+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11459 | ||||||||||||||||||
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タイトル | The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism | ||||||||||||||||||
マップデータ | |||||||||||||||||||
試料 |
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キーワード | RIBOSOME INTERNAL RIBOSOME ENTRY SITE RNA DICISTROVIRUS Halastavi arva virus Intergenic region pseudoknot CrPV IGR IRES SERBP1 / TRANSLATION | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 ...Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / Downstream TCR signaling / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / FCERI mediated NF-kB activation / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / RAD18 and ubiquitinated PCNA-mediated recruitment of translesion polymerases / Nucleotide Excision Repair / Deactivation of the beta-catenin transactivating complex / TRAF6 mediated induction of proinflammatory cytokines / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / NFkB activation mediated by RIP1 complexed with activated TLR3 / Activated TAK1 mediates p38 MAP kinase phosphorylation / Activated TAK1 mediates Jun kinases (JNK) phosphorylation and activation / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog ligand biogenesis / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / NFkB and MAPK activation mediated by TRAF6 upon TLR7 or TLR21 stimulation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / Neddylation / ER Quality Control Compartment (ERQC) / NOTCH3 Activation and Transmission of Signal to the Nucleus / Peroxisomal protein import / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Halastavi arva RNA virus (ウイルス) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.49 Å | ||||||||||||||||||
データ登録者 | Abaeva IS / Vicens Q | ||||||||||||||||||
資金援助 | 米国, フランス, 5件
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引用 | ジャーナル: Cell Rep / 年: 2020 タイトル: The Halastavi árva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism. 著者: Irina S Abaeva / Quentin Vicens / Anthony Bochler / Heddy Soufari / Angelita Simonetti / Tatyana V Pestova / Yaser Hashem / Christopher U T Hellen / 要旨: Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the ...Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the elongation cycle via formation of IRES/80S complexes resembling the pre-translocation state. eEF2 then translocates the [codon-anticodon]-mimicking pseudoknot I (PKI) from ribosomal A sites to P sites, bringing the first sense codon into the decoding center. Halastavi árva virus (HalV) contains an IGR that is related to previously described IGR IRESs but lacks domain 2, which enables these IRESs to bind to individual 40S ribosomal subunits. By using in vitro reconstitution and cryoelectron microscopy (cryo-EM), we now report that the HalV IGR IRES functions by the simplest initiation mechanism that involves binding to 80S ribosomes such that PKI is placed in the P site, so that the A site contains the first codon that is directly accessible for decoding without prior eEF2-mediated translocation of PKI. | ||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_11459.map.gz | 164.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11459-v30.xml emd-11459.xml | 109.7 KB 109.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_11459.png | 126.4 KB | ||
Filedesc metadata | emd-11459.cif.gz | 19.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11459 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11459 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11459_validation.pdf.gz | 709 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_11459_full_validation.pdf.gz | 708.6 KB | 表示 | |
