- EMDB-0208: OBP chaperonin in the ATPgammaS-bound state -
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基本情報
登録情報
データベース: EMDB / ID: EMD-0208
タイトル
OBP chaperonin in the ATPgammaS-bound state
マップデータ
A symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the ATPgammaS-bound state.
ジャーナル: J Struct Biol / 年: 2020 タイトル: Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin. 著者: Tatiana B Stanishneva-Konovalova / Pavel I Semenyuk / Lidia P Kurochkina / Evgeny B Pichkur / Alexander L Vasilyev / Mikhail V Kovalchuk / Mikhail P Kirpichnikov / Olga S Sokolova / 要旨: Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They ...Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both of these groups do not include recently discovered viral chaperonins. Here, we solved the symmetry-free cryo-EM structures of a single-ring chaperonin encoded by the gene 246 of bacteriophage OBP Pseudomonas fluorescens, in the nucleotide-free, ATPγS-, and ADP-bound states, with resolutions of 4.3 Å, 5.0 Å, and 6 Å, respectively. The structure of OBP chaperonin reveals a unique subunit arrangement, with three pairs of subunits and one unpaired subunit. Each pair combines subunits in two possible conformations, differing in nucleotide-binding affinity. The binding of nucleotides results in the increase of subunits' conformational variability. Due to its unique structural and functional features, OBP chaperonin can represent a new group.
ダウンロード / ファイル: emd_0208.map.gz / 形式: CCP4 / 大きさ: 8.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
A symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the ATPgammaS-bound state.
ボクセルのサイズ
X=Y=Z: 1.72 Å
密度
表面レベル
登録者による: 0.226 / ムービー #1: 0.226
最小 - 最大
-0.32981038 - 0.72862643
平均 (標準偏差)
0.00005425383 (±0.046707384)
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
132
132
132
Spacing
132
132
132
セル
A=B=C: 227.04001 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
1.72
1.72
1.72
M x/y/z
132
132
132
origin x/y/z
0.000
0.000
0.000
length x/y/z
227.040
227.040
227.040
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
132
132
132
D min/max/mean
-0.330
0.729
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 : OBP chaperonin in complex with ATPgammaS
全体
名称: OBP chaperonin in complex with ATPgammaS
要素
複合体: OBP chaperonin in complex with ATPgammaS
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超分子 #1: OBP chaperonin in complex with ATPgammaS
超分子
名称: OBP chaperonin in complex with ATPgammaS / タイプ: complex / ID: 1 / 親要素: 0
由来(天然)
生物種: Pseudomonas phage OBP (ファージ)
組換発現
生物種: Escherichia coli BL21(DE3) (大腸菌)
分子量
実験値: 420 KDa
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実験情報
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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
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試料調製
濃度
2.5 mg/mL
緩衝液
pH: 7.5
凍結
凍結剤: ETHANE
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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: FEI FALCON II (4k x 4k) 平均電子線量: 6.0 e/Å2