- EMDB-5469: Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likel... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-5469
タイトル
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
マップデータ
Cryo-EM reconstruction of the structure standard deviation of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
試料
試料: Cryo-EM reconstruction of the structure variance of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
ウイルス: Nudaurelia capensis omega virus (ウイルス)
キーワード
time-resolved / single particle reconstruction / virus maturation / protein folding / quasi-equivalence / cryo electron microscopy / Nudaurelia Capensis Omega Virus / maximum likelihood estimation / expectation maximization algorithm / heterogeneous particles / variance map
ジャーナル: J Struct Biol / 年: 2013 タイトル: Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps. 著者: Qiu Wang / Tsutomu Matsui / Tatiana Domitrovic / Yili Zheng / Peter C Doerschuk / John E Johnson / 要旨: CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. ...CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. Regions of high variation in the data set are apparent in the image reconstruction due to the poor density that results from the lack of superposition of these regions. These observations are qualitative and, to date, only preliminary efforts have been made to quantitate the heterogeneity in the ensemble of particles that are individually imaged. We developed and tested a quantitative method for simultaneously computing a reconstruction of the particle and a map of the space-varying heterogeneity of the particle based on an entire data set. The method uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle. The result describes the heterogeneity of the particle as a variance to be plotted at every voxel of the reconstructed density. The test, employing time resolved data sets of virus maturation, not only recapitulated local variations obtained with difference map analysis, but revealed a remarkable time dependent reduction in the overall particle dynamics that was unobservable with classical methods of analysis.
ダウンロード / ファイル: emd_5469.map.gz / 形式: CCP4 / 大きさ: 29.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Cryo-EM reconstruction of the structure standard deviation of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
ボクセルのサイズ
X=Y=Z: 2.768 Å
密度
表面レベル
登録者による: 0.00000033 / ムービー #1: 3.0E-7
最小 - 最大
0.0 - 0.00003064
平均 (標準偏差)
0.00000008 (±0.0000002)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
-100
-100
-100
サイズ
200
200
200
Spacing
200
200
200
セル
A=B=C: 553.6 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
2.768
2.768
2.768
M x/y/z
200
200
200
origin x/y/z
0.000
0.000
0.000
length x/y/z
553.600
553.600
553.600
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-150
-150
0
NX/NY/NZ
301
301
151
MAP C/R/S
1
2
3
start NC/NR/NS
-100
-100
-100
NC/NR/NS
200
200
200
D min/max/mean
0.000
0.000
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 : Cryo-EM reconstruction of the structure variance of Nudaurelia ca...
全体
名称: Cryo-EM reconstruction of the structure variance of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
要素
試料: Cryo-EM reconstruction of the structure variance of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
ウイルス: Nudaurelia capensis omega virus (ウイルス)
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超分子 #1000: Cryo-EM reconstruction of the structure variance of Nudaurelia ca...
超分子
名称: Cryo-EM reconstruction of the structure variance of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation タイプ: sample / ID: 1000 / 集合状態: Icosahedral virus / Number unique components: 1
詳細: Data were collected using the Leginon automated electron microscopy package and data processing was performed using the Appion pipeline.
電子線
加速電圧: 120 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
試料ステージ
試料ホルダーモデル: GATAN LIQUID NITROGEN
実験機器
モデル: Tecnai F20 / 画像提供: FEI Company
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画像解析
詳細
The reconstruction uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle.