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- PDB-7b5h: Cryo-EM structure of the contractile injection system base plate ... -

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Basic information

Entry
Database: PDB / ID: 7b5h
TitleCryo-EM structure of the contractile injection system base plate from Anabaena PCC7120
Components
  • All3314 protein
  • All3315 protein
  • All3316 protein
  • All3317 protein
  • All3318 protein
  • All3320 protein
  • All3321 protein
  • All3323 protein
  • All3324 protein
  • All3325 protein
  • Asl3322 protein
KeywordsPROTEIN TRANSPORT / contractile tail / injection system / macromolecular machine
Function / homology
Function and homology information


structural molecule activity / membrane
Similarity search - Function
Protein of unknown function DUF5908 / Family of unknown function (DUF5908) / YegP-like superfamily / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / Type VI secretion system, RhsGE-associated Vgr protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube ...Protein of unknown function DUF5908 / Family of unknown function (DUF5908) / YegP-like superfamily / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / Type VI secretion system, RhsGE-associated Vgr protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Baseplate protein J-like / Baseplate J-like protein barrel domain / 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
Similarity search - Domain/homology
All3325 protein / All3324 protein / All3323 protein / Asl3322 protein / All3321 protein / All3320 protein / All3318 protein / All3317 protein / All3316 protein / All3315 protein / All3314 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsEisenstein, F. / Weiss, G.L. / 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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
AA: All3314 protein
AB: All3314 protein
AC: All3314 protein
AD: All3315 protein
AE: All3316 protein
AF: All3316 protein
AG: All3316 protein
AH: All3317 protein
AJ: All3320 protein
AL: Asl3322 protein
AI: All3318 protein
AK: All3321 protein
AM: All3323 protein
AN: All3324 protein
AO: All3325 protein
AP: All3325 protein
AQ: All3325 protein
BA: All3314 protein
BB: All3314 protein
BC: All3314 protein
BD: All3315 protein
BE: All3316 protein
BF: All3316 protein
BG: All3316 protein
BH: All3317 protein
BI: All3318 protein
BK: All3321 protein
BM: All3323 protein
BN: All3324 protein
BO: All3325 protein
BP: All3325 protein
BQ: All3325 protein
CA: All3314 protein
CB: All3314 protein
CC: All3314 protein
CD: All3315 protein
CE: All3316 protein
CF: All3316 protein
CG: All3316 protein
CH: All3317 protein
CJ: All3320 protein
CL: Asl3322 protein
CI: All3318 protein
CK: All3321 protein
CM: All3323 protein
CN: All3324 protein
CO: All3325 protein
CP: All3325 protein
CQ: All3325 protein
DA: All3314 protein
DB: All3314 protein
DC: All3314 protein
DD: All3315 protein
DE: All3316 protein
DF: All3316 protein
DG: All3316 protein
DH: All3317 protein
DI: All3318 protein
DK: All3321 protein
DM: All3323 protein
DN: All3324 protein
DO: All3325 protein
DP: All3325 protein
DQ: All3325 protein
EA: All3314 protein
EB: All3314 protein
EC: All3314 protein
ED: All3315 protein
EE: All3316 protein
EF: All3316 protein
EG: All3316 protein
EH: All3317 protein
EJ: All3320 protein
EL: Asl3322 protein
EI: All3318 protein
EK: All3321 protein
EM: All3323 protein
EN: All3324 protein
EO: All3325 protein
EP: All3325 protein
EQ: All3325 protein
FA: All3314 protein
FB: All3314 protein
FC: All3314 protein
FD: All3315 protein
FE: All3316 protein
FF: All3316 protein
FG: All3316 protein
FH: All3317 protein
FI: All3318 protein
FK: All3321 protein
FM: All3323 protein
FN: All3324 protein
FO: All3325 protein
FP: All3325 protein
FQ: All3325 protein


Theoretical massNumber of molelcules
Total (without water)6,722,33296
Polymers6,722,33296
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, in situ structures of the full assembly have been determined by cryo-electron tomography
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area737000 Å2
ΔGint-3342 kcal/mol
Surface area1836010 Å2
MethodPISA

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Components

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Protein , 10 types, 93 molecules AAABACBABBBCCACBCCDADBDCEAEBECFAFBFCADBDCDDDEDFDAEAFAGBEBFBG...

#1: Protein
All3314 protein


Mass: 166114.344 Da / Num. of mol.: 18 / Fragment: crown protein Cis19 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRX8
#2: Protein
All3315 protein


Mass: 154377.031 Da / Num. of mol.: 6 / Fragment: baseplate protein Cis12 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRX7
#3: Protein
All3316 protein


Mass: 18335.021 Da / Num. of mol.: 18 / Fragment: tail fibre protein Cis13 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRX6
#4: Protein
All3317 protein


Mass: 139003.422 Da / Num. of mol.: 6 / Fragment: baseplate protein Cis11 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRX5
#5: Protein All3320 protein


Mass: 63636.625 Da / Num. of mol.: 3 / Fragment: spike protein Cis8 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRX2
#7: Protein
All3318 protein


Mass: 16764.764 Da / Num. of mol.: 6 / Fragment: baseplate protein Cis9 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRX4
#8: Protein
All3321 protein


Mass: 27090.568 Da / Num. of mol.: 6 / Fragment: tube adapter protein Cis7 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRX1
#9: Protein
All3323 protein


Mass: 19204.932 Da / Num. of mol.: 6 / Fragment: tube adapter protein Cis5 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRW9
#10: Protein
All3324 protein


Mass: 16459.543 Da / Num. of mol.: 6 / Fragment: tube protein Cis1 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRW8
#11: Protein
All3325 protein


Mass: 53236.160 Da / Num. of mol.: 18 / Fragment: sheath protein Cis2 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRW7

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Protein/peptide , 1 types, 3 molecules ALCLEL

#6: Protein/peptide Asl3322 protein


Mass: 5226.893 Da / Num. of mol.: 3 / Fragment: spike plug protein Cis6 / Source method: isolated from a natural source / Details: cell culture
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YRX0

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Base plate and spike complex (C3) of the Anabaena PCC7120 contractile injection system
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated defocus min: 900 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 19000
Image scansMovie frames/image: 50

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 228163
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36909 / Symmetry type: POINT

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