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- PDB-5wby: Crystal structure of mTOR(deltaN)-mLST8-PRAS40(beta-strand) complex -

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基本情報

登録情報
データベース: PDB / ID: 5wby
タイトルCrystal structure of mTOR(deltaN)-mLST8-PRAS40(beta-strand) complex
要素
  • Proline-rich AKT1 substrate 1
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8
キーワードTRANSFERASE / WD40 / PRAS40 beta / complex
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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability ...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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / 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 / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / voluntary musculoskeletal movement / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of lysosome organization / Amino acids regulate mTORC1 / cellular response to L-leucine / MTOR signalling / cellular response to nutrient / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / energy reserve metabolic process / ruffle organization / serine/threonine protein kinase complex / negative regulation of cell size / cellular response to methionine / positive regulation of ubiquitin-dependent protein catabolic process / inositol hexakisphosphate binding / cellular response to osmotic stress / negative regulation of TOR signaling / anoikis / negative regulation of protein localization to nucleus / AKT phosphorylates targets in the cytosol / cardiac muscle cell development / protein serine/threonine kinase inhibitor activity / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / positive regulation of actin filament polymerization / regulation of cell size / Macroautophagy / positive regulation of myotube differentiation / protein kinase inhibitor activity / Constitutive Signaling by AKT1 E17K in Cancer / oligodendrocyte differentiation / germ cell development / neurotrophin TRK receptor signaling pathway / behavioral response to pain / TOR signaling / mTORC1-mediated signalling / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / CD28 dependent PI3K/Akt signaling / positive regulation of TOR signaling / response to amino acid / HSF1-dependent transactivation / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to nutrient levels / vascular endothelial cell response to laminar fluid shear stress / positive regulation of lipid biosynthetic process / neuronal action potential / heart morphogenesis / positive regulation of epithelial to mesenchymal transition / regulation of cellular response to heat / positive regulation of lamellipodium assembly / cardiac muscle contraction / regulation of neuron apoptotic process / phagocytic vesicle / positive regulation of stress fiber assembly / negative regulation of TORC1 signaling / T cell costimulation / cytoskeleton organization / endomembrane system / negative regulation of autophagy / cellular response to amino acid starvation / protein serine/threonine kinase activator activity / positive regulation of glycolytic process / cellular response to starvation / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / positive regulation of translation / negative regulation of protein kinase activity / VEGFR2 mediated vascular permeability / post-embryonic development / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / phosphoprotein binding / non-specific protein-tyrosine kinase / cellular response to amino acid stimulus / regulation of cell growth
類似検索 - 分子機能
Proline-rich AKT1 substrate 1 protein / : / Proline-rich AKT1 substrate 1 / Proline-rich AKT1 substrate 1, N-terminal domain / 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 ...Proline-rich AKT1 substrate 1 protein / : / Proline-rich AKT1 substrate 1 / Proline-rich AKT1 substrate 1, N-terminal domain / 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 / : / 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. / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Mainly Beta
類似検索 - ドメイン・相同性
Serine/threonine-protein kinase mTOR / Proline-rich AKT1 substrate 1 / Target of rapamycin complex subunit LST8
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å
データ登録者Pavletich, N.P. / Yang, H.
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6月29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10日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
A: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8
P: Proline-rich AKT1 substrate 1
O: Proline-rich AKT1 substrate 1


分子量 (理論値)分子数
合計 (水以外)362,5116
ポリマ－362,5116
非ポリマー00
水00
1
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
P: Proline-rich AKT1 substrate 1


分子量 (理論値)分子数
合計 (水以外)181,2563
ポリマ－181,2563
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8
O: Proline-rich AKT1 substrate 1


分子量 (理論値)分子数
合計 (水以外)181,2563
ポリマ－181,2563
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)138.926, 163.044, 206.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11B
21A
12B
22A
13B
23A
14B
24A
15B
25A
16B
26A
17B
27A
18B
28A
19B
29A
110B
210A
111B
211A
112B
212A
113B
213A
114B
214A
115B
215A
116B
216A
117D
217C
118P
218O

