Pvc16, N-terminal / Pvc16 N-terminal domain / 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 ...Pvc16, N-terminal / Pvc16 N-terminal domain / 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 類似検索 - ドメイン・相同性
Baseplate_J domain-containing protein / Baseplate_J domain-containing protein / Putative tail lysozyme / LysM domain-containing protein / Phospholipid/glycerol acyltransferase / Phage tail protein / Putative phage tail sheath protein FI / Uncharacterized protein / Uncharacterized protein 類似検索 - 構成要素
ジャーナル: Nat Microbiol / 年: 2022 タイトル: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. 著者: Jingwei Xu / Charles F Ericson / Yun-Wei Lien / Florentine U N Rutaganira / Fabian Eisenstein / Miki Feldmüller / Nicole King / Martin Pilhofer / 要旨: 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.
ダウンロード / ファイル: emd_11746.map.gz / 形式: CCP4 / 大きさ: 1.9 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
ボクセルのサイズ
X=Y=Z: 2.2 Å
密度
表面レベル
登録者による: 0.02 / ムービー #1: 0.02
最小 - 最大
-0.10040828 - 0.19695058
平均 (標準偏差)
0.00013043448 (±0.0028570362)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
800
800
800
Spacing
800
800
800
セル
A=B=C: 1760.0 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.2
2.2
2.2
M x/y/z
800
800
800
origin x/y/z
0.000
0.000
0.000
length x/y/z
1760.000
1760.000
1760.000
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
800
800
800
D min/max/mean
-0.100
0.197
0.000
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添付データ
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試料の構成要素
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全体 : The whole extracellular contractile injection system in marine ba...
全体
名称: The whole extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 3-fold symmetry.
要素
複合体: The whole extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 3-fold symmetry.
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超分子 #1: The whole extracellular contractile injection system in marine ba...
超分子
名称: The whole extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 3-fold symmetry. タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#9
由来(天然)
生物種: Algoriphagus machipongonensis (バクテリア)
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実験情報
-
構造解析
手法
クライオ電子顕微鏡法
解析
単粒子再構成法
試料の集合状態
particle
-
試料調製
緩衝液
pH: 8
凍結
凍結剤: ETHANE-PROPANE / 装置: FEI VITROBOT MARK IV
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電子顕微鏡法
顕微鏡
FEI TITAN KRIOS
撮影
フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 60.0 e/Å2
電子線
加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系
照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD
実験機器
モデル: Titan Krios / 画像提供: FEI Company
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画像解析
初期モデル
モデルのタイプ: NONE 詳細: The initial model is generated based on the orientation determined from responding baseplate complex.
最終 再構成
想定した対称性 - 点群: C3 (3回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF 詳細: the resolution of reconstruction reaches the Nyquist frequency of data at binning=2. However, the reconstruction map is good enough to assemble all structural models together to generate the ...詳細: the resolution of reconstruction reaches the Nyquist frequency of data at binning=2. However, the reconstruction map is good enough to assemble all structural models together to generate the complete atomic model. In addition, it will cost lots of calculation resources if pursuing at the binning=1 due to huge boxsize of particles. 使用した粒子像数: 52837