ジャーナル: Cell / 年: 2006 タイトル: Cryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN. 著者: Elena Pokidysheva / Ying Zhang / Anthony J Battisti / Carol M Bator-Kelly / Paul R Chipman / Chuan Xiao / G Glenn Gregorio / Wayne A Hendrickson / Richard J Kuhn / Michael G Rossmann / 要旨: Dengue virus (DENV) is a significant human pathogen that causes millions of infections and results in about 24,000 deaths each year. Dendritic cell-specific ICAM3 grabbing nonintegrin (DC-SIGN), ...Dengue virus (DENV) is a significant human pathogen that causes millions of infections and results in about 24,000 deaths each year. Dendritic cell-specific ICAM3 grabbing nonintegrin (DC-SIGN), abundant in immature dendritic cells, was previously reported as being an ancillary receptor interacting with the surface of DENV. The structure of DENV in complex with the carbohydrate recognition domain (CRD) of DC-SIGN was determined by cryo-electron microscopy at 25 A resolution. One CRD monomer was found to bind to two glycosylation sites at Asn67 of two neighboring glycoproteins in each icosahedral asymmetric unit, leaving the third Asn67 residue vacant. The vacancy at the third Asn67 site is a result of the nonequivalence of the glycoprotein environments, leaving space for the primary receptor binding to domain III of E. The use of carbohydrate moieties for receptor binding sites suggests a mechanism for avoiding immune surveillance.
#222 - 2018年6月 タンパク質とナノ粒子 (Proteins and Nanoparticles) 類似性 (1)
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マップ
ファイル
ダウンロード / ファイル: emd_1166.map.gz / 形式: CCP4 / 大きさ: 13.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
EM map of dengue virus in complex with CRD domain of DC-SIGN
ボクセルのサイズ
X=Y=Z: 4.34 Å
密度
表面レベル
1: 2.36
最小 - 最大
-2.99261 - 4.39911
平均 (標準偏差)
0.00208941 (±0.999885)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
Y
X
Z
Origin
-77
-77
-77
サイズ
154
154
154
Spacing
154
154
154
セル
A=B=C: 668.36 Å α=β=γ: 90 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
4.34
4.34
4.34
M x/y/z
154
154
154
origin x/y/z
0.000
0.000
0.000
length x/y/z
668.360
668.360
668.360
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-77
-77
-77
NX/NY/NZ
154
154
154
MAP C/R/S
2
1
3
start NC/NR/NS
-77
-77
-77
NC/NR/NS
154
154
154
D min/max/mean
-2.993
4.399
0.002
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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 : Dengue virus complexed with CRD domain of DC-SIGN
全体
名称: Dengue virus complexed with CRD domain of DC-SIGN
要素
試料: Dengue virus complexed with CRD domain of DC-SIGN
ウイルス: Dengue-2
タンパク質・ペプチド: CRD domain of DC-SIGN
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超分子 #1000: Dengue virus complexed with CRD domain of DC-SIGN
超分子
名称: Dengue virus complexed with CRD domain of DC-SIGN / タイプ: sample / ID: 1000 / 詳細: Calcium should be present in the sample. / 集合状態: one monomer of CRD binds virus ico / Number unique components: 2
pH: 7.5 / 詳細: 50mM Tris 50mM NaCl 0.5 mM EDTA, 5 mM CaCl2, pH 7.5
グリッド
詳細: 400 mesh copper grid
凍結
凍結剤: ETHANE / 装置: HOMEMADE PLUNGER 詳細: Vitrification instrument: Guillotine-style plunge freezeing device 手法: Small aliquots of sample were applied to 400 mesh copper grids coated with holey carbon film and rapidly frozen by plunging into an ethane slush
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電子顕微鏡法
顕微鏡
FEI/PHILIPS CM300FEG/T
温度
平均: 103 K
アライメント法
Legacy - 非点収差: objective lens astigmatism was corrected at 98,000 times magnification