- EMDB-11744: Focused refined cryo-EM structure of an extracellular contractile... -
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Basic information
Entry
Database: EMDB / ID: EMD-11744
Title
Focused refined cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the baseplate complex in extended state applied 6-fold symmetry
Map data
Sample
Complex: The focused refined baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 6-fold symmetry.
Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / Baseplate protein J-like / Baseplate J-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : ...Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / Baseplate protein J-like / Baseplate J-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / LysM domain profile. / LysM domain Similarity search - Domain/homology
Uncharacterized protein / Baseplate protein J-like domain-containing protein / Putative tail lysozyme / LysM domain-containing protein / Phospholipid/glycerol acyltransferase / Phage tail protein / Putative phage tail sheath protein FI Similarity search - Component
Biological species
Algoriphagus machipongonensis (bacteria)
Method
single particle reconstruction / cryo EM / Resolution: 2.9 Å
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
Deposition
Sep 17, 2020
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Header (metadata) release
Feb 16, 2022
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Map release
Feb 16, 2022
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Update
Mar 16, 2022
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Current status
Mar 16, 2022
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_11744.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel size
X=Y=Z: 1.1 Å
Density
Contour Level
By AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum
-0.06659989 - 0.13430272
Average (Standard dev.)
0.0008114426 (±0.0054758824)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
400
400
400
Spacing
400
400
400
Cell
A=B=C: 440.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.1
1.1
1.1
M x/y/z
400
400
400
origin x/y/z
0.000
0.000
0.000
length x/y/z
440.000
440.000
440.000
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
400
400
400
D min/max/mean
-0.067
0.134
0.001
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Supplemental data
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Sample components
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Entire : The focused refined baseplate complex of an extracellular contrac...
Entire
Name: The focused refined baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 6-fold symmetry.
Components
Complex: The focused refined baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 6-fold symmetry.
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Supramolecule #1: The focused refined baseplate complex of an extracellular contrac...
Supramolecule
Name: The focused refined 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: #1-#7
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