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Yorodumi- EMDB-11743: Cryo-EM structure of an extracellular contractile injection syste... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11743 | ||||||||||||
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Title | Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the baseplate complex in extended state applied 6-fold symmetry. | ||||||||||||
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Sample |
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Keywords | extracellular contractile injection system / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Algoriphagus machipongonensis (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
Authors | Xu J / Ericson C | ||||||||||||
Funding support | Switzerland, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11743.map.gz | 38.7 MB | EMDB map data format | |
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Header (meta data) | emd-11743-v30.xml emd-11743.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_11743.png | 77.7 KB | ||
Filedesc metadata | emd-11743.cif.gz | 7.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11743 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11743 | HTTPS FTP |
-Validation report
Summary document | emd_11743_validation.pdf.gz | 510.5 KB | Display | EMDB validaton report |
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Full document | emd_11743_full_validation.pdf.gz | 510.1 KB | Display | |
Data in XML | emd_11743_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_11743_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11743 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11743 | HTTPS FTP |
-Related structure data
Related structure data | 7aebMC 7adzC 7ae0C 7aefC 7aekC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11743.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : The baseplate complex of an extracellular contractile injection s...
Entire | Name: The baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 6-fold symmetry. |
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Components |
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-Supramolecule #1: The baseplate complex of an extracellular contractile injection s...
Supramolecule | Name: The baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 6-fold symmetry. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
-Macromolecule #1: baseplate protein (Algo12)
Macromolecule | Name: baseplate protein (Algo12) / type: protein_or_peptide / ID: 1 Details: the residues (552-end) could not be built up due to the poor map density. Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
Molecular weight | Theoretical: 107.770953 KDa |
Sequence | String: 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 |
-Macromolecule #2: Baseplate_J domain-containing protein
Macromolecule | Name: Baseplate_J domain-containing protein / type: protein_or_peptide / ID: 2 Details: The C terminal part (residues 916-1012aa) is built up by poly-alanine chain due to the poor map density. Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
Molecular weight | Theoretical: 119.37932 KDa |
Sequence | String: 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 |
-Macromolecule #3: LysM domain-containing protein
Macromolecule | Name: LysM domain-containing protein / type: protein_or_peptide / ID: 3 Details: The residue S169 is not found in relative map, which might be cleaved in the structure. Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
Molecular weight | Theoretical: 26.571104 KDa |
Sequence | String: 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 |
-Macromolecule #4: Putative tail lysozyme
Macromolecule | Name: Putative tail lysozyme / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
Molecular weight | Theoretical: 15.762021 KDa |
Sequence | String: MMEKSKDFLG TGWGFPPEFE TSIGQVKTTS GVEDIQKSLE ILFSTKIGER IMQPTYGCNL DELLFSPINR TLKTYVIELI KNAILYHEP RIDPEKIDIT QGNEIEGELL IHLQYIVRAT NSRKNMVYPF YLEEGTNI UniProtKB: Putative tail lysozyme |
-Macromolecule #5: Phospholipid/glycerol acyltransferase
Macromolecule | Name: Phospholipid/glycerol acyltransferase / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
Molecular weight | Theoretical: 17.063238 KDa |
Sequence | String: MATYYPPSSF HFLVEFTGID AKNNDHEFQS VSGLSVDIDT EEFAEGGENR FKHKFPVKTK YPNLVLKRGV LVDSKVISWC RDAIEDFEF KPIDLTVKLL NEEHQPLMTW NVVHAYPVKW SVEDFNAQES KMAIESVELS YNYFKTIV UniProtKB: Phospholipid/glycerol acyltransferase |
-Macromolecule #6: Putative phage tail sheath protein FI
Macromolecule | Name: Putative phage tail sheath protein FI / type: protein_or_peptide / ID: 6 Details: the residues 288-320aa could not be built up in the model, with residues 430-446aa assigned with poly-alanine chain. Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
Molecular weight | Theoretical: 76.319039 KDa |
Sequence | String: 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 |
-Macromolecule #7: Phage tail protein
Macromolecule | Name: Phage tail protein / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
Molecular weight | Theoretical: 16.375458 KDa |
Sequence | String: MSYPLSKFHF SVEWGGTKIG FTEVSGLDLE TEIIEYRHGA SPEYSKIKMP GMQKFSNITL KRGTFKSDNE YFQWYNTINL NKVERRDLT ISLLNEEHEP VVTWKVKNAW PLKVQSTDLK GDGNEVAIES MELAHEGLVI QNE UniProtKB: Phage tail protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82969 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7aeb: |