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- PDB-8ppl: MERS-CoV Nsp1 bound to the human 43S pre-initiation complex -

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基本情報

登録情報
データベース: PDB / ID: 8ppl
タイトルMERS-CoV Nsp1 bound to the human 43S pre-initiation complex
要素
  • (40S ribosomal protein ...) x 28
  • (Eukaryotic translation initiation factor ...) x 15
  • (Small ribosomal subunit protein ...) x 2
  • 18S rRNA
  • 60S ribosomal protein L41
  • Host translation inhibitor nsp1
  • Met-tRNAi(Met)
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
キーワードTRANSLATION / Nsp1 / MERS / SARS / SARS-CoV2 / ribosome / 40S ribosomal subunit / translation inhibition / coronavirus / 43S PIC / 43S pre-initiation complex / mRNA channel / initiation factor / eIF2 / eIF3 / eIF1 / eIF1A / VIRAL PROTEIN
機能・相同性
機能・相同性情報


male germ cell proliferation / positive regulation of mRNA binding / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / viral translational termination-reinitiation / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress ...male germ cell proliferation / positive regulation of mRNA binding / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / viral translational termination-reinitiation / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / eukaryotic translation initiation factor 3 complex, eIF3e / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / cap-dependent translational initiation / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / PERK regulates gene expression / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / cytoplasmic translational initiation / multi-eIF complex / regulation of translational initiation in response to stress / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / 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 peptidyl-serine phosphorylation / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / translation at postsynapse / TNFR1-mediated ceramide production / protein-synthesizing GTPase / negative regulation of DNA repair / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / mammalian oogenesis stage / regulation of translational initiation / supercoiled DNA binding / activation-induced cell death of T cells / neural crest cell differentiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / NF-kappaB complex / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / translation at presynapse / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of phagocytosis / erythrocyte homeostasis / rRNA modification in the nucleus and cytosol / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / pigmentation / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / monocyte chemotaxis / negative regulation of translational frameshifting / Protein hydroxylation / BH3 domain binding / TOR signaling / SARS-CoV-1 modulates host translation machinery / regulation of cell division / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / iron-sulfur cluster binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
類似検索 - 分子機能
RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M ...RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / : / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / AAA domain / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ubiquitin-like protein FUBI / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / S1 domain profile. / : / 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 S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Translation elongation factor EFTu-like, domain 2 / 40S Ribosomal protein S10
類似検索 - ドメイン・相同性
GUANOSINE-5'-TRIPHOSPHATE / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Replicase polyprotein 1ab / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D ...GUANOSINE-5'-TRIPHOSPHATE / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Replicase polyprotein 1ab / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 2 subunit 1 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Eukaryotic translation initiation factor 2 subunit 2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 1 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Eukaryotic translation initiation factor 1A, X-chromosomal / Eukaryotic translation initiation factor 3 subunit E / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / 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 uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / 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 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit L
類似検索 - 構成要素
生物種Middle East respiratory syndrome-related coronavirus (ウイルス)
Homo sapiens (ヒト)
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: 2.65 Å
データ登録者Schubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. ...Schubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. / Puglisi, J.D. / Muehlemann, O. / Ban, N.
資金援助 スイス, 米国, 13件
組織認可番号国
Swiss National Science Foundation182341 スイス
