or_peptide / ID: 2
Details: The C-terminal part (residues 916-1012aa) is assigned with poly-alanine due to the poor map density.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 119.37932 KDa
SequenceString: MSENCNHIVT TLKRDGTGRR DLLDPKLAPE SVQLQDFELS DWLIFALNFA RKIHFFPSDL ANEPLGDWRN FFSTIVSDKT LISDIENLD DFEKLRGNIE EFLAAYDQSG KLTPHLTLFV SFLKLLETSK KRFNQLTKRH LDFYYQEILH LEKQALSPDH V FLIFELAK ...String:
MSENCNHIVT TLKRDGTGRR DLLDPKLAPE SVQLQDFELS DWLIFALNFA RKIHFFPSDL ANEPLGDWRN FFSTIVSDKT LISDIENLD DFEKLRGNIE EFLAAYDQSG KLTPHLTLFV SFLKLLETSK KRFNQLTKRH LDFYYQEILH LEKQALSPDH V FLIFELAK NVSQEKLDEG TEVDGGKDDT GKKNTYLTSF ETVLNKTKVG QLKSLYNEIS VEKEEIKELN TPISTGTFVM AP MANSFDG LGEDFPKGSE KWWPFGYTKI CNASTVLPAL PKARLGCSIS SKLLKLSEGT RDIILEFTFN KPILPNGEDY TAL NKAMSI ELTGEKGWIA GLPMTLKSDS GINSGSKKMK LSLTLDSEQP AVVPYQTELH EGSYEVDEPL LRVLFKTNEK EGYN LYRLF NENVLTDLKI TVEVSDITSV QLENDLGVLN PQKPFFPFGP RPIKGSSFIV KYPEAMEKPV TAISYQMDYL NLPEN LVNH YSAYTIGDDE PLVSDMDYFS VKSFPKSSND SDQLFSEKSG GGYESDFEFQ IENGVWESGL KKELKISLER SFLHEK YAH YFTLVAISKD TDPTIELLPN EPYAPLAENL VLGYTAISSI DFSSSSSENQ VSLIHEMPFG FQQVFTPGDT DNSLYLV PD YCHGGELYIG LENGKNLQQV TLLLQFLEGS ENPDITDIFT GNQKIKWQYL SQNQWQDFQS GEIIQNQTPR FLKSGIFQ F SIPKQANLDN TVLPPGYHWI KASMVKPFDV VSQLINIHAQ AVEAVFEDQG SSGNHLEKGL PAETISKLQE RLSWIKSIQ QPYPSTKGKA QESDEDYYRR VSERLRHKKR AITLWDYEHL ILQKFPKVYK VKCLNHTCSS SFQSPGNATL ILVPDTVQQS VFDIYQPRV SQGTLNDVAA FVNELNSFHV QAKVINPNYE EVKVDVKVKF REGLDVSFYL TKVKEDIKKF LSPWAYDQES S VEFGVTLH RSQMIHYLEQ LTYVDYITDL RLLKRQAGSS PCNPIFIETT EKEYIQPSNP KSILVSAKEH LVTPITQNCS SI SLNNEEE CQH

UniProtKB: Baseplate protein J-like domain-containing protein

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Macromolecule #3: LysM domain-containing protein

MacromoleculeName: LysM domain-containing protein / type: protein_or_peptide / ID: 3
Details: The residue S169 is not observed in the responding map density, which might be cleaved in the complex.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 26.571104 KDa
SequenceString: MSEGKLEKLR IVAYKDSKFS DEVENGEFIT LLNPEKYKFQ YRVEQNEDQA SGTSSAPIRF NKILPQTLEF DFLFDRTGVI AGYEVTEDG IINDIDHFKK VVYDYNGEKH KPNYLMITWG SLLFKGYLKE MDIEYKLFRP DGTPIRAMAT TKIGEFVEEE L RTAQENNQ ...String:
MSEGKLEKLR IVAYKDSKFS DEVENGEFIT LLNPEKYKFQ YRVEQNEDQA SGTSSAPIRF NKILPQTLEF DFLFDRTGVI AGYEVTEDG IINDIDHFKK VVYDYNGEKH KPNYLMITWG SLLFKGYLKE MDIEYKLFRP DGTPIRAMAT TKIGEFVEEE L RTAQENNQ SPDMSHYRTV KEGDTLPLMT YRIYGDSKYY LEVAKANGLT NFRRLKTGTE LIFPPLQKQK

UniProtKB: LysM domain-containing protein

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Macromolecule #4: Putative tail lysozyme

MacromoleculeName: Putative tail lysozyme / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 15.762021 KDa
SequenceString:
MMEKSKDFLG TGWGFPPEFE TSIGQVKTTS GVEDIQKSLE ILFSTKIGER IMQPTYGCNL DELLFSPINR TLKTYVIELI KNAILYHEP RIDPEKIDIT QGNEIEGELL IHLQYIVRAT NSRKNMVYPF YLEEGTNI

UniProtKB: Putative tail lysozyme

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Macromolecule #5: Phospholipid/glycerol acyltransferase

MacromoleculeName: Phospholipid/glycerol acyltransferase / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 17.063238 KDa
SequenceString:
MATYYPPSSF HFLVEFTGID AKNNDHEFQS VSGLSVDIDT EEFAEGGENR FKHKFPVKTK YPNLVLKRGV LVDSKVISWC RDAIEDFEF KPIDLTVKLL NEEHQPLMTW NVVHAYPVKW SVEDFNAQES KMAIESVELS YNYFKTIV

UniProtKB: Phospholipid/glycerol acyltransferase

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Macromolecule #6: Putative phage tail sheath protein FI

MacromoleculeName: Putative phage tail sheath protein FI / type: protein_or_peptide / ID: 6
Details: the residues 288-320 aa could not be built up due to the poor map density, with the residues 430-446 assigned poly-alanine chain.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 76.319039 KDa
SequenceString: MATYKTPGVY IEEITKFPPS VAQVETAIPA FIGYTQFART KPSVDSDDLI LKPKRISSLL DFTTYYGGAQ NEQGITVKLT DTLIEGAEN RTINVPEPTF KSPYLMFYSL QMYFANGGGP CYIVSTGVYD DWSDSETPPT INFSDLESGL AVIRKEDEPT L LLFPDATN ...String:
MATYKTPGVY IEEITKFPPS VAQVETAIPA FIGYTQFART KPSVDSDDLI LKPKRISSLL DFTTYYGGAQ NEQGITVKLT DTLIEGAEN RTINVPEPTF KSPYLMFYSL QMYFANGGGP CYIVSTGVYD DWSDSETPPT INFSDLESGL AVIRKEDEPT L LLFPDATN LPTDDEFYSL YNSALMQCND LQDRFTILDT YSDQTYNDGV EDLDPIPALR NGINLTKDYL KYGAAYYPFV QT ILNYQYS ADEIVIQHLS YNPNAIATAL DNLNAVNGPT FIDAILDDLR DLSLPDISGE ISDAVGFMYD DVDGFDIDGT FTT NSVKVA NFASLVESVL STLNELIDAK EEINKDVNSA IASSEEDNAI KTAISDALDV FNEDFEGADK IESVAKNLSD LLIK IKQAD TNTKVENVLS INALNFSAEF EKLLTYDVNT GLTASVTLDL FANIGTRLDD IIAAVSAAEP IDVNNGKLNG RLLSD IEPL DNATYNTILL EINSHKVTLP PSSSMAGAYA RVDNDRGVWK SPANIGLNYV SKPSVTVSHE EQESMNVHGT GKSVNA IRS FVGKGTLVWG ARTLAGNDNE WRYISVRRFF NMAEESIKKA TEQFVFEPND GNTWVRVRAM IENFLILQWR AGALAGA KP EHAFYVKVGL GQTMTAQDIL EGNMNVEIGL AVVRPAEFII LKFSHKMQES

UniProtKB: Putative phage tail sheath protein FI

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Macromolecule #7: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 16.375458 KDa
SequenceString:
MSYPLSKFHF SVEWGGTKIG FTEVSGLDLE TEIIEYRHGA SPEYSKIKMP GMQKFSNITL KRGTFKSDNE YFQWYNTINL NKVERRDLT ISLLNEEHEP VVTWKVKNAW PLKVQSTDLK GDGNEVAIES MELAHEGLVI QNE

UniProtKB: Phage tail protein

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Macromolecule #8: inner protein (Algo6)

MacromoleculeName: inner protein (Algo6) / type: protein_or_peptide / ID: 8
Details: the residues (19-28) attributing to the flexible loop are not built up in the model.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 5.714442 KDa
SequenceString:
MPIEIKELHI KITVDDSNNA GRGGASSGED KQQLVAQCVE QVLDVLKSQK ER

UniProtKB: Uncharacterized protein

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Macromolecule #9: Phosphoserine phosphatase SerB

MacromoleculeName: Phosphoserine phosphatase SerB / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 63.787738 KDa
SequenceString: MNNSGTIETS QSVDRVTHKI LIDGSEIPGT YQVKSIQVTK EVNRIPTARL VILDGDAAER DFKVSNSDHF VPGKEIEITV GYHSDDETI FKGVVIRQNL KIRNNQSILI VESRDMAVKM TLRRKSKYFY ELSDSDILEE LISNHGLEAD VASTENQHTE L VQYDVTDW ...String:
MNNSGTIETS QSVDRVTHKI LIDGSEIPGT YQVKSIQVTK EVNRIPTARL VILDGDAAER DFKVSNSDHF VPGKEIEITV GYHSDDETI FKGVVIRQNL KIRNNQSILI VESRDMAVKM TLRRKSKYFY ELSDSDILEE LISNHGLEAD VASTENQHTE L VQYDVTDW DFMMLRLQAN GLLCLVDDGK VSIQKPDLSS EALETVTFGA TILEFDAEMD ARNQLPKVVS QAWNMSDQEL LE KEGVDPS LETNGNISSS DLASLFDQEE EVLRHGGSKK DGSLQEWANA KWTFQQLAKT RGRIKFQGIP TVKPGVNLLL EGV GDRFNG KVFITGVNHQ ISEGNWTVDA QFGLNPEWFS ESESNIHTPP AAGLTAAISG LHVGLVTDLE DPDGEDRIKV KIPI INNEE EGVWCRQAFP DAGNERGITF RPEIEDEVIV GFINEDPNDA VVLGMLHSSA NPNPIEASND NHEKGIQTRS GIKMI FNDE KSILQIETPT GNLVTLDDDA GSITIEDQNG NKTVMDSDGI TMESAKDMNL KASGDINLEG TNVNIKANAE FKAEGS AGA EVSTSAVAVL KGSLVQIN

UniProtKB: Phosphoserine phosphatase SerB

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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: 8
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: EMDB MAP
EMDB ID:

11743

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82969
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7aef:
Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the baseplate complex in extended state applied 3-fold symmetry.

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