登録情報 データベース : PDB / ID : 5jpq 構造の表示 ダウンロードとリンクタイトル Cryo-EM structure of the 90S pre-ribosome 要素(WD40 domain proteins) x 2 18S ribosomal RNA Bms1 Emg1 Imp3 KRR1 small subunit processome component Kre33 Nop1 Pre mRNA splicing protein Putative U3 small nucleolar ribonucleoprotein Rcl1 Snu13 NHP2L1 U3 RNA U3 small nucleolar RNA-associated protein 21 UTP-A oligomerization domain UTP-B oligomerisation domain UTP10 UTP6 Utp24 Utp30 eS1 eS24 eS28 eS4 eS6 eS7 eS8 rrp9 uS11 uS15 uS17 uS4 uS7 uS8 uS9 残り31件を表示 表示を減らす 詳細キーワード RIBOSOME (リボソーム) / nuclear RNP機能・相同性 機能・相同性情報分子機能 ドメイン・相同性 構成要素
tRNA N-acetyltransferase activity / tRNA wobble cytosine modification / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / t-UTP complex ... tRNA N-acetyltransferase activity / tRNA wobble cytosine modification / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / t-UTP complex / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / rRNA base methylation / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / rRNA methylation / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / tRNA processing / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of translational fidelity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / RNA nuclease activity / enzyme activator activity / 90S preribosome / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / RNA endonuclease activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / maturation of LSU-rRNA / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / リボソーム生合成 / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / リボソーム / structural constituent of ribosome / ribonucleoprotein complex / 翻訳 (生物学) / GTPase activity / mRNA binding / 核小体 / GTP binding / ATP hydrolysis activity / ミトコンドリア / RNA binding / 核質 / ATP binding / identical protein binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 : / : / Archaeal Nop5/56-rel, N-terminal domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / : ... : / : / Archaeal Nop5/56-rel, N-terminal domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / : / : / : / ヘリカーゼ / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / KRR1 small subunit processome component, second KH domain / Ribosomal RNA assembly KRR1 / rRNA-processing protein Fcf1, PIN domain / rRNA-processing protein Fcf1/Utp23 / Fcf1 / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / RNA 3'-terminal phosphate cyclase signature. / BP28CT (NUC211) domain / Ribosomal RNA-processing protein Rrp9-like / Small-subunit processome, Utp21 / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Nucleolar protein Nop56/Nop58 / Krr1, KH1 domain / Krr1 KH1 domain / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / U3 snoRNP protein/Ribosome production factor 1 / Large family of predicted nucleotide-binding domains / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / PIN domain / Ribosomal protein L7Ae, archaea / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Anaphase-promoting complex subunit 4, WD40 domain / Brix domain / Brix domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Brix domain profile. / Brix / Anaphase-promoting complex subunit 4 WD40 domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / K Homology domain, type 1 superfamily / PIN-like domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / RS4NT (NUC023) domain / GNAT domain / Ribosomal family S4e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S4e signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal S24e conserved site 類似検索 - ドメイン・相同性 リボ核酸 / RNA (> 10) / RNA (> 100) / RNA (> 1000) / C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S6 / RNA cytidine acetyltransferase / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein ... リボ核酸 / RNA (> 10) / RNA (> 100) / RNA (> 1000) / C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S6 / RNA cytidine acetyltransferase / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein / Uncharacterized protein / PIN domain-containing protein / U3 small nucleolar ribonucleoprotein protein IMP4 / 40S ribosomal protein S24 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL8 / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / RNA 3'-terminal phosphate cyclase-like protein / Ribosome biogenesis protein BMS1 / 40S ribosomal protein S8 / 40S ribosomal protein S11, putative / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS28A 類似検索 - 構成要素生物種 Chaetomium thermophilum (菌類)Saccharomyces cerevisiae (パン酵母)手法 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度 : 7.3 Å 詳細データ登録者 Turk, M. / Cheng, J. / Berninghausen, O. / Kornprobst, M. / Flemming, D. / Kos-Braun, I.C. / Kos, M. / Thoms, M. / Hurt, E. / Beckmann, R. 引用ジャーナル : Cell / 年 : 2016タイトル : Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.著者 : Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt / 要旨 : The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that ... The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding. 履歴 登録 2016年5月4日 登録サイト : RCSB / 処理サイト : PDBE改定 1.0 2016年7月27日 Provider : repository / タイプ : Initial release改定 1.1 2016年8月3日 Group : Other改定 1.2 2017年7月5日 Group : Structure summary / カテゴリ : entity / Item : _entity.pdbx_description改定 1.3 2018年10月24日 Group : Advisory / Data collection / Derived calculationsカテゴリ : em_image_scans / ndb_struct_na_base_pair ... em_image_scans / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn 改定 1.4 2018年11月21日 Group : Advisory / Data collection / Derived calculationsカテゴリ : pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn改定 1.5 2019年1月23日 Group : Advisory / Data collection / Derived calculationsカテゴリ : pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ... pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type 改定 1.6 2020年3月11日 Group : Source and taxonomy / カテゴリ : entity_src_nat / Item : _entity_src_nat.pdbx_ncbi_taxonomy_id改定 1.7 2024年5月8日 Group : Data collection / Database references / カテゴリ : chem_comp_atom / chem_comp_bond / database_2Item : _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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