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- PDB-6bcu: Cryo-EM structure of the activated RHEB-mTORC1 refined to 3.4 angstrom -

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基本情報

登録情報
データベース: PDB / ID: 6bcu
タイトルCryo-EM structure of the activated RHEB-mTORC1 refined to 3.4 angstrom
要素
  • Eukaryotic translation initiation factor 4E-binding protein 1
  • GTP-binding protein Rheb
  • Regulatory-associated protein of mTOR,Regulatory-associated protein of mTOR
  • Serine/threonine-protein kinase 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


regulation of type B pancreatic cell development / 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 / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of wound healing, spreading of epidermal cells / eukaryotic initiation factor 4E binding ...regulation of type B pancreatic cell development / 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 / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of wound healing, spreading of epidermal cells / eukaryotic initiation factor 4E binding / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / negative regulation of lysosome organization / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / TORC1 complex / voluntary musculoskeletal movement / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of lysosome organization / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / energy reserve metabolic process / cellular response to L-leucine / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / ruffle organization / serine/threonine protein kinase complex / cellular response to methionine / negative regulation of cell size / positive regulation of osteoclast differentiation / positive regulation of ubiquitin-dependent protein catabolic process / inositol hexakisphosphate binding / cellular response to osmotic stress / anoikis / negative regulation of protein localization to nucleus / cardiac muscle cell development / negative regulation of cold-induced thermogenesis / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / small GTPase-mediated signal transduction / Macroautophagy / positive regulation of myotube differentiation / regulation of cell size / positive regulation of actin filament polymerization / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / TOR signaling / behavioral response to pain / mTORC1-mediated signalling / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / protein kinase activator activity / social behavior / protein serine/threonine kinase inhibitor activity / CD28 dependent PI3K/Akt signaling / positive regulation of TOR signaling / HSF1-dependent transactivation / regulation of macroautophagy / enzyme-substrate adaptor activity / positive regulation of G1/S transition of mitotic cell cycle / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / vascular endothelial cell response to laminar fluid shear stress / neuronal action potential / positive regulation of lipid biosynthetic process / cellular response to nutrient levels / regulation of cellular response to heat / positive regulation of lamellipodium assembly / cardiac muscle contraction / phagocytic vesicle / T cell costimulation / positive regulation of stress fiber assembly / translation initiation factor binding / translation repressor activity / positive regulation of endothelial cell proliferation / 14-3-3 protein binding / cytoskeleton organization / negative regulation of translational initiation / positive regulation of TORC1 signaling / endomembrane system / negative regulation of autophagy / negative regulation of insulin receptor signaling pathway / positive regulation of mitotic cell cycle / cellular response to amino acid starvation / cellular response to starvation / positive regulation of glycolytic process
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 / Serine/threonine-protein kinase ATR-like, HEAT repeats / HEAT repeat / HEAT repeat / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Small GTPase, Ras-type / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Small GTPase Ras domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Serine/threonine-protein kinase mTOR / Eukaryotic translation initiation factor 4E-binding protein 1 / GTP-binding protein Rheb / 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: 3.8 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 1.12018年1月17日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22018年1月24日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32018年10月3日Group: Data collection / Refinement description / カテゴリ: refine
改定 1.42019年11月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52024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-7086
  • 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,Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
W: Regulatory-associated protein of mTOR,Regulatory-associated protein of mTOR
X: Eukaryotic translation initiation factor 4E-binding protein 1
S: GTP-binding protein Rheb
B: Serine/threonine-protein kinase mTOR,Serine/threonine-protein kinase mTOR
E: Target of rapamycin complex subunit LST8
Y: Regulatory-associated protein of mTOR,Regulatory-associated protein of mTOR
Z: Eukaryotic translation initiation factor 4E-binding protein 1
R: GTP-binding protein Rheb
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,016,87720
ポリマ－1,014,67110
非ポリマー2,20710
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 , 5種, 10分子 ABDEWYXZSR

#1: タンパク質 Serine/threonine-protein kinase mTOR,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


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 / 細胞株 (発現宿主): HEK293 / 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 / 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,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
#5: タンパク質 GTP-binding protein Rheb / Ras homolog enriched in brain


分子量: 20877.826 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: RHEB, RHEB2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q15382

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非ポリマー , 3種, 10分子

#6: 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
#7: 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: 6 / 由来タイプ: 合成 / 式: Mg
#8: 化合物 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM

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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: active complex / タイプ: COMPLEX / Entity ID: #1-#5 / 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: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 198237 / 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: 3.8→3.8 Å / Cor.coef. Fo:Fc: 0.869 / SU B: 44.652 / SU ML: 0.268 / ESU R: 0.473
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
Rwork0.32438 --
obs0.32438 568359 100 %
溶媒の処理イオンプローブ半径: 0.9 Å / 減衰半径: 0.9 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: 40.812 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-2.13 Å2-0.53 Å2
2--0.63 Å2-0.37 Å2
3---0.87 Å2
精密化ステップサイクル: 1 / 合計: 59662
拘束条件
Refine-IDタイプDev idealDev ideal target数
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01960942
ELECTRON MICROSCOPYr_bond_other_d0.0020.0257194
ELECTRON MICROSCOPYr_angle_refined_deg1.5751.95882676
ELECTRON MICROSCOPYr_angle_other_deg1.1953132344
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.31457444
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.64723.8072758
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.6491510624
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.44515436
ELECTRON MICROSCOPYr_chiral_restr0.0880.29378
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.02166922
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0212376
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_it3.5381.99729926
ELECTRON MICROSCOPYr_mcbond_other3.5371.99729925
ELECTRON MICROSCOPYr_mcangle_it6.2513.98837320
ELECTRON MICROSCOPYr_mcangle_other6.2513.98837321
ELECTRON MICROSCOPYr_scbond_it4.1032.20131016
ELECTRON MICROSCOPYr_scbond_other4.1042.20131003
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other7.324.29945337
ELECTRON MICROSCOPYr_long_range_B_refined10.98978.465132281
ELECTRON MICROSCOPYr_long_range_B_other10.98978.465132279
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS精密化 シェル解像度: 3.43→3.519 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rwork0.741 42011 -
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)
15.93730.15371.08642.6699-0.3123.24280.13250.36980.355-0.3247-0.2679-0.1493-0.10540.29620.13541.34120.25860.04961.2413-0.07120.749146.9129158.456127.2824
25.68490.3073-1.05362.73910.32223.03220.11510.3663-0.3377-0.3278-0.27780.17410.1252-0.34250.16261.32810.242-0.03061.25090.08660.765145.573775.495127.278
33.6538-0.9389-2.80020.44450.93892.39850.0841-0.01291.0731-0.1484-0.03430.31340.0095-0.06-0.04982.09220.25750.11912.11840.23082.3075170.488798.746127.843
47.5742-0.21641.90641.8916-1.61382.7324-0.04770.36670.3762-0.03270.39330.4034-0.07110.2981-0.34571.26140.45470.18311.40820.19210.8548172.531778.857828.7773
56.856-0.0143-3.61246.9333.05053.3321-0.08890.4339-0.90510.2987-0.0922-0.21690.3849-0.43510.1811.34170.284-0.07241.51520.22850.88186.672463.964928.715
67.07925.1268-1.12725.09540.08810.7842-0.1439-0.4491-0.35070.03370.2163-0.5930.09920.3234-0.07251.53680.2174-0.32351.37570.08881.175208.866572.071724.6017
76.2437-2.5258-1.60589.39491.7282.09190.1684-0.3460.03150.2106-0.173-0.61360.36090.38750.00461.06020.1932-0.24561.1265-0.06730.6386213.7838101.289233.3375
85.85970.4463-2.49153.46540.60886.48310.01260.2139-0.5552-0.23260.11740.05110.70410.076-0.130.54450.106-0.06910.2967-0.00480.3941191.1799117.957454.2716
93.61952.1447-0.75779.4413-4.87725.9417-0.2043-0.1144-0.24440.03790.01990.51630.6846-0.76650.18440.99650.1532-0.0310.7233-0.08330.76174.274397.43869.0758
106.1446-3.44962.594611.56270.45184.8709-0.2513-0.04130.2862-0.16940.0644-0.31420.41660.43980.18680.8830.2610.13751.00310.08640.5083146.159581.835957.8133
116.1142-2.66432.30413.731-1.28663.98980.16910.747-0.019-0.4782-0.20040.038-0.01450.37240.03130.71370.19930.07130.63210.06360.3316116.817799.010642.5378
127.394-4.05762.35795.5695-3.04835.97420.68221.2381-0.2505-0.6696-0.4627-0.07490.71980.7431-0.21941.02280.68230.24180.9890.11940.2818163.162564.758254.8258
133.34080.01430.05217.28351.14134.0928-0.0043-0.2750.23530.2613-0.10490.08350.43410.04060.10920.36150.25080.05010.22180.01120.0243156.825963.629296.5528
140.181-0.68910.17494.6313-0.74240.24880.06970.0671-0.22810.19230.0802-0.69020.3338-0.1619-0.14991.76060.1164-0.06991.74050.06111.6888196.54864.414177.28
154.2445-0.2463-0.00263.6941.0157.7026-0.10460.1499-0.1631-0.47930.08010.01090.35790.23840.02451.00360.54230.06070.75280.050.248189.542986.225676.8836
168.7944-1.0513-0.35292.16320.83732.53920.0333-0.84910.13640.1162-0.19830.17410.24650.46930.1650.80330.33570.04770.45320.04210.2624171.445790.6917114.9921
1711.39181.8914-0.5278.4865-0.2448.17180.12890.76830.9284-0.4846-0.23330.756-0.3825-0.86820.10440.39180.3136-0.17610.3314-0.10940.3693135.152788.028795.5483
183.71871.6894-3.65272.4377-0.96174.9605-0.3433-0.6751-0.62410.6438-0.53020.98760.9869-0.63640.87361.3279-0.00770.03611.6613-0.00681.5256115.560870.6637108.7933
196.19381.0194-0.02917.2308-1.40096.0456-0.0124-0.7137-0.6130.76530.0365-0.04460.8108-0.1356-0.02411.28310.22220.13420.8742-0.2050.4651150.064228.5075111.4896
205.648-1.5882-0.34357.4252-0.54045.07860.00240.196-0.6842-0.1039-0.0071-0.07120.76060.21440.00470.44990.2980.09560.22550.05120.124106.133272.292166.5201
219.11771.86891.30279.38541.36039.9255-0.0158-0.67670.46290.58410.0836-0.5453-0.81850.3179-0.06790.33750.18910.03410.27290.01640.0929100.843696.477671.227
2213.28572.6444-0.10436.7827-0.95752.773-0.0202-0.053-0.4559-0.0058-0.24610.16780.4696-0.61090.26630.37940.19770.01830.5049-0.09290.183177.242995.898167.7659
2310.4098-0.39661.2435.0529-0.34264.6825-0.022-0.2391-0.59380.01520.14310.37710.3276-0.5483-0.12110.69090.205-0.08460.7171-0.01790.581151.733693.307670.8833
241.92761.4852-0.10176.0838-2.81184.4344-0.21280.1684-1.4941-0.44220.0324-0.01331.3285-1.09760.18041.7058-0.0401-0.08291.6321-0.30341.879434.121285.360658.3115
255.7132-0.73730.31744.65040.23242.9758-0.20060.80780.6575-0.57690.08770.4829-0.4227-0.35760.11292.04350.37240.03111.77340.29011.112734.2452118.628340.517
