- EMDB-2438: Mechanism of Membranous Tunnelling Nanotube Formation in Viral Ge... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-2438
タイトル
Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery
マップデータ
Contour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. The recommended contour level for the visualization of the internal vesicle is about 0.35 sigma
ジャーナル: Nature / 年: 2004 タイトル: Membrane structure and interactions with protein and DNA in bacteriophage PRD1. 著者: Joseph J B Cockburn / Nicola G A Abrescia / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / James M Benevides / George J Thomas / Jaana K H Bamford / Dennis H Bamford / David I Stuart / 要旨: Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated ...Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated proteins present considerable difficulties for structural analysis. Although enveloped viruses have been imaged at about 9 A resolution by cryo-electron microscopy and image reconstruction, no detailed crystallographic structure of a membrane system has been described. The structure of the bacteriophage PRD1 particle, determined by X-ray crystallography at about 4 A resolution, allows the first detailed analysis of a membrane-containing virus. The architecture of the viral capsid and its implications for virus assembly are presented in the accompanying paper. Here we show that the electron density also reveals the icosahedral lipid bilayer, beneath the protein capsid, enveloping the viral DNA. The viral membrane contains about 26,000 lipid molecules asymmetrically distributed between the membrane leaflets. The inner leaflet is composed predominantly of zwitterionic phosphatidylethanolamine molecules, facilitating a very close interaction with the viral DNA, which we estimate to be packaged to a pressure of about 45 atm, factors that are likely to be important during membrane-mediated DNA translocation into the host cell. In contrast, the outer leaflet is enriched in phosphatidylglycerol and cardiolipin, which show a marked lateral segregation within the icosahedral asymmetric unit. In addition, the lipid headgroups show a surprising degree of order.
ダウンロード / ファイル: emd_2438.map.gz / 形式: CCP4 / 大きさ: 3.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Contour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. The recommended contour level for the visualization of the internal vesicle is about 0.35 sigma
ボクセルのサイズ
X=Y=Z: 8.8 Å
密度
表面レベル
登録者による: 1.5 / ムービー #1: 0.7
最小 - 最大
-2.83609939 - 3.94621778
平均 (標準偏差)
-0.19220899 (±0.84541529)
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
96
96
96
Spacing
96
96
96
セル
A=B=C: 844.80005 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
8.8
8.8
8.8
M x/y/z
96
96
96
origin x/y/z
0.000
0.000
0.000
length x/y/z
844.800
844.800
844.800
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
-40
NX/NY/NZ
55
55
81
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
96
96
96
D min/max/mean
-2.836
3.946
-0.192
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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 : Lipid-containing bacteriophage PRD1
全体
名称: Lipid-containing bacteriophage PRD1
要素
試料: Lipid-containing bacteriophage PRD1
ウイルス: Enterobacteria phage PRD1 (ファージ)
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超分子 #1000: Lipid-containing bacteriophage PRD1
超分子
名称: Lipid-containing bacteriophage PRD1 / タイプ: sample / ID: 1000 詳細: Please keep in mind that these are PRD1 particles with a protruding tube. Therefore the icosahedral symmetry is broken and never applied during data processing and averaging 集合状態: A pseudo T=25 assembly / Number unique components: 1
分子量
理論値: 70 MDa
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超分子 #1: Enterobacteria phage PRD1
超分子
名称: Enterobacteria phage PRD1 / タイプ: virus / ID: 1 / Name.synonym: bacteriophage PRD1 詳細: Infects both Escherichia coli and Salmonella enterica NCBI-ID: 10658 / 生物種: Enterobacteria phage PRD1 / ウイルスタイプ: VIRION / ウイルス・単離状態: SPECIES / ウイルス・エンベロープ: No / ウイルス・中空状態: No / Syn species name: bacteriophage PRD1