Swiss National Science Foundation182831 スイス
Swiss National Science Foundation204161 スイス
Swiss National Science Foundation51NF40-182880 スイス
Swiss National Science Foundation51NF40--205601 スイス
Other governmentETH-23 18-2 スイス
Other government スイス
Other private スイス
Other private スイス
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM011378 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145306 米国
National Institutes of Health/National Institute on Aging (NIH/NIA)AG064690 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM144678 米国
引用
ジャーナル: Mol Cell / 年: 2023
タイトル: Universal features of Nsp1-mediated translational shutdown by coronaviruses.
著者: Katharina Schubert / Evangelos D Karousis / Ivo Ban / Christopher P Lapointe / Marc Leibundgut / Emilie Bäumlin / Eric Kummerant / Alain Scaiola / Tanja Schönhut / Jana Ziegelmüller / ...著者: Katharina Schubert / Evangelos D Karousis / Ivo Ban / Christopher P Lapointe / Marc Leibundgut / Emilie Bäumlin / Eric Kummerant / Alain Scaiola / Tanja Schönhut / Jana Ziegelmüller / Joseph D Puglisi / Oliver Mühlemann / Nenad Ban /
要旨: Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ...Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ribosomal mRNA channel to inhibit translation, but it is unclear whether this mechanism is broadly used by coronaviruses, whether the Nsp1 N-terminal domain binds the ribosome, or how Nsp1 allows viral RNAs to be translated. Here, we investigated Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV coronaviruses using structural, biophysical, and biochemical experiments, revealing a conserved role for the C-terminal domain. Additionally, the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A accommodation. Structure-based experiments demonstrated the importance of decoding center interactions in all three coronaviruses and showed that the same regions of Nsp1 are necessary for the selective translation of viral RNAs. Our results provide a mechanistic framework to understand how Nsp1 controls preferential translation of viral RNAs.
#1: ジャーナル: Mol.Cell / 年: 2023
タイトル: Universal features of Nsp1-mediated translational shutdown by coronaviruses
著者: Schubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. / Puglisi, J.D. / Muehlemann, O. / Ban, N.
履歴
登録2023年7月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年10月18日Provider: repository / タイプ: Initial release
改定 2.02023年11月15日Group: Atomic model / Data collection / Derived calculations
カテゴリ: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
改定 2.12024年4月24日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
I3: Eukaryotic translation initiation factor 3 subunit K
I4: Eukaryotic translation initiation factor 3 subunit F
I5: Eukaryotic translation initiation factor 3 subunit L
I6: Eukaryotic translation initiation factor 3 subunit M
I8: Eukaryotic translation initiation factor 3 subunit H
Io: Eukaryotic translation initiation factor 3 subunit G
Ip: Eukaryotic translation initiation factor 1
Iq: Eukaryotic translation initiation factor 1A, X-chromosomal
Ir: Eukaryotic translation initiation factor 2 subunit 1
Is: Eukaryotic translation initiation factor 2 subunit 2
It: Eukaryotic translation initiation factor 2 subunit 3
Iu: Eukaryotic translation initiation factor 3 subunit A
Iv: Eukaryotic translation initiation factor 3 subunit E
Iw: Met-tRNAi(Met)
Ix: Eukaryotic translation initiation factor 3 subunit D
Iy: Eukaryotic translation initiation factor 3 subunit C
A2: 18S rRNA
AA: 40S ribosomal protein SA
AB: 40S ribosomal protein S3a
AC: 40S ribosomal protein S2
AD: 40S ribosomal protein S3
AE: 40S ribosomal protein S4, X isoform
AF: 40S ribosomal protein S5
AG: 40S ribosomal protein S6
AH: 40S ribosomal protein S7
AI: 40S ribosomal protein S8
AJ: 40S ribosomal protein S9
AK: 40S ribosomal protein S10
AL: 40S ribosomal protein S11
AM: 40S ribosomal protein S12
AN: 40S ribosomal protein S13
AO: 40S ribosomal protein S14
AP: 40S ribosomal protein S15
AQ: 40S ribosomal protein S16
AR: 40S ribosomal protein S17
AS: Small ribosomal subunit protein uS13
AT: Small ribosomal subunit protein eS19
AU: 40S ribosomal protein S20
AV: 40S ribosomal protein S21
AW: 40S ribosomal protein S15a
AX: 40S ribosomal protein S23
AY: 40S ribosomal protein S24
AZ: 40S ribosomal protein S25
Aa: 40S ribosomal protein S26
Ab: 40S ribosomal protein S27
Ac: 40S ribosomal protein S28
Ad: 40S ribosomal protein S29
Ae: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Af: Ubiquitin-40S ribosomal protein S27a
Ag: Receptor of activated protein C kinase 1
Ah: 60S ribosomal protein L41
Aj: Host translation inhibitor nsp1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,078,202303
ポリマ－2,074,44852
非ポリマー3,753251
水362
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_555x,y,z1

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要素

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Eukaryotic translation initiation factor ... , 15種, 15分子 I3I4I5I6I8IoIpIqIrIsItIuIvIxIy

