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Yorodumi- EMDB-12034: Cryo-EM structure of the contractile injection system cap complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12034 | |||||||||
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Title | Cryo-EM structure of the contractile injection system cap complex from Anabaena PCC7120 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Eisenstein F / Weiss GL / Pilhofer M | |||||||||
Citation | Journal: Nat Microbiol / Year: 2022 Title: Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria. Authors: Gregor L Weiss / Fabian Eisenstein / Ann-Katrin Kieninger / Jingwei Xu / Hannah A Minas / Milena Gerber / Miki Feldmüller / Iris Maldener / Karl Forchhammer / Martin Pilhofer / Abstract: Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 ...Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 secretion systems (T6SSs) are attached to the cytoplasmic membrane and function upon cell-cell contact. Here, we characterized a CIS in the multicellular cyanobacterium Anabaena, with features distinct from extracellular CISs and T6SSs. Cryo-electron tomography of focused ion beam-milled cells revealed that CISs were anchored in thylakoid membrane stacks, facing the cell periphery. Single particle cryo-electron microscopy showed that this unique in situ localization was mediated by extensions of tail fibre and baseplate components. On stress, cyanobacteria induced the formation of ghost cells, presenting thylakoid-anchored CISs to the environment. Functional assays suggest that these CISs may mediate ghost cell formation and/or interactions of ghost cells with other organisms. Collectively, these data provide a framework for understanding the evolutionary re-engineering of CISs and potential roles of these CISs in cyanobacterial programmed cell death. | |||||||||
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_12034.map.gz | 479.3 MB | EMDB map data format | |
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Header (meta data) | emd-12034-v30.xml emd-12034.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12034_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_12034.png | 213.5 KB | ||
Others | emd_12034_half_map_1.map.gz emd_12034_half_map_2.map.gz | 407.8 MB 407.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12034 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12034 | HTTPS FTP |
-Validation report
Summary document | emd_12034_validation.pdf.gz | 530.6 KB | Display | EMDB validaton report |
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Full document | emd_12034_full_validation.pdf.gz | 530.2 KB | Display | |
Data in XML | emd_12034_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | emd_12034_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12034 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12034 | HTTPS FTP |
-Related structure data
Related structure data | 7b5iMC 7b5hC 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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-Map
File | Download / File: emd_12034.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Half map: #1
File | emd_12034_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12034_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cap complex of the Anabaena PCC7120 contractile injection system
Entire | Name: Cap complex of the Anabaena PCC7120 contractile injection system |
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Components |
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-Supramolecule #1: Cap complex of the Anabaena PCC7120 contractile injection system
Supramolecule | Name: Cap complex of the Anabaena PCC7120 contractile injection system type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
-Macromolecule #1: All3327 protein
Macromolecule | Name: All3327 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 21.935064 KDa |
Sequence | String: MISDAMRLIQ VALQRYILEF EPELGLSQVV IIENIAMAEE LGGQNNQING HVVMSLVNLQ EETTLKNSPH YRLDNGRTIY QNPPVNLNL FILFSALHNQ YETSLRLLSR VVEFFQWQKE LSFTTTPGIG GISRDLRILP DLYSLTFEQL NHLWGALGGK Q VPFVLYRA ...String: MISDAMRLIQ VALQRYILEF EPELGLSQVV IIENIAMAEE LGGQNNQING HVVMSLVNLQ EETTLKNSPH YRLDNGRTIY QNPPVNLNL FILFSALHNQ YETSLRLLSR VVEFFQWQKE LSFTTTPGIG GISRDLRILP DLYSLTFEQL NHLWGALGGK Q VPFVLYRA RILSLEAPKR QAEGSTITEI YINE |
-Macromolecule #2: All3326 protein
Macromolecule | Name: All3326 protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 45.348633 KDa |
Sequence | String: MKILYKKILN LELWHDFYLG QPNTPGSLPN NYDISRTLAL VPTQECLRVL ANLRWVFRPQ LYGASLFANV NAAPSGQFPT IFPIDRVYR LTFWLVVSDR YFANFTNLSL INSRNQIYYF SNLSGNEGHA LFLTQPLSAY TTNNEYQLGQ LVTHADKTLE S LTYQGNAT ...String: MKILYKKILN LELWHDFYLG QPNTPGSLPN NYDISRTLAL VPTQECLRVL ANLRWVFRPQ LYGASLFANV NAAPSGQFPT IFPIDRVYR LTFWLVVSDR YFANFTNLSL INSRNQIYYF SNLSGNEGHA LFLTQPLSAY TTNNEYQLGQ LVTHADKTLE S LTYQGNAT NIPNPSDWDS LPASQYVSEL DHLPRQGTYR TQVITNANPD NTYNFTLVNT NEQESWAIDV IVPDTHKSGE PF STSLNFV GQTPGHYRLL ENDTQVAEFV LVDNSLPEAF ALVEVILNPE LVPSAFSLLQ ASAGQTFIQP KTYVIRFKNR ATR WRYRYE QPHGCSAANL PSYFNLIDTH TYATARPIGL RQRPDSLLND CQDRPLPAPS ITLIQPETDG SQRIARIFSD IYL |
-Macromolecule #3: All3325 protein
Macromolecule | Name: All3325 protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 53.23616 KDa |
Sequence | String: MPSTYKTPGV YIEEISKFPP SIAQVETAIP AFIGYTQIAK VGVENFHTDA DNLILRPVRI TSLLEYEQFF GKAINETTIQ VVIQDTTDS RGNLTERKAS ARITSPSPHN LYYSMQAYFA NGGGPCYIVS VGPMSNTGTI QLEALQNGLA EVAKEDEVTL L VFPESQSL ...String: MPSTYKTPGV YIEEISKFPP SIAQVETAIP AFIGYTQIAK VGVENFHTDA DNLILRPVRI TSLLEYEQFF GKAINETTIQ VVIQDTTDS RGNLTERKAS ARITSPSPHN LYYSMQAYFA NGGGPCYIVS VGPMSNTGTI QLEALQNGLA EVAKEDEVTL L VFPESQSL SDENYAALMS AALEQCANLQ DRFTVMDLKL PATRPIPANA IVGASNAFRD LSLPQDNLKY GACYAPDIET IF NYFYQED AVTIFRSVNG GAEEQDTLTM AGYNPANGGD GIQYALIESA IDQLPLILPP SPLVVGQYAR TDNTRGVWKA PAN VALSSV IKPVLKITNE QQNNLNVHPT GKSINAIRAF TGKGTLIWGA RTLAGNDNEW RYVSVRRFFN MAEESIKKGS EPFV FEPND ANTWTKVKAM IENFLTLQWR AGALAGAKPE QAFYVKIGLN ETMTALDILE GRMIVEIGMA VVRPAEFIIL KFSHK MQES |
-Macromolecule #4: All3324 protein
Macromolecule | Name: All3324 protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 16.459543 KDa |
Sequence | String: MAEYPLPKFH FQVDWGGSRL GFTEVSGLDV ETEVIEYREG NLPQYHKLKM PGMQKFSNIT MKRGTFQGDN DFYKWWNTVA LNTIERRDL TISLLNEKHE PVVVWKVNRA WPTKVQSTDL KGDGNEVAIE SIEVAHEGLT IQNG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 19000 / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |