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- EMDB-12034: Cryo-EM structure of the contractile injection system cap complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-12034
TitleCryo-EM structure of the contractile injection system cap complex from Anabaena PCC7120
Map data
Sample
  • Complex: Cap complex of the Anabaena PCC7120 contractile injection system
    • Protein or peptide: All3327 protein
    • Protein or peptide: All3326 protein
    • Protein or peptide: All3325 protein
    • Protein or peptide: All3324 protein
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / 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
All3327 protein / All3326 protein / All3325 protein / All3324 protein
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsEisenstein F / Weiss GL / Pilhofer M
CitationJournal: 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
DepositionDec 3, 2020-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b5i
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b5i
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12034.png

Downloads & links

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Map

FileDownload / File: emd_12034.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.09187173 - 0.20301405
Average (Standard dev.)0.0004968329 (±0.009501554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z563.200563.200563.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0920.2030.000

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Supplemental data

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Half map: #1

Fileemd_12034_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12034_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cap complex of the Anabaena PCC7120 contractile injection system

EntireName: Cap complex of the Anabaena PCC7120 contractile injection system
Components
  • Complex: Cap complex of the Anabaena PCC7120 contractile injection system
    • Protein or peptide: All3327 protein
    • Protein or peptide: All3326 protein
    • Protein or peptide: All3325 protein
    • Protein or peptide: All3324 protein

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Supramolecule #1: Cap complex of the Anabaena PCC7120 contractile injection system

SupramoleculeName: Cap complex of the Anabaena PCC7120 contractile injection system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Macromolecule #1: All3327 protein

MacromoleculeName: All3327 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 21.935064 KDa
SequenceString: 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

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Macromolecule #2: All3326 protein

MacromoleculeName: All3326 protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 45.348633 KDa
SequenceString: 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

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Macromolecule #3: All3325 protein

MacromoleculeName: All3325 protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 53.23616 KDa
SequenceString: 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

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Macromolecule #4: All3324 protein

MacromoleculeName: All3324 protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 16.459543 KDa
SequenceString:
MAEYPLPKFH FQVDWGGSRL GFTEVSGLDV ETEVIEYREG NLPQYHKLKM PGMQKFSNIT MKRGTFQGDN DFYKWWNTVA LNTIERRDL TISLLNEKHE PVVVWKVNRA WPTKVQSTDL KGDGNEVAIE SIEVAHEGLT IQNG

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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: 7.5
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 281 K / 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 opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 433028
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: related structure
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 22598
FSC plot (resolution estimation)

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