#1: タンパク質 Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / ...eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / PLAC-24 / eIF-3 p25 / eIF-3 p28


分子量: 25083.619 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: Q9UBQ5
#2: タンパク質 Eukaryotic translation initiation factor 3 subunit F / eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF- ...eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


分子量: 37593.645 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: O00303, ubiquitinyl hydrolase 1
#3: タンパク質 Eukaryotic translation initiation factor 3 subunit L / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


分子量: 66803.734 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: Q9Y262
#4: タンパク質 Eukaryotic translation initiation factor 3 subunit M / eIF3m / Fetal lung protein B5 / hFL-B5 / PCI domain-containing protein 1


分子量: 42555.832 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: Q7L2H7
#5: タンパク質 Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


分子量: 39979.277 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: O15372
#6: タンパク質 Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Eukaryotic translation initiation factor 3 subunit 4 / eIF-3-delta / eIF3 p42 / eIF3 p44


分子量: 35662.016 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: O75821
#7: タンパク質 Eukaryotic translation initiation factor 1 / eIF1 / A121 / Protein translation factor SUI1 homolog / Sui1iso1


分子量: 12752.498 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: N-terminus built as UNK / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P41567
#8: タンパク質 Eukaryotic translation initiation factor 1A, X-chromosomal / eIF-1A X isoform / Eukaryotic translation initiation factor 4C / eIF-4C


分子量: 16488.449 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P47813
#9: タンパク質 Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


分子量: 36161.180 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P05198
#10: タンパク質 Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


分子量: 38454.484 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P20042
#11: タンパク質 Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


分子量: 51178.406 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P41091, protein-synthesizing GTPase
#12: タンパク質 Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 ...eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


分子量: 166903.781 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code Q14152 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q14152
#13: タンパク質 Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 ...eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 homolog / eIF-3 p48


分子量: 52281.633 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P60228 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P60228
#15: タンパク質 Eukaryotic translation initiation factor 3 subunit D / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 / eIF-3-zeta / eIF3 p66


分子量: 64060.758 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code O15371 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O15371
#16: タンパク質 Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


分子量: 105503.945 Da / 分子数: 1 / 由来タイプ: 天然
詳細: One linker built as UNK. UniProt accession code Q99613
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: Q99613

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RNA鎖 , 2種, 2分子 IwA2

#14: RNA鎖 Met-tRNAi(Met)


分子量: 24463.807 Da / 分子数: 1 / 由来タイプ: 天然
詳細: Aminoacylated initiator tRNA with base modifications. (XXX) refers to methionine residue attached to CCA-3'OH of tRNA. Sequence obtained from gtrnadb.
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E
#17: RNA鎖 18S rRNA


分子量: 603609.188 Da / 分子数: 1 / 由来タイプ: 天然
詳細: unmodified sequence: >18S_rRNA_taoka_unmodified UACCUGGUUGAUCCUGCCAGUAGCAUaUGCUUGuCuCAAAGAUUAAGCCAUGCAUGUCUA AGUACGCACGGCCGGUACAGUGAAACUGCGAAuGGCUCaUUAAAuCAGuUAUGGUuCCuU ...詳細: unmodified sequence: >18S_rRNA_taoka_unmodified UACCUGGUUGAUCCUGCCAGUAGCAUaUGCUUGuCuCAAAGAUUAAGCCAUGCAUGUCUA AGUACGCACGGCCGGUACAGUGAAACUGCGAAuGGCUCaUUAAAuCAGuUAUGGUuCCuU uGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAaUUCUAGaGCUAAuAcAUGCCG ACGGGCGCUGACCCCCUUCGCGGGGGGGAuGCGUGCAuUUAUCAGAUCAAAACCAACCCG GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCuAGAU AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCuGCCCUA UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGuGACGGGGAAUCAGG GUUCGAUuCCGGAGAgGGAGCCUGAGAAACGGCUACCACAUcCAAGGaAGGCAGCAGGCG CGCaAAUUACCCACUCCCGACCCGGGGAgGUaGUGAcGAAAAAUAACAAUACAGGACUCU UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUuUAAaUCCUUUAACGAGGaUCCAUUGGAG gGCAAGUCuGGUGCCAGCAGcCGCGGuAAUUCCAGCUCCAAUAgCGUAuAuUAAAGUUGC UGCAGUUaAAAAGCUCGUAGuUgGAuCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU CCCGCGGGGCCCGAAGcGuUuACUUUGAAAAAAuuAGAGUGuUCAAAGCAGGCCCGAGCC GCCUGGAUACCGCAGCUAGGAAuAAugGAAUAGGACCGCGGUUCUAUUUUGUUGGUuUUC GGAACUGAGGCCAUGAUuAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU GAAAUuCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUuGCCAAGAAUGUUUUCA UUAAUCAAGAaCGAAAGUCGGAGGuuCGAAGACGAuCAGAUACCGUCGUAGUUCCGACCA uAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCuUCCG GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAuGGuUGCAAAGCUGAAACUUAAAGGAA UUGACGGAAGGGCACCACCAGGAGUGGAGCCuGCGGCuUAAUUuGACuCAACACGGGAAA CCUCACCCGGCcCGGACACGGACAGGAuUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG GGUGGuGgUGCAUGGCcGUUCUUAGUuGGUGGAGCGAUUUGUCUGGuUAAUUCCGAUAAC GAaCGAGACUcUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC UuCUuAgAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAgGUCUGUGAUG CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA UUAUuCCCCAUGAACGAGgAAUuCCCAGUAAGUGCGGGUCAUAAGCUuGCGUUGAUUaAG UCCCUGCCCUUuGUACACACCGcCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA ACUuGACUAUCUAGAGGAAGUAAAAGUCGUAaCAAGGUUUCcGUAGGUGaaCCUGCGGAA GGAUCAUUA
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E

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40S ribosomal protein ... , 28種, 28分子 AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARAUAVAWAXAYAZAaAbAcAd

#18: タンパク質 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


分子量: 32925.973 Da / 分子数: 1 / 由来タイプ: 天然
詳細: UniProt accession code P08865 S2: acetylserine (SAC)
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P08865
#19: タンパク質 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


分子量: 30002.061 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P61247 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P61247
#20: タンパク質 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


分子量: 31376.516 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P15880 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P15880
#21: タンパク質 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


分子量: 26729.369 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P23396 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E
参照: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#22: タンパク質 40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


分子量: 29654.869 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62701 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62701
#23: タンパク質 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


分子量: 22913.453 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P46782 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P46782
#24: タンパク質 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


分子量: 28751.906 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62753 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62753
#25: タンパク質 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


分子量: 22168.914 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62081 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62081
#26: タンパク質 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


分子量: 24263.387 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Uniprot accession code P62241 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62241
#27: タンパク質 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


分子量: 22641.564 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P46781 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P46781
#28: タンパク質 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


分子量: 18933.846 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P46783 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P46783
#29: タンパク質 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


分子量: 18468.826 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62280 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62280
#30: タンパク質 40S ribosomal protein S12 / Small ribosomal subunit protein eS12


分子量: 14538.987 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P25398 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P25398
#31: タンパク質 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


分子量: 17259.389 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62277 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62277
#32: タンパク質 40S ribosomal protein S14 / Small ribosomal subunit protein uS11


分子量: 16302.772 Da / 分子数: 1 / 由来タイプ: 天然
詳細: D138: isoaspartate (IAS) UniProt accession code P62263
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62263
#33: タンパク質 40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


分子量: 17076.207 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62841 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62841
#34: タンパク質 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


分子量: 16477.377 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: P62249 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62249
#35: タンパク質 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


分子量: 15578.156 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P08708 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P08708
#38: タンパク質 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


分子量: 13398.763 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P60866 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P60866
#39: タンパク質 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


分子量: 9166.426 Da / 分子数: 1 / 由来タイプ: 天然
詳細: UniProt accession code P63220 M1: acetylmethionine (AME)
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P63220
#40: タンパク質 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


分子量: 14865.555 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62244 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62244
#41: タンパク質 40S ribosomal protein S23


分子量: 15860.666 Da / 分子数: 1 / 由来タイプ: 天然
詳細: UniProt accession code P62266 P62: hydroxyproline (HY3)
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: A0A4W2DI10
#42: タンパク質 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


分子量: 15463.333 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62847 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62847
#43: タンパク質 40S ribosomal protein S25 / Small ribosomal subunit protein eS25


分子量: 13776.224 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62851 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62851
#44: タンパク質 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


分子量: 13047.532 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62854 zinc finger protein / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62854
#45: タンパク質 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


分子量: 9480.186 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P42677 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P42677
#46: タンパク質 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


分子量: 7855.052 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62857 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62857
#47: タンパク質 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


分子量: 6690.821 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62273 zinc finger protein / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62273

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Small ribosomal subunit protein ... , 2種, 2分子 ASAT

#36: タンパク質 Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3


分子量: 17801.814 Da / 分子数: 1 / 由来タイプ: 天然
詳細: UniProt accession code P62269 S2: acetylserine (SAC)
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62269
#37: タンパク質 Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


分子量: 16104.579 Da / 分子数: 1 / 由来タイプ: 天然
詳細: R67: omega-methylarginine (NMM) UniProt accession code P39019
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P39019

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タンパク質 , 4種, 4分子 AeAfAgAj

#48: タンパク質 Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / FAU ubiquitin like and ribosomal protein S30 fusion


分子量: 14415.724 Da / 分子数: 1 / 由来タイプ: 天然
詳細: P62861 (UniProt) NP_001988.1 (GeneBank) residues 1-74: ubiquitin
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62861
#49: タンパク質 Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


分子量: 18004.041 Da / 分子数: 1 / 由来タイプ: 天然
詳細: residues 1-76: ubiquitin zinc finger protein UniProt accession code P62979
由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P62979
#50: タンパク質 Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


分子量: 35115.652 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P63244 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293E / 参照: UniProt: P63244
#52: タンパク質 Host translation inhibitor nsp1 / nsp1 / Leader protein


分子量: 24328.531 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: residues 1-193 of MERS polyprotein ORF1ab UniProt accession number K9N7C7 (R1AB_MERS1)
由来: (組換発現) Middle East respiratory syndrome-related coronavirus (ウイルス)
遺伝子: rep, 1a-1b / プラスミド: pcDNA3.1(+) / 細胞株 (発現宿主): HEK293E / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: K9N7C7

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タンパク質・ペプチド , 1種, 1分子 Ah

#51: タンパク質・ペプチド 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


分子量: 3473.451 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: UniProt accession code P62945 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HEK293 / 参照: UniProt: P62945

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非ポリマー , 6種, 253分子

#53: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn
#54: 化合物 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#55: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 116 / 由来タイプ: 合成 / 式: Mg
#56: 化合物 ChemComp-MET / METHIONINE / メチオニン


タイプ: L-peptide linking / 分子量: 149.211 Da / 分子数: 1 / 由来タイプ: 組換発現 / 式: C5H11NO2S
#57: 化合物...
ChemComp-UNX / UNKNOWN ATOM OR ION


分子数: 129 / 由来タイプ: 合成
#58: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: MERS-CoV Nsp1 - 43S pre-initiation complex / タイプ: RIBOSOME / Entity ID: #1-#13, #15-#52 / 由来: NATURAL
由来(天然)生物種: Homo sapiens (ヒト)
緩衝液pH: 7.4
緩衝液成分
ID濃度名称Buffer-ID
150 mMHEPES-KOH1
2100 mMKOAc1
310 mMMg(OAc)21
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: f.c. 100 nM
試料支持詳細: 15 sec in easiGlow Discharge cleaning system (PELCO) at 15 mA
グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R2/2
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE-PROPANE / 湿度: 100 % / 凍結前の試料温度: 277 K

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 81000 X / 最大 デフォーカス（公称値）: 3000 nm / 最小 デフォーカス（公称値）: 600 nm
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 60 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 8932

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解析

EMソフトウェア
ID名称バージョンカテゴリ詳細
7Coot0.9.8.5モデルフィッティング
9PHENIX1.20.1モデル精密化phenix.real_space_refine
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 2.65 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 218516 / 対称性のタイプ: POINT
原子モデル構築プロトコル: OTHER / 空間: REAL / 詳細: phenix.real_space_refine
原子モデル構築

3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model

IDPDB-IDAccession code詳細Initial refinement model-ID
16ZOK

6zok

6ZOK40S body1
26ZOL

6zol

6ZOL40S head2

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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