NCSドメイン領域:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUBA1385 - 144213 - 70
21GLUGLUGLUGLUAC1385 - 144213 - 70
12LEULEUVALVALBA1443 - 150471 - 132
22LEULEUVALVALAC1443 - 150471 - 132
13ASNASNPROPROBA1505 - 1537133 - 165
23ASNASNPROPROAC1505 - 1537133 - 165
14ARGARGGLYGLYBA1538 - 1580166 - 208
24ARGARGGLYGLYAC1538 - 1580166 - 208
15GLUGLUTYRTYRBA1581 - 1605209 - 233
25GLUGLUTYRTYRAC1581 - 1605209 - 233
16ARGARGGLYGLYBA1612 - 1678240 - 306
26ARGARGGLYGLYAC1612 - 1678240 - 306
17VALVALTHRTHRBA1679 - 1734307 - 362
27VALVALTHRTHRAC1679 - 1734307 - 362
18GLUGLULYSLYSBA1735 - 1814363 - 442
28GLUGLULYSLYSAC1735 - 1814363 - 442
19LYSLYSILEILEBA1867 - 1930495 - 558
29LYSLYSILEILEAC1867 - 1930495 - 558
110GLNGLNHISHISBA1931 - 2001559 - 629
210GLNGLNHISHISAC1931 - 2001559 - 629
111SERSERILEILEBA2002 - 2021630 - 649
211SERSERILEILEAC2002 - 2021630 - 649
112LEULEULEULEUBA2022 - 2115650 - 743
212LEULEULEULEUAC2022 - 2115650 - 743
113PROPROGLUGLUBA2116 - 2190744 - 818
213PROPROGLUGLUAC2116 - 2190744 - 818
114ASPASPASPASPBA2191 - 2212819 - 840
214ASPASPASPASPAC2191 - 2212819 - 840
115PROPROPROPROBA2213 - 2241841 - 869
215PROPROPROPROAC2213 - 2241841 - 869
116HISHISTRPTRPBA2242 - 2549870 - 1177
216HISHISTRPTRPAC2242 - 2549870 - 1177
117VALVALVALVALDB8 - 32410 - 326
217VALVALVALVALCD8 - 32410 - 326
118SERSERLYSLYSPE187 - 19678 - 87
218SERSERLYSLYSOF187 - 19678 - 87

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2given(0.999973, -0.007384, 0.000186), (-0.007386, -0.999823, 0.017318), (5.8E-5, -0.017319, -0.99985)-69.721687, -31.5979, -102.920921
3given(1), (1), (1)
4given(0.999676, -0.012174, -0.022333), (-0.011942, -0.999873, 0.01051), (-0.022458, -0.01024, -0.999695)-71.616333, -31.80653, -100.876343
5given(1), (1), (1)
6given(0.999834, -0.006294, -0.017069), (-0.006308, -0.99998, -0.000781), (-0.017064, 0.000889, -0.999854)-70.896301, -33.261791, -100.962967
7given(1), (1), (1)
8given(0.999633, -0.020611, -0.017579), (-0.020801, -0.999726, -0.010739), (-0.017353, 0.011101, -0.999788)-71.454193, -33.158482, -100.762711
9given(1), (1), (1)
10given(0.999792, 0.004595, -0.019854), (0.004865, -0.999896, 0.013548), (-0.01979, -0.013642, -0.999711)-71.016693, -32.98035, -101.174683
11given(1), (1), (1)
12given(0.999847, 0.00743, -0.015861), (0.007578, -0.999928, 0.009288), (-0.015791, -0.009407, -0.999831)-70.589417, -33.776451, -101.101448
13given(1), (1), (1)
14given(0.99977, 0.020708, -0.005645), (0.020927, -0.998899, 0.041993), (-0.004769, -0.042101, -0.999102)-69.571709, -32.41103, -102.542084
15given(1), (1), (1)
16given(0.999949, 0.005613, -0.008454), (0.005913, -0.99934, 0.035846), (-0.008247, -0.035894, -0.999322)-69.747383, -31.27895, -102.332062
17given(1), (1), (1)
18given(0.999991, 0.003362, -0.00258), (0.00342, -0.999736, 0.022699), (-0.002503, -0.022708, -0.999739)-69.431091, -31.621099, -103.195023
19given(1), (1), (1)
20given(0.999986, 0.00479, -0.002046), (0.004825, -0.999835, 0.017532), (-0.001962, -0.017542, -0.999844)-69.400627, -31.935209, -103.386292
21given(1), (1), (1)
22given(0.99996, 0.008668, 0.002178), (0.008613, -0.999672, 0.024131), (0.002386, -0.024111, -0.999706)-69.312927, -31.887529, -103.477966
23given(1), (1), (1)
24given(0.999829, 0.013438, -0.012708), (0.013793, -0.999505, 0.028265), (-0.012322, -0.028436, -0.99952)-69.912338, -31.873739, -102.915489
25given(1), (1), (1)
26given(0.999966, 0.008156, 0.001065), (0.008131, -0.999718, 0.022324), (0.001247, -0.022315, -0.99975)-69.340233, -31.894831, -103.455849
27given(1), (1), (1)
28given(0.999999, 0.001063, 0.000381), (0.001052, -0.999588, 0.028693), (0.000411, -0.028693, -0.999588)-69.293953, -31.25392, -103.345261
29given(1), (1), (1)
30given(0.999959, 0.007712, -0.004753), (0.007873, -0.999364, 0.034765), (-0.004482, -0.034801, -0.999384)-69.590233, -31.381359, -102.991798
31given(1), (1), (1)
32given(0.999949, 0.010037, -0.000649), (0.010048, -0.999736, 0.020651), (-0.000442, -0.020657, -0.999786)-69.316872, -32.359402, -103.135262
33given(1), (1), (1)
34given(0.999955, 0.004915, 0.008095), (0.004914, -0.999988, 0.000132), (0.008095, -9.2E-5, -0.999967)-69.155327, -32.97868, -103.127113
35given(1), (1), (1)
36given(0.998327, -0.03443, 0.04646), (-0.03416, -0.999395, -0.006587), (0.046659, 0.004989, -0.998898)-69.001007, -29.43128, -106.350609

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要素

#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 / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1


分子量: 134865.453 Da / 分子数: 2 / 断片: residues 1376-2549 / 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: 36054.219 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 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9BVC4
#3: タンパク質 Proline-rich AKT1 substrate 1 / 40 kDa proline-rich AKT substrate


分子量: 10336.045 Da / 分子数: 2 / 断片: residues 114-207 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AKT1S1, PRAS40 / プラスミド: pET2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q96B36

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.23 Å3/Da / 溶媒含有率: 66.91 % / Mosaicity: 0.304 °
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: tacsimate

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2014年2月12日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9792 Å / 相対比: 1
反射解像度: 3.1→80 Å / Num. obs: 71263 / % possible obs: 97.2 % / 冗長度: 3.9 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.064 / Rrim(I) all: 0.131 / Χ2: 0.556 / Net I/σ(I): 4.6 / Num. measured all: 278987
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.1140.69271260.8260.3860.7980.55598.5
3.11-3.233.90.4750.8950.2690.550.56598.3
3.23-3.383.70.3380.9380.1990.3950.56896.9
3.38-3.563.90.2490.9640.1410.2880.55897.5
3.56-3.7840.1680.9820.0930.1930.55498.1
3.78-4.0740.110.990.0620.1280.55697.9
4.07-4.483.80.080.9940.0470.0940.5696.3
4.48-5.134.10.0790.9950.0440.0910.55597.2
5.13-6.463.90.070.9960.040.0810.55197.3
6.46-803.90.0330.9980.0190.0380.54194.5

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0189精密化
SCALEPACKデータスケーリング
PDB_EXTRACT3.22データ抽出
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4JSN

4jsn


解像度: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 54.095 / SU ML: 0.436 / 交差検証法: THROUGHOUT / ESU R Free: 0.522 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.27587 1707 2.4 %RANDOM
Rwork0.23287 ---
obs0.2339 69072 82.54 %-
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: 1.1 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 98.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---4.64 Å20 Å2
3---5.54 Å2
精密化ステップサイクル: 1 / 解像度: 3.1→50.01 Å
タンパク質核酸リガンド溶媒全体
原子数22243 0 0 0 22243
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01922757
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220893
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.94130849
X-RAY DIFFRACTIONr_angle_other_deg0.901348454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2952753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15323.9631090
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33154008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.39615157
X-RAY DIFFRACTIONr_chiral_restr0.0640.23386
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024662
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8692.32611045
X-RAY DIFFRACTIONr_mcbond_other2.8692.32611044
X-RAY DIFFRACTIONr_mcangle_it4.8924.64713787
X-RAY DIFFRACTIONr_mcangle_other4.8924.64813788
X-RAY DIFFRACTIONr_scbond_it2.9132.41311712
X-RAY DIFFRACTIONr_scbond_other2.9132.41311713
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.034.77217063
X-RAY DIFFRACTIONr_long_range_B_refined7.81151.85825048
X-RAY DIFFRACTIONr_long_range_B_other7.81151.86325049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-ID数タイプRms dev position (Å)Weight position
1010A419tight positional0.010.05
1111A120tight positional0.010.05
1212A556tight positional0.010.05
1313A439tight positional0.010.05
1414A131tight positional0.010.05
1515A169tight positional0.010.05
1616A1500tight positional0.010.05
1717C1866tight positional0.010.05
1818O58tight positional00.05
11A556medium positional0.010.5
22A627medium positional0.010.5
33A280medium positional0.010.5
44A387medium positional0.010.5
55A226medium positional0.010.5
66A727medium positional0.010.5
77A545medium positional0.010.5
88A816medium positional0.010.5
99A634medium positional0.010.5
1010A710medium positional0.010.5
1111A187medium positional0.010.5
1212A980medium positional0.010.5
1313A744medium positional0.010.5
1414A216medium positional0.010.5
1515A281medium positional0.010.5
1616A2552medium positional0.010.5
1717C2783medium positional0.010.5
1818O110medium positional0.010.5
11A342tight thermal3.1399
22A368tight thermal11.1299
33A195tight thermal12.0299
44A256tight thermal9.999
55A149tight thermal8.3299
66A397tight thermal6.7199
77A332tight thermal3.4399
88A477tight thermal3.599
99A378tight thermal2.4799
1010A419tight thermal2.7299
1111A120tight thermal2.9199
1212A556tight thermal12.5599
1313A439tight thermal4.0999
1414A131tight thermal2.999
1515A169tight thermal2.9399
1616A1500tight thermal3.9899
1717C1866tight thermal4.499
1818O58tight thermal7.5699
11A556medium thermal499
22A627medium thermal10.9899
33A280medium thermal11.0499
44A387medium thermal8.3299
55A226medium thermal10.0399
66A727medium thermal7.8999
77A545medium thermal3.8699
88A816medium thermal4.0999
99A634medium thermal2.9499
1010A710medium thermal3.8599
1111A187medium thermal3.1999
1212A980medium thermal11.3999
1313A744medium thermal3.7799
1414A216medium thermal4.1799
1515A281medium thermal3.2799
1616A2552medium thermal4.6599
1717C2783medium thermal4.8199
1818O110medium thermal7.899
LS精密化 シェル解像度: 3.1→3.18 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.412 54 -
Rwork0.355 2082 -
obs--34.31 %
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