264.9085-0.59383.30870.4149-0.6912.48750.1432-0.1333-1.3454-0.24980.0108-0.56780.0956-0.0067-0.1542.14010.3044-0.10222.1397-0.26162.2029122.0209135.23127.839
277.95870.0006-2.18861.11211.57563.62480.00580.3427-0.3878-0.05890.3394-0.35740.102-0.3774-0.34521.28410.4578-0.13531.4065-0.17620.8705119.9685155.118928.7687
287.6938-0.23613.79996.7051-3.07933.2407-0.15160.47710.93460.3792-0.04560.1938-0.3130.44560.19721.30880.27960.10091.5208-0.22080.8945105.8197170.004528.7051
297.03244.96391.15824.7565-0.0420.8058-0.1386-0.41510.3319-0.00610.22090.587-0.0515-0.2748-0.08231.50360.21320.3221.3523-0.04851.154483.6289161.885324.5977
306.4512-2.56781.35249.2824-1.70512.03910.2028-0.3325-0.03120.1642-0.17480.642-0.3655-0.4454-0.0281.05130.16320.27871.12650.09210.632278.7292132.668333.3419
316.40270.53512.79353.5479-0.52056.6097-0.00170.18930.5921-0.24190.094-0.059-0.6939-0.0936-0.09230.54620.10450.13480.2920.05290.3796101.3492116.02154.2757
323.90332.14190.56679.17624.6526.348-0.2229-0.11560.236-0.0008-0.0135-0.4917-0.73690.73410.23640.99430.16430.06040.72110.1090.7547118.2443136.550569.072
335.7594-3.2315-2.949211.1408-0.28675.2777-0.2394-0.0761-0.2692-0.16580.05910.2668-0.3595-0.40060.18030.86740.2579-0.10620.9975-0.04960.5356146.3555152.140657.817
345.7893-2.582-2.24753.69561.24263.92050.13780.6985-0.0074-0.4513-0.1645-0.02630.0491-0.34180.02670.70660.202-0.00490.6419-0.02430.3388175.7074134.972942.5397
355.8107-2.9529-1.30264.66821.73084.43240.41140.89860.2891-0.5041-0.22460.1057-0.4386-0.5083-0.18680.91790.5149-0.12270.9228-0.07310.3285129.3553169.228354.8256
363.28070.0682-0.14527.2334-1.19574.0829-0.0067-0.2732-0.2280.2735-0.1046-0.0671-0.4316-0.03460.11130.36640.25220.00620.22050.03170.0194135.7025170.364896.5504
370.2179-0.8171-0.19814.76330.72210.2380.08810.03380.2130.15830.08450.7086-0.32550.1514-0.17251.75280.13640.08691.764-0.02141.698495.972169.566377.2851
384.2681-0.2627-0.04673.8025-0.9087.5143-0.10660.11810.152-0.50840.0693-0.0305-0.3181-0.23770.03731.01050.5398-0.01140.744-0.01910.2634102.9824147.757176.8885
398.5657-1.05680.38712.2012-0.82532.45150.046-0.8344-0.12250.123-0.2133-0.1646-0.1913-0.44790.16730.79150.32620.00340.4574-0.00120.2715121.0883143.2982114.9945
4011.42281.93290.77228.81680.16898.09360.13910.7866-0.9571-0.4778-0.2359-0.71840.37350.86870.09680.39430.3240.24640.34260.14560.3518157.3788145.967995.5435
413.99891.55433.51822.74610.57314.0146-0.3775-0.66970.71820.5852-0.579-1.0901-0.93250.43240.95651.3494-0.04420.05831.66690.07841.4669176.9663163.3353108.7844
426.20551.00640.02627.34871.48696.1269-0.0394-0.68610.5920.76980.03150.0563-0.79360.16080.00791.28330.2227-0.09180.87050.2480.4572142.4369205.4549111.4825
435.5958-1.61070.3027.33890.61725.0074-0.02650.18830.6804-0.09680.01220.0766-0.7657-0.21940.01430.44970.2954-0.05960.2308-0.02630.1118186.41161.719366.5228
449.06852.0603-1.26179.2605-1.37449.8203-0.025-0.6707-0.45580.54940.06540.53440.8369-0.3135-0.04040.34120.18170.01840.26450.01590.098191.6858137.532571.2367
