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- PDB-6bcx: mTORC1 structure refined to 3.0 angstroms -

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基本情報

登録情報
データベース: PDB / ID: 6bcx
タイトルmTORC1 structure refined to 3.0 angstroms
要素
  • Eukaryotic translation initiation factor 4E-binding protein 1
  • Regulatory-associated protein of mTOR
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8
キーワードTRANSFERASE / PIKK
機能・相同性
機能・相同性情報


RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / eukaryotic initiation factor 4E binding / TORC2 complex ...RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / eukaryotic initiation factor 4E binding / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / regulation of membrane permeability / negative regulation of lysosome organization / heart valve morphogenesis / nucleus localization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / voluntary musculoskeletal movement / TORC1 signaling / regulation of osteoclast differentiation / positive regulation of odontoblast differentiation / positive regulation of keratinocyte migration / cellular response to L-leucine / Amino acids regulate mTORC1 / MTOR signalling / cellular response to nutrient / regulation of autophagosome assembly / cellular response to methionine / Energy dependent regulation of mTOR by LKB1-AMPK / energy reserve metabolic process / negative regulation of cell size / ruffle organization / positive regulation of osteoclast differentiation / cellular response to osmotic stress / protein serine/threonine kinase inhibitor activity / enzyme-substrate adaptor activity / negative regulation of protein localization to nucleus / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of actin filament polymerization / regulation of cell size / negative regulation of macroautophagy / positive regulation of oligodendrocyte differentiation / lysosome organization / Macroautophagy / positive regulation of myotube differentiation / protein kinase activator activity / behavioral response to pain / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / mTORC1-mediated signalling / germ cell development / : / CD28 dependent PI3K/Akt signaling / social behavior / HSF1-dependent transactivation / neuronal action potential / positive regulation of TOR signaling / response to amino acid / TOR signaling / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / regulation of macroautophagy / positive regulation of translational initiation / positive regulation of G1/S transition of mitotic cell cycle / cellular response to nutrient levels / positive regulation of lamellipodium assembly / phagocytic vesicle / heart morphogenesis / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / phosphorylation / cardiac muscle contraction / regulation of cellular response to heat / translation repressor activity / negative regulation of translational initiation / positive regulation of stress fiber assembly / cytoskeleton organization / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / T cell costimulation / translation initiation factor binding / cellular response to amino acid starvation / cellular response to starvation / post-embryonic development / positive regulation of glycolytic process / negative regulation of autophagy / positive regulation of mitotic cell cycle / protein serine/threonine kinase activator activity / response to nutrient / response to nutrient levels / VEGFR2 mediated vascular permeability / regulation of signal transduction by p53 class mediator / positive regulation of peptidyl-threonine phosphorylation
類似検索 - 分子機能
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function ...Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / HEAT repeat / HEAT repeat / : / PIK-related kinase, FAT / FAT domain / FATC domain / FAT domain profile. / FATC domain profile. / FATC / FATC domain / PIK-related kinase / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / Serine/threonine-protein kinase mTOR / Eukaryotic translation initiation factor 4E-binding protein 1 / Regulatory-associated protein of mTOR / Target of rapamycin complex subunit LST8
類似検索 - 構成要素
生物種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: 3.23 Å
データ登録者Pavletich, N.P. / Yang, H.
資金援助 米国, 1件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
引用ジャーナル: Nature / 年: 2017
タイトル: Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40.
著者: Haijuan Yang / Xiaolu Jiang / Buren Li / Hyo J Yang / Meredith Miller / Angela Yang / Ankita Dhar / Nikola P Pavletich /
要旨: The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the ...The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the RAPTOR subunit that binds to the Tor signalling sequence (TOS) motif of substrates and regulators. mTORC1 is activated by the small GTPase RHEB (Ras homologue enriched in brain) and inhibited by PRAS40. Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB-mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis. Cancer-associated hyperactivating mutations map to structural elements that maintain the inactive state, and we provide biochemical evidence that they mimic RHEB relieving auto-inhibition. We also present crystal structures of RAPTOR-TOS motif complexes that define the determinants of TOS recognition, of an mTOR FKBP12-rapamycin-binding (FRB) domain-substrate complex that establishes a second substrate-recruitment mechanism, and of a truncated mTOR-PRAS40 complex that reveals PRAS40 inhibits both substrate-recruitment sites. These findings help explain how mTORC1 selects its substrates, how its kinase activity is controlled, and how it is activated by cancer-associated mutations.
履歴
登録2017年10月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年12月20日Provider: repository / タイプ: Initial release
改定 1.12017年12月27日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22018年1月10日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32018年1月17日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42018年10月3日Group: Data collection / Refinement description / カテゴリ: refine
改定 1.52019年11月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.62024年3月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-7087
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
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
A: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
W: Regulatory-associated protein of mTOR
X: Eukaryotic translation initiation factor 4E-binding protein 1
B: Serine/threonine-protein kinase mTOR
E: Target of rapamycin complex subunit LST8
Y: Regulatory-associated protein of mTOR
Z: Eukaryotic translation initiation factor 4E-binding protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)974,02714
ポリマ－972,9158
非ポリマー1,1126
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_5551

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要素

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タンパク質 , 4種, 8分子 ABDEWYXZ

#1: タンパク質 Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR


分子量: 287399.125 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: P42345, non-specific serine/threonine protein kinase
#2: タンパク質 Target of rapamycin complex subunit LST8 / TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 ...TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 protein 8 / mLST8


分子量: 35910.090 Da / 分子数: 2 / Fragment: mLST8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MLST8, GBL, LST8 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9BVC4
#3: タンパク質 Regulatory-associated protein of mTOR / Raptor / p150 target of rapamycin (TOR)-scaffold protein


分子量: 150197.000 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RPTOR, KIAA1303, RAPTOR / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8N122
#4: タンパク質 Eukaryotic translation initiation factor 4E-binding protein 1 / eIF4E-binding protein 1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I


分子量: 12951.344 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EIF4EBP1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q13541

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非ポリマー , 2種, 6分子

#5: 化合物 ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / コメント: ATP, エネルギー貯蔵分子*YM
#6: 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: 4 / 由来タイプ: 合成 / 式: Mg

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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: Dimer of two mTOR-mLST8-RAPTOR-4EBP1 complexes. / タイプ: COMPLEX / Entity ID: #1-#4 / 由来: RECOMBINANT
分子量実験値: NO
由来(天然)生物種: Homo sapiens (ヒト)
由来(組換発現)生物種: Homo sapiens (ヒト)
緩衝液pH: 8
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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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
撮影電子線照射量: 56 e/Å2
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)

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解析

ソフトウェア名称: REFMAC / バージョン: 5.8.0158 / 分類: 精密化
EMソフトウェア
ID名称バージョンカテゴリ
9REFMACモデル精密化
13RELION2３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C2 (2回回転対称)
3次元再構成解像度: 3.23 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 580768 / 対称性のタイプ: POINT
原子モデル構築プロトコル: AB INITIO MODEL
精密化解像度: 3.23→3.23 Å / Cor.coef. Fo:Fc: 0.859 / SU B: 23.164 / SU ML: 0.172 / ESU R: 0.272
立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射
Rwork0.31946 --
obs0.31946 926567 100 %
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 31.329 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0.45 Å2-0.09 Å2
2--1.79 Å2-0.09 Å2
3----1.11 Å2
精密化ステップサイクル: 1 / 合計: 56580
拘束条件
Refine-IDタイプDev idealDev ideal target数
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01957784
ELECTRON MICROSCOPYr_bond_other_d0.0010.0254296
ELECTRON MICROSCOPYr_angle_refined_deg1.191.95678396
ELECTRON MICROSCOPYr_angle_other_deg0.913125572
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.01757054
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.52723.7252620
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.2121510062
ELECTRON MICROSCOPYr_dihedral_angle_4_deg13.01715424
ELECTRON MICROSCOPYr_chiral_restr0.0670.28906
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02163450
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0211780
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.0963.02128384
ELECTRON MICROSCOPYr_mcbond_other6.0963.02128383
ELECTRON MICROSCOPYr_mcangle_it9.6314.535382
ELECTRON MICROSCOPYr_mcangle_other9.6314.535383
ELECTRON MICROSCOPYr_scbond_it8.0833.3829400
ELECTRON MICROSCOPYr_scbond_other8.0833.3829401
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.3924.83543015
ELECTRON MICROSCOPYr_long_range_B_refined16.01737.71564130
ELECTRON MICROSCOPYr_long_range_B_other16.01737.71564131
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS精密化 シェル解像度: 3→3.078 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rwork0.859 68685 -
Rfree-0 -
obs--100 %
精密化 TLS

手法: refined / Refine-ID: ELECTRON MICROSCOPY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.14370.06730.69970.04740.37433.65150.109-0.06020.01460.03360.13550.01550.64750.1998-0.24451.57070.00220.0571.5328-0.01421.5845190.6454102.386224.9193
20.04980.00930.00650.0020.00090.00640.0781-0.22520.23780.0169-0.0850.02840.12660.01320.00692.64390.0340.10942.59220.10492.2615191.974382.599725.9233
30.54670.87840.46811.44610.76380.4048-0.0071-0.17090.19730.0585-0.07630.13150.0184-0.07920.08342.67590.00190.03252.6078-0.0382.3013206.709467.654524.4136
40.0140.0007-0.00230.00020.00130.0125-0.0163-0.0127-0.17260.0190.0044-0.01070.1742-0.00190.01192.4439-0.0913-0.02432.0754-0.01122.1623228.448974.886726.1057
58.3137-2.7812-1.6646.47530.32093.39940.02120.2752-0.9799-0.2886-0.3156-0.5920.85570.56520.29441.1890.2235-0.17751.3021-0.06480.826231.962103.079437.1766
65.74960.1823-1.71742.57770.47074.92180.2098-0.2194-0.3726-0.1411-0.0491-0.13690.39170.4543-0.16070.26070.1287-0.0510.10190.02060.1336207.1914119.355955.359
73.71933.26670.05349.6461-4.12244.09020.327-0.03880.1433-0.0927-0.25710.25830.5408-0.4564-0.06990.42860.1283-0.13330.5178-0.17930.2298187.510898.755666.0723
84.3198-3.78531.92466.44480.71752.8347-0.11850.20450.13570.08110.1942-0.62590.09160.3592-0.07570.73070.1270.10250.5980.08390.7744148.553180.311154.2979
97.4541-1.66162.48482.9982-1.00163.1628-0.00760.1361-0.1645-0.1534-0.10360.17040.1775-0.01750.11120.33510.09190.03080.0389-0.03720.2516117.183196.831942.5227
105.797-2.42121.4492.9626-0.65793.53910.27411.1361-0.2754-0.53630.0151-0.0770.17060.3894-0.28920.69150.08670.06440.56550.02870.5485165.198863.287250.2806
111.6557-0.06360.05143.66980.62373.03090.052-0.23930.00050.09940.01110.07120.1921-0.0186-0.06320.12410.1233-0.0440.2183-0.02060.0518165.38964.281592.7885
127.29544.70750.2256.4329-1.14792.20850.0702-0.0527-1.2593-0.7643-0.2591-1.06460.64140.21340.18890.90810.1457-0.01940.8187-0.14370.822205.596964.271275.9074
134.6316-0.7566-0.08373.0342-0.77376.6817-0.0449-0.01370.0456-0.41680.12910.09420.16320.2818-0.08420.68560.12-0.0040.28790.00510.4338201.292986.235476.943
147.7329-0.86990.20091.23090.58662.1786-0.1933-0.6320.16030.0190.0226-0.13330.14760.27420.17070.34930.12710.09020.31940.07540.3379178.107590.4432113.7738
158.30040.52570.85686.36311.60356.49740.02950.54020.3842-0.5538-0.30870.3916-0.1589-0.54960.27920.28560.186-0.12550.3968-0.07460.1439142.929488.178193.1771
166.04831.346-2.22366.1048-4.11155.0338-0.3635-1.6272-1.18320.9640.12130.70880.9128-0.48880.24221.3898-0.24240.2581.39180.13871.1613124.182471.4762108.0996
174.77010.3143-0.37986.9748-1.84275.58050.0618-0.4958-0.40120.4935-0.0314-0.16920.65560.0906-0.03040.61740.0631-0.06040.8142-0.22580.3609162.829129.2775109.7475
182.647-1.7182-0.76645.9145-0.73323.4389-0.0389-0.0039-0.1679-0.1739-0.0665-0.02930.25230.00910.10540.27880.13590.02250.1823-0.03410.037109.986471.756669.3231
196.93440.84350.24647.77280.16956.5132-0.0734-0.3380.26320.43920.0766-0.6164-0.56890.4936-0.00330.23830.105-0.00050.17770.01180.0748105.818296.175273.3644
2010.39611.742-3.29664.1552-1.53171.64180.10590.1821-0.3105-0.0467-0.18470.0870.3561-0.0950.07880.49030.0325-0.03970.2174-0.08380.043381.953695.939773.7187
2111.3815-0.71830.65283.4978-0.37244.3663-0.0527-0.3053-0.29060.09940.14090.18450.1207-0.2935-0.08820.57130.2016-0.07030.1147-0.05880.232457.333994.168781.0044
224.06321.09510.4227.295-2.08468.72680.0768-0.2611-1.4424-0.2515-0.0260.52471.4607-0.9406-0.05081.31950.1447-0.2010.66920.02530.861137.902185.964171.949
235.8935-1.01040.79365.5826-0.15354.782-0.05181.0241.0253-0.4540.02520.0722-0.5913-0.34450.02661.68430.330.07581.04590.27350.570835.7872118.234552.5191
240.3220.0252-0.95580.0086-0.08012.96510.1331-0.0294-0.0099-0.02870.0738-0.0418-0.6285-0.2336-0.20691.6294-0.001-0.0661.5650.01411.5983120.2943131.741124.8442
250.7080.13660.13920.2077-0.70443.04630.1799-0.3546-0.3045-0.00290.04020.00080.0467-0.2139-0.22011.5319-0.0214-0.00821.5618-0.05841.5618118.8462151.520625.8308
260.09170.1029-0.06270.1332-0.07730.0459-0.0406-0.1646-0.20370.025-0.0654-0.13140.01010.03860.1062.6208-0.0424-0.04062.54460.00562.2645104.0109166.371924.3655
270.02030.00180.00210.0005-0.00040.0118-0.0254-0.04990.19930.00980.01930.0254-0.16760.02810.00612.444-0.09690.05522.0425-0.00192.126782.326159.007826.1582
288.4186-2.95881.55566.629-0.52373.2362-0.0230.2440.9509-0.2078-0.29090.5573-0.7087-0.64560.31391.15960.17550.2041.29580.08670.779879.0367130.809737.2767
295.73660.06421.77832.6434-0.45224.86710.2185-0.22530.3594-0.1499-0.04850.1395-0.3657-0.4527-0.170.2550.12830.0620.1052-0.01190.123103.9909114.714855.3741
303.53973.2333-0.00239.77884.13013.99110.2718-0.0157-0.1032-0.0741-0.2278-0.2448-0.51230.4225-0.04410.41560.13380.13310.52220.18540.2267123.5882135.440565.9847
314.5083-4.0557-1.9986.4483-0.53732.9864-0.11580.2093-0.1612-0.00330.16190.6084-0.0569-0.3736-0.0460.74860.1308-0.10590.5855-0.0720.7799162.5911153.781854.305
327.725-1.7836-2.63573.24421.063.2858-0.00120.14120.1893-0.1607-0.1131-0.1825-0.1690.01860.11440.32780.0906-0.02050.03920.0410.2305194.027137.309642.5216
335.8388-2.4615-1.34342.9940.68233.56920.27691.12990.2766-0.54760.01370.0754-0.1477-0.3921-0.29060.69210.0841-0.05030.5596-0.02090.5588145.9687170.835650.2733
341.6469-0.0494-0.07593.658-0.63833.05670.046-0.24820.00310.09790.0107-0.0672-0.19290.0237-0.05660.13190.12650.05190.21690.02980.0488145.8106169.848692.781
357.33024.9561-0.17376.78031.42372.29950.0187-0.1041.2948-0.8271-0.24761.1023-0.6771-0.24270.22890.91890.14120.04780.8060.16620.837105.5852169.85375.9243
364.641-0.76310.17873.06160.87266.5505-0.0534-0.0177-0.0552-0.40540.1266-0.0927-0.1607-0.2871-0.07320.68610.1120.03660.28110.02120.4447109.892147.890476.9598
377.8193-0.8687-0.18721.1961-0.59362.1808-0.1943-0.6333-0.14860.02180.02750.1327-0.1388-0.26840.16690.35460.1328-0.06970.3164-0.06080.3291133.1024143.6874113.7775
388.29310.4846-0.85816.6428-1.6646.48410.00640.5456-0.3886-0.5624-0.2959-0.40920.16540.54510.28950.28040.18910.14150.39640.08650.1462168.2674145.951793.1582
395.73831.34342.51426.22914.13574.6929-0.3932-1.59631.17850.92480.1794-0.7362-0.82180.46870.21381.4459-0.3051-0.24511.4398-0.12761.1602187.0195162.6548108.0666
404.85740.31290.41867.02281.80945.68990.0547-0.49590.4020.5164-0.03040.1765-0.6538-0.0837-0.02440.61860.07410.04050.80890.2140.3408148.2516204.7797109.7236
412.6032-1.71910.78355.91250.69263.4628-0.0361-0.01130.1664-0.1748-0.06420.0314-0.2421-0.0130.10030.27970.1334-0.01630.18320.03880.0365201.2183162.41369.3198
426.98640.9947-0.16147.8021-0.12186.4841-0.0577-0.329-0.28260.44510.0680.60170.5725-0.498-0.01030.2430.10170.00580.1707-0.00450.0721205.34137.993673.4013
4310.41811.67343.32734.10851.48221.67370.10120.18350.2854-0.0381-0.1767-0.0981-0.37650.10080.07550.50060.03110.04070.21780.09210.0454229.2058138.177973.7242
4411.5797-0.6552-0.63123.40660.39974.3156-0.0581-0.32110.27050.07830.1447-0.2-0.12090.2737-0.08670.59380.20510.06960.1140.05730.2135253.8346139.908180.9756
454.18751.0371-0.3827.51571.90718.42450.0838-0.23971.4412-0.2569-0.0112-0.5718-1.41250.9053-0.07271.35990.17040.2010.6646-0.03390.8396273.2678148.048971.8776
465.606-0.8403-0.86035.49120.15264.7032-0.07970.9944-1.0701-0.43620.0471-0.05010.56020.28250.03261.70480.3299-0.07211.0368-0.27030.5896275.2812115.733652.5086
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1A17 - 100
2ELECTRON MICROSCOPY2A101 - 186
3ELECTRON MICROSCOPY3A187 - 275
4ELECTRON MICROSCOPY4A276 - 490
5ELECTRON MICROSCOPY5A497 - 633
6ELECTRON MICROSCOPY6A644 - 786
7ELECTRON MICROSCOPY7A791 - 903
8ELECTRON MICROSCOPY8A933 - 1005
9ELECTRON MICROSCOPY9A1006 - 1222
10ELECTRON MICROSCOPY10A1261 - 1391
11ELECTRON MICROSCOPY11A2241 - 3002
12ELECTRON MICROSCOPY11A2192 - 2228
13ELECTRON MICROSCOPY11A1392 - 1442
14ELECTRON MICROSCOPY12A1443 - 1537
15ELECTRON MICROSCOPY13A1538 - 1677
16ELECTRON MICROSCOPY14A1678 - 2001
17ELECTRON MICROSCOPY15A2002 - 2021
18ELECTRON MICROSCOPY15A2119 - 2191
19ELECTRON MICROSCOPY15A2229 - 2240
20ELECTRON MICROSCOPY16A2022 - 2118
21ELECTRON MICROSCOPY17D8 - 324
22ELECTRON MICROSCOPY18W54 - 270
23ELECTRON MICROSCOPY18W341 - 371
24ELECTRON MICROSCOPY19W271 - 340
25ELECTRON MICROSCOPY19W372 - 406
26ELECTRON MICROSCOPY20W45 - 53
27ELECTRON MICROSCOPY20W407 - 512
28ELECTRON MICROSCOPY20X111 - 118
29ELECTRON MICROSCOPY21W39 - 44
30ELECTRON MICROSCOPY21W513 - 631
31ELECTRON MICROSCOPY21W958 - 970
32ELECTRON MICROSCOPY22W632 - 840
33ELECTRON MICROSCOPY22W950 - 957
34ELECTRON MICROSCOPY23W18 - 38
35ELECTRON MICROSCOPY23W971 - 1331
36ELECTRON MICROSCOPY24B17 - 100
37ELECTRON MICROSCOPY25B101 - 186
38ELECTRON MICROSCOPY26B187 - 275
39ELECTRON MICROSCOPY27B276 - 490
40ELECTRON MICROSCOPY28B497 - 633
41ELECTRON MICROSCOPY29B644 - 786
42ELECTRON MICROSCOPY30B791 - 903
43ELECTRON MICROSCOPY31B933 - 1005
44ELECTRON MICROSCOPY32B1006 - 1222
45ELECTRON MICROSCOPY33B1261 - 1391
46ELECTRON MICROSCOPY34B2241 - 3002
47ELECTRON MICROSCOPY34B2192 - 2228
48ELECTRON MICROSCOPY34B1392 - 1442
49ELECTRON MICROSCOPY35B1443 - 1537
50ELECTRON MICROSCOPY36B1538 - 1677
51ELECTRON MICROSCOPY37B1678 - 2001
52ELECTRON MICROSCOPY38B2002 - 2021
53ELECTRON MICROSCOPY38B2119 - 2191
54ELECTRON MICROSCOPY38B2229 - 2240
55ELECTRON MICROSCOPY39B2022 - 2118
56ELECTRON MICROSCOPY40E8 - 324
57ELECTRON MICROSCOPY41Y54 - 270
58ELECTRON MICROSCOPY41Y341 - 371
59ELECTRON MICROSCOPY42Y271 - 340
60ELECTRON MICROSCOPY42Y372 - 406
61ELECTRON MICROSCOPY43Y45 - 53
62ELECTRON MICROSCOPY43Y407 - 512
63ELECTRON MICROSCOPY43Z111 - 118
64ELECTRON MICROSCOPY44Y39 - 44
65ELECTRON MICROSCOPY44Y513 - 631
66ELECTRON MICROSCOPY44Y958 - 970
67ELECTRON MICROSCOPY45Y632 - 840
68ELECTRON MICROSCOPY45Y950 - 957
69ELECTRON MICROSCOPY46Y18 - 38
70ELECTRON MICROSCOPY46Y971 - 1331

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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

他の情報も見る