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)
16.91882.2317-1.84.482-1.31525.0370.1887-0.79790.24980.459-0.3951-0.09-0.29850.44080.20640.68320.0299-0.02220.7121-0.17880.433-10.275-6-31.986
26.66370.9826-0.30920.5978-0.6460.8208-0.15-0.1480.55460.2836-0.1816-0.1564-0.43210.28470.33161.30880.0227-0.12011.0591-0.09230.869916.1380.423-25.046
32.3164-0.9105-1.87141.78570.65562.1282-0.0339-0.19440.22690.7175-0.10280.6135-0.154-0.59750.13671.0741-0.03030.05281.4255-0.22540.852412.902-18.662-12.3
44.52291.83831.09461.97130.70230.74340.09830.2456-0.0131-0.00770.0446-0.24790.14920.2465-0.1430.24860.05470.02360.20720.00870.130916.013-45.388-50.556
50.15170.04850.62120.33690.32943.6225-0.08110.31930.0233-0.51690.0145-0.4006-0.7610.51480.06661.1935-0.00920.1281.32030.23941.1276-27.647-43.279-84.499
60.82950.1078-0.01773.6122-0.99390.29960.0663-0.0117-0.172-0.1037-0.03460.2450.0724-0.0368-0.03160.1543-0.03780.01570.2428-0.00140.1669-13.443-27.796-53.928
74.8808-2.94881.42784.591-1.83544.66990.06540.7852-0.0216-0.5389-0.2808-0.0970.2340.37680.21530.8068-0.04110.04170.8006-0.11960.679859.466-27.236-70.954
82.48151.2762-0.58331.6814-1.8712.5736-0.09430.4745-0.497-0.37-0.0991-0.25540.63660.53560.19341.3390.16640.11721.2715-0.08831.079785.834-34.055-77.958
90.1427-0.04940.21570.1444-0.30180.8062-0.08080.1420.2501-0.17740.09190.14860.0395-0.2833-0.01111.3969-0.111-0.12461.6208-0.10481.401782.393-15.676-90.149
103.7748-1.7114-0.74222.31010.48890.73380.0388-0.24590.1722-0.02330.0692-0.1177-0.10230.2729-0.1080.2746-0.0632-0.06430.25650.01030.377185.41412.735-53.459
110.0518-0.00960.12710.2296-0.75613.37540.1392-0.20360.00370.24540.0110.03770.21290.2718-0.15031.49480.14830.16661.47010.01941.297342.07111.386-19.783
120.85180.2838-0.11093.7668-0.92130.2598-0.0026-0.02420.27110.15210.02220.187-0.0946-0.0492-0.01970.15460.04330.02850.2586-0.00710.455756.09-4.941-49.658
132.65950.14940.18324.09950.67943.8167-0.12350.4063-0.0032-0.40860.1485-0.2042-0.09730.0864-0.0250.2035-0.00110.0010.1172-0.0170.0135-1.2369.104-78.44
143.1985-0.0197-0.7113.75840.16053.4878-0.0732-0.7490.00690.68660.0676-0.5158-0.00460.20470.00560.34150.028-0.12240.2790.01590.404268.482-41.74-24.537
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1385 - 1442
2X-RAY DIFFRACTION2B1443 - 1504
3X-RAY DIFFRACTION3B1505 - 1678
4X-RAY DIFFRACTION4B1679 - 2021
5X-RAY DIFFRACTION5B2022 - 2115
6X-RAY DIFFRACTION6B2116 - 2459
7X-RAY DIFFRACTION7A1385 - 1442
8X-RAY DIFFRACTION8A1443 - 1504
9X-RAY DIFFRACTION9A1505 - 1678
10X-RAY DIFFRACTION10A1679 - 2021
11X-RAY DIFFRACTION11A2022 - 2115
12X-RAY DIFFRACTION12A2116 - 2459
13X-RAY DIFFRACTION13D8 - 324
14X-RAY DIFFRACTION13P187 - 196
15X-RAY DIFFRACTION14C8 - 324
16X-RAY DIFFRACTION14O187 - 196

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万見について

-
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

-
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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