ジャーナル: Cell / 年: 2018 タイトル: Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. 著者: Eva-Maria Weick / M Rhyan Puno / Kurt Januszyk / John C Zinder / Michael A DiMattia / Christopher D Lima / 要旨: The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4- ...The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.
ダウンロード / ファイル: emd_7819.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Overall reconstruction of a small class for human nuclear exosome-MTR4 complex with the MTR4 KOW domain in a closed conformation
ボクセルのサイズ
X=Y=Z: 1.07 Å
密度
表面レベル
登録者による: 0.012 / ムービー #1: 0.012
最小 - 最大
-0.012411459 - 0.034145005
平均 (標準偏差)
0.00013792339 (±0.0015943364)
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
384
384
384
Spacing
384
384
384
セル
A=B=C: 410.88 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
1.07
1.07
1.07
M x/y/z
384
384
384
origin x/y/z
0.000
0.000
0.000
length x/y/z
410.880
410.880
410.880
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
0
NX/NY/NZ
384
384
384
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
384
384
384
D min/max/mean
-0.012
0.034
0.000
-
添付データ
-
試料の構成要素
+
全体 : Human nuclear exosome-MTR4 helicase captured after unwinding a DN...
全体
名称: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
要素
複合体: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
タンパク質・ペプチド: EXOSC9
タンパク質・ペプチド: EXOSC4
タンパク質・ペプチド: EXOSC8
タンパク質・ペプチド: EXOSC5
タンパク質・ペプチド: EXOSC7
タンパク質・ペプチド: EXOSC6
タンパク質・ペプチド: EXOSC3
タンパク質・ペプチド: EXOSC2
タンパク質・ペプチド: EXOSC1
タンパク質・ペプチド: EXOSC10
タンパク質・ペプチド: DIS3
タンパク質・ペプチド: MPP6, MPHOSPH6
タンパク質・ペプチド: MTR4, MTREX
タンパク質・ペプチド: C1D, Rrp47
RNA: synthetic RNA
Other: DNA-RNA chimera
+
超分子 #1: Human nuclear exosome-MTR4 helicase captured after unwinding a DN...
超分子
名称: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: Human C1D/Rrp47 also in the sample, but was not observed in density
名称: EXOSC3 / タイプ: protein_or_peptide / ID: 7 詳細: N-terminal DP cloning artifact Y to H at position 225, Natural variant (VAR_054098, dbSNP:rs3208406) 光学異性体: LEVO
使用したクラス数: 1 / 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: 8.22 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2.1b1) 詳細: Overall reconstruction for a small class that shows the MTR4 KOW domain in an open conformation 使用した粒子像数: 2973
初期 角度割当
タイプ: RANDOM ASSIGNMENT / ソフトウェア - 名称: cryoSPARC (ver. 0.6.1) / ソフトウェア - 詳細: from 0.6.1 to 0.6.5