EMDB-0598: Structure of a drug-like molecule stalled ribosome nascent chain ...

基本情報

• 登録情報: データベース: EMDB / ID: EMD-0598
• タイトル: Structure of a drug-like molecule stalled ribosome nascent chain complex (PCSK9_RNC) in non-rotated state with PP tRNA
• マップデータ: PF846 stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA. Map is sharpened.

試料

• 複合体: Drug-like molecule stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA
  • RNA: human ribosome with nascent chain

機能・相同性

分子機能:

low-density lipoprotein particle receptor catabolic process / : / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / PCSK9-LDLR complex / : / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / LDL clearance / very-low-density lipoprotein particle receptor binding / embryonic brain development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / axial mesoderm development / ribosomal protein import into nucleus / positive regulation of respiratory burst involved in inflammatory response / negative regulation of receptor internalization / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / : / protein-DNA complex disassembly / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / : / IRE1-RACK1-PP2A complex / regulation of signaling receptor activity / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / endolysosome membrane / translation at postsynapse / sodium channel inhibitor activity / TNFR1-mediated ceramide production / signaling receptor inhibitor activity / negative regulation of DNA repair / negative regulation of RNA splicing / TORC2 complex binding / mammalian oogenesis stage / GAIT complex / A band / supercoiled DNA binding / activation-induced cell death of T cells / G1 to G0 transition / oxidized purine DNA binding / NF-kappaB complex / neural crest cell differentiation / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / alpha-beta T cell differentiation / ubiquitin-like protein conjugating enzyme binding / translation at presynapse / regulation of establishment of cell polarity / exit from mitosis / rRNA modification in the nucleus and cytosol / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / lysosomal transport / laminin receptor activity / negative regulation of peptidyl-serine phosphorylation / protein kinase A binding / triglyceride metabolic process / optic nerve development / low-density lipoprotein particle receptor binding / negative regulation of ubiquitin protein ligase activity / pigmentation / retinal ganglion cell axon guidance / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / Translation initiation complex formation / homeostatic process / positive regulation of mitochondrial depolarization / COPII-coated ER to Golgi transport vesicle / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / lung morphogenesis / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / monocyte chemotaxis / Protein hydroxylation

ドメイン・相同性:

Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proteinase K-like catalytic domain / 40S ribosomal protein SA / Peptidase S8 propeptide/proteinase inhibitor I9 / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Peptidase inhibitor I9 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Ribosomal protein L28e / : / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L10e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L19/L19e conserved site / : / Ribosomal protein L19e signature. / Ribosomal protein S7e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S27a / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal

構成要素:

FAU ubiquitin like and ribosomal protein S30 fusion / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein eS4, Y isoform 1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Proprotein convertase subtilisin/kexin type 9 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL36

• 生物種: Homo sapiens (ヒト)
• 手法: 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å
• データ登録者: Li W / Cate JHD

資金援助

米国, 1件

Organization	Grant number	国
National Institutes of Health/National Human Genome Research Institute	R01-GM065050	米国

• 引用: ジャーナル: Nat Struct Mol Biol / 年: 2019; タイトル: Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.; 著者: Wenfei Li / Fred R Ward / Kim F McClure / Stacey Tsai-Lan Chang / Elizabeth Montabana / Spiros Liras / Robert G Dullea / Jamie H D Cate / ; 要旨: The drug-like molecule PF-06446846 (PF846) binds the human ribosome and selectively blocks the translation of a small number of proteins by an unknown mechanism. In structures of PF846-stalled human ribosome nascent chain complexes, PF846 binds in the ribosome exit tunnel in a eukaryotic-specific pocket formed by 28S ribosomal RNA, and alters the path of the nascent polypeptide chain. PF846 arrests the translating ribosome in the rotated state of translocation, in which the peptidyl-transfer RNA 3'-CCA end is improperly docked in the peptidyl transferase center. Selections of messenger RNAs from mRNA libraries using translation extracts reveal that PF846 can stall translation elongation, arrest termination or even enhance translation, depending on nascent chain sequence context. These results illuminate how a small molecule selectively targets translation by the human ribosome, and provides a foundation for developing small molecules that modulate the production of proteins of therapeutic interest.

履歴

登録	2019年2月21日	-
ヘッダ(付随情報) 公開	2019年3月20日	-
マップ公開	2019年3月20日	-
更新	2019年6月19日	-
現状	2019年6月19日	処理サイト: RCSB / 状態: 公開

マップ

• ファイル: ダウンロード / ファイル: emd_0598.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• 注釈: PF846 stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA. Map is sharpened.
• ボクセルのサイズ: X=Y=Z: 1.22 Å

密度

表面レベル	登録者による: 0.022 / ムービー #1: 0.024
最小 - 最大	-0.057956874 - 0.10376459
平均 (標準偏差)	0.000268779 (±0.007156887)

• 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 400 400 400 Spacing 400 400 400
セル	A=B=C: 488.0 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	1.22	1.22	1.22
M x/y/z	400	400	400
origin x/y/z	0.000	0.000	0.000
length x/y/z	488.000	488.000	488.000
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	400	400	400
D min/max/mean	-0.058	0.104	0.000

添付データ

追加マップ: PF846 stalled human ribosome nascent chain complex (PCSK9-RNC)...

• ファイル: emd_0598_additional.map
• 注釈: PF846 stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA. Map is not sharpened.

ハーフマップ: Half map of PF846 stalled human ribosome nascent...

• ファイル: emd_0598_half_map_1.map
• 注釈: Half map of PF846 stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA.

ハーフマップ: Half map of PF846 stalled human ribosome nascent...

• ファイル: emd_0598_half_map_2.map
• 注釈: Half map of PF846 stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA.

試料の構成要素

全体 : Drug-like molecule stalled human ribosome nascent chain complex (...

• 全体: 名称: Drug-like molecule stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA

要素

• 複合体: Drug-like molecule stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA
  • RNA: human ribosome with nascent chain

超分子 #1: Drug-like molecule stalled human ribosome nascent chain complex (...

• 超分子: 名称: Drug-like molecule stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA; タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all
• 由来(天然): 生物種: Homo sapiens (ヒト)
• 組換発現: 生物種: Homo sapiens (ヒト) / 組換細胞: HeLa
• 分子量: 理論値: 4.3 MDa

分子 #1: human ribosome with nascent chain

• 分子: 名称: human ribosome with nascent chain / タイプ: rna / ID: 1 ; 詳細: Nascent chain sequence including CDH1 domain V and PCSK9 1-35
• 由来(天然): 生物種: Homo sapiens (ヒト)

配列

文字列:

SDVNDNAPIP EPRTIFFCER NPKPQVINII DADLPPNTSP FTAELTHGAS ANWTIQYNDP TQESIILKPK MALEVGDYKI NLKLMDNQNK DQVTTLEVSV CDCEGAAGVC RKAQPVEAGL QIPAILGILG MGTVSSRRS WWPLPLLLLL LLLLGPAGAR AQEDED

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

試料調製

• 緩衝液: pH: 7.8
• グリッド: 詳細: unspecified
• 凍結: 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 4 K

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: GATAN K2 SUMMIT (4k x 4k); 平均電子線量: 50.0 e/Ų
• 電子線: 加速電圧: 300 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
• 実験機器: モデル: Titan Krios / 画像提供: FEI Company

画像解析

• 最終 再構成: 解像度のタイプ: BY AUTHOR / 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 7214
• 初期 角度割当: タイプ: ANGULAR RECONSTITUTION
• 最終 角度割当: タイプ: ANGULAR RECONSTITUTION

原子モデル構築 1

• 精密化: 空間: REAL / 温度因子: 80

得られたモデル

PDB-6olz:
Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNA