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- EMDB-11747: Cryo-EM structure of an extracellular contractile injection syste... -

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Basic information

Entry
Database: EMDB / ID: EMD-11747
TitleCryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the contracted sheath shell.
Map data
Sample
  • Complex: The contracted sheath shell of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis.
    • Protein or peptide: Putative phage tail sheath protein FI
Keywordsextracellular contractile injection system / STRUCTURAL PROTEIN
Function / homology: / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Putative phage tail sheath protein FI
Function and homology information
Biological speciesAlgoriphagus machipongonensis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.5 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 16, 2022-
Map releaseFeb 16, 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: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7aek
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7aek
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11747.png

Downloads & links

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Map

FileDownload / File: emd_11747.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. 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: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.19583882 - 0.29862234
Average (Standard dev.)0.0012833801 (±0.012837992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z528.000528.000528.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1960.2990.001

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Supplemental data

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Sample components

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Entire : The contracted sheath shell of an extracellular contractile injec...

EntireName: The contracted sheath shell of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis.
Components
  • Complex: The contracted sheath shell of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis.
    • Protein or peptide: Putative phage tail sheath protein FI

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Supramolecule #1: The contracted sheath shell of an extracellular contractile injec...

SupramoleculeName: The contracted sheath shell of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)

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Macromolecule #1: Putative phage tail sheath protein FI

MacromoleculeName: Putative phage tail sheath protein FI / type: protein_or_peptide / ID: 1
Details: the residues 288-320aa are not built up in the model due to the poor map density, with residues 430-446aa assigned by poly-alanine chain.
Number of copies: 18 / 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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Experimental details

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Structure determination

Methodcryo EM
Processinghelical 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 18.04 Å
Applied symmetry - Helical parameters - Δ&Phi: 32.20 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92922
Startup modelType of model: EMDB MAP
EMDB ID:

11743

Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7aek:
Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the contracted sheath shell.

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