4513.14332.70210.10387.04010.98823.0929-0.0035-0.06330.4461-0.0136-0.2638-0.1547-0.5010.59530.26730.37490.20990.02660.50170.12240.183215.2852138.09467.7683
4610.5267-0.5235-1.09975.03970.45475.0409-0.0493-0.22430.5939-0.0180.1402-0.3969-0.30680.5424-0.09090.69360.21060.11510.72140.03460.5622240.7947140.665270.8771
471.89681.72160.41476.3332.51433.847-0.27060.17061.4117-0.3871-0.02150.0232-1.31771.05960.29211.6784-0.02440.0941.64210.2931.7883258.4069148.592258.2965
485.5552-0.6272-0.34214.4542-0.17352.8552-0.23390.7904-0.6863-0.52040.1371-0.47060.42190.29590.09692.07950.3907-0.0071.7712-0.27281.141258.2524115.316740.516
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1R4 - 202
2ELECTRON MICROSCOPY2S4 - 202
3ELECTRON MICROSCOPY3A17 - 100
4ELECTRON MICROSCOPY4A101 - 186
5ELECTRON MICROSCOPY5A187 - 275
6ELECTRON MICROSCOPY6A276 - 490
7ELECTRON MICROSCOPY7A497 - 633
8ELECTRON MICROSCOPY8A644 - 786
9ELECTRON MICROSCOPY9A791 - 903
10ELECTRON MICROSCOPY10A933 - 1005
11ELECTRON MICROSCOPY11A1006 - 1222
12ELECTRON MICROSCOPY12A1261 - 1391
13ELECTRON MICROSCOPY13A2241 - 3002
14ELECTRON MICROSCOPY13A2192 - 2228
15ELECTRON MICROSCOPY13A1392 - 1442
16ELECTRON MICROSCOPY14A1443 - 1537
17ELECTRON MICROSCOPY15A1538 - 1677
18ELECTRON MICROSCOPY16A1678 - 2001
19ELECTRON MICROSCOPY17A2002 - 2021
20ELECTRON MICROSCOPY17A2119 - 2191
21ELECTRON MICROSCOPY17A2229 - 2240
22ELECTRON MICROSCOPY18A2022 - 2118
23ELECTRON MICROSCOPY19D8 - 324
24ELECTRON MICROSCOPY20W54 - 270
25ELECTRON MICROSCOPY20W341 - 371
26ELECTRON MICROSCOPY21W271 - 340
27ELECTRON MICROSCOPY21W372 - 406
28ELECTRON MICROSCOPY22W45 - 53
29ELECTRON MICROSCOPY22W407 - 512
30ELECTRON MICROSCOPY22X111 - 118
31ELECTRON MICROSCOPY23W39 - 44
32ELECTRON MICROSCOPY23W513 - 631
33ELECTRON MICROSCOPY23W958 - 970
34ELECTRON MICROSCOPY24W632 - 840
35ELECTRON MICROSCOPY24W950 - 957
36ELECTRON MICROSCOPY25W18 - 38
37ELECTRON MICROSCOPY25W971 - 1331
38ELECTRON MICROSCOPY26B17 - 100
39ELECTRON MICROSCOPY27B101 - 186
40ELECTRON MICROSCOPY28B187 - 275
41ELECTRON MICROSCOPY29B276 - 490
42ELECTRON MICROSCOPY30B497 - 633
43ELECTRON MICROSCOPY31B644 - 786
44ELECTRON MICROSCOPY32B791 - 903
45ELECTRON MICROSCOPY33B933 - 1005
46ELECTRON MICROSCOPY34B1006 - 1222
47ELECTRON MICROSCOPY35B1261 - 1391
48ELECTRON MICROSCOPY36B2241 - 3002
49ELECTRON MICROSCOPY36B2192 - 2228
50ELECTRON MICROSCOPY36B1392 - 1442
51ELECTRON MICROSCOPY37B1443 - 1537
52ELECTRON MICROSCOPY38B1538 - 1677
53ELECTRON MICROSCOPY39B1678 - 2001
54ELECTRON MICROSCOPY40B2002 - 2021
55ELECTRON MICROSCOPY40B2119 - 2191
56ELECTRON MICROSCOPY40B2229 - 2240
57ELECTRON MICROSCOPY41B2022 - 2118
58ELECTRON MICROSCOPY42E8 - 324
59ELECTRON MICROSCOPY43Y54 - 270
60ELECTRON MICROSCOPY43Y341 - 371
61ELECTRON MICROSCOPY44Y271 - 340
62ELECTRON MICROSCOPY44Y372 - 406
63ELECTRON MICROSCOPY45Y45 - 53
64ELECTRON MICROSCOPY45Y407 - 512
65ELECTRON MICROSCOPY45Z111 - 118
66ELECTRON MICROSCOPY46Y39 - 44
67ELECTRON MICROSCOPY46Y513 - 631
68ELECTRON MICROSCOPY46Y958 - 970
69ELECTRON MICROSCOPY47Y632 - 840
70ELECTRON MICROSCOPY47Y950 - 957
71ELECTRON MICROSCOPY48Y18 - 38
72ELECTRON MICROSCOPY48Y971 - 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