ジャーナル: Nat Commun / 年: 2020 タイトル: MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments. 著者: Klemens Wild / Milan Aleksić / Karine Lapouge / Keven D Juaire / Dirk Flemming / Stefan Pfeffer / Irmgard Sinning / 要旨: Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature ...Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature 80S ribosomes for translational control. Here, we present a cryo-EM single particle analysis reconstruction of Ebp1 bound to non-translating human 80S ribosomes at a resolution range from 3.3 to ~8 Å. Ebp1 blocks the tunnel exit with major interactions to the general uL23/uL29 docking site for nascent chain-associated factors complemented by eukaryote-specific eL19 and rRNA helix H59. H59 is defined as dynamic adaptor undergoing significant remodeling upon Ebp1 binding. Ebp1 recruits rRNA expansion segment ES27L to the tunnel exit via specific interactions with rRNA consensus sequences. The Ebp1-ribosome complex serves as a template for MetAP binding and provides insights into the structural principles for spatial coordination of co-translational events and molecular triage at the ribosomal tunnel exit.
ダウンロード / ファイル: emd_10608.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
ボクセルのサイズ
X=Y=Z: 1.5218 Å
密度
表面レベル
登録者による: 0.025 / ムービー #1: 0.025
最小 - 最大
-0.395412 - 0.52741325
平均 (標準偏差)
0.001479043 (±0.008448959)
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
360
360
360
Spacing
360
360
360
セル
A=B=C: 547.848 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
1.5218
1.5218
1.5218
M x/y/z
360
360
360
origin x/y/z
0.000
0.000
0.000
length x/y/z
547.848
547.848
547.848
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
360
360
360
D min/max/mean
-0.395
0.527
0.001
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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 : Human Ebp1-ribosome complex
全体
名称: Human Ebp1-ribosome complex
要素
複合体: Human Ebp1-ribosome complex
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超分子 #1: Human Ebp1-ribosome complex
超分子
名称: Human Ebp1-ribosome complex / タイプ: complex / ID: 1 / 親要素: 0 詳細: Puromycin-treated ribosomes from HeLa cells in complex with recombinantly expressed Ebp1
由来(天然)
生物種: Homo sapiens (ヒト)
組換発現
生物種: Escherichia coli (大腸菌)
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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
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試料調製
緩衝液
pH: 7.5 詳細: 20 mM HEPES KOH pH 7.5 5 mM Mg(OAc)2 175 mM KOAc 1 mM Tris(2-carboxyethyl)phosphin
凍結
凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 293 K / 装置: FEI VITROBOT MARK IV
想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.0) 詳細: Ebp1-60S density segment after 3D classification focused on ES27L and 2-body multibody refinement; filtered to local resolution 使用した粒子像数: 4864
初期 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0)
最終 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0)