XML形式データ | emd_11459_validation.xml.gz | 6.7 KB | 表示 | |
CIF形式データ | emd_11459_validation.cif.gz | 7.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11459 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11459 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_11459.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : COMPLEX BETWEEN 870S RIBOSOME AND HALV IGR IRES
+超分子 #1: COMPLEX BETWEEN 870S RIBOSOME AND HALV IGR IRES
+超分子 #2: RIBOSOME
+超分子 #3: HALV IGR IRES
+分子 #1: Ribosomal protein L14
+分子 #5: 60S RIBOSOMAL PROTEIN EL38
+分子 #6: 60S RIBOSOMAL PROTEIN UL13
+分子 #7: uL22
+分子 #8: 60S RIBOSOMAL PROTEIN EL18
+分子 #9: 60S RIBOSOMAL PROTEIN EL19
+分子 #10: uL3
+分子 #11: 60S RIBOSOMAL PROTEIN EL20
+分子 #12: eL21
+分子 #13: Ribosomal protein L22
+分子 #14: eL14
+分子 #15: Ribosomal protein L24
+分子 #16: 60S RIBOSOMAL PROTEIN UL23
+分子 #17: Ribosomal protein L26
+分子 #18: uL15
+分子 #19: 60S ribosomal protein L29
+分子 #20: Ribosomal protein L30
+分子 #21: uL4
+分子 #22: eL31
+分子 #23: eL32
+分子 #24: eL33
+分子 #25: eL34
+分子 #26: 60S RIBOSOMAL PROTEIN UL2
+分子 #27: uL29
+分子 #28: 60S ribosomal protein L36
+分子 #29: Ribosomal protein L37
+分子 #30: ribosomal protein eL39
+分子 #31: 60S RIBOSOMAL PROTEIN EL40
+分子 #32: eL42
+分子 #33: 60S ribosomal protein L5
+分子 #34: ribosomal protein eL43
+分子 #35: 60S RIBOSOMAL PROTEIN EL28
+分子 #36: 60S acidic ribosomal protein P0
+分子 #37: Ribosomal protein L10 (Predicted)
+分子 #38: Uncharacterized protein
+分子 #39: Ribosomal_L6e_N domain-containing protein
+分子 #40: 60S ribosomal protein L6
+分子 #41: uL30
+分子 #42: 60S RIBOSOMAL PROTEIN EL8
+分子 #43: 60S RIBOSOMAL PROTEIN UL6
+分子 #44: Ribosomal protein L10 (Predicted)
+分子 #45: Ribosomal protein L11
+分子 #46: 60S ribosomal protein L13
+分子 #47: Ribosomal protein L15
+分子 #48: 60S ribosomal protein L27
+分子 #49: Ribosomal protein
+分子 #51: Ribosomal_S10 domain-containing protein
+分子 #52: 40S RIBOSOMAL PROTEIN ES30
+分子 #53: Ribosomal protein S11
+分子 #54: ribosomal protein eS28
+分子 #56: 40S RIBOSOMAL PROTEIN ES7
+分子 #57: 40S RIBOSOMAL PROTEIN US11
+分子 #58: ribosomal protein uS19
+分子 #59: 40S RIBOSOMAL PROTEIN US9
+分子 #60: 40S RIBOSOMAL PROTEIN ES17
+分子 #61: 40S RIBOSOMAL PROTEIN ES21
+分子 #62: ribosomal protein uS13
+分子 #63: 40S RIBOSOMAL PROTEIN ES19
+分子 #64: Ribosomal protein S15a
+分子 #65: 40S ribosomal protein S24
+分子 #66: 40S ribosomal protein S27
+分子 #67: ribosomal protein eS25
+分子 #68: 40S RIBOSOMAL PROTEIN ES26
+分子 #69: 40S RIBOSOMAL PROTEIN ES31
+分子 #70: ribosomal protein RACK1
+分子 #71: Ribosomal protein S23
+分子 #72: 40S_SA_C domain-containing protein
+分子 #73: 40S ribosomal protein S3a
+分子 #74: S5 DRBM domain-containing protein
+分子 #75: 60s ribosomal protein l41
+分子 #76: Ribosomal protein S3
+分子 #77: 40S ribosomal protein S4
+分子 #78: Ribosomal protein S5
+分子 #79: 40S ribosomal protein S6
+分子 #80: 40S ribosomal protein S8
+分子 #81: Ribosomal protein S9 (Predicted)
+分子 #82: 40S ribosomal protein S12
+分子 #83: ribosomal protein uS15
+分子 #84: S10_plectin domain-containing protein
+分子 #85: ribosomal protein uS14
+分子 #2: 28S RIBOSOMAL RNA
+分子 #3: 5S RIBOSOMAL RNA
+分子 #4: 5.8S RIBOSOMAL RNA
+分子 #50: INTERNAL RIBOSOME ENTRY SITE
+分子 #55: 18S RIBOSOMAL RNA
+分子 #86: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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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: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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: 60.0 e/Å2 |
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
初期モデル | モデルのタイプ: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.49 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 55589 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |