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- PDB-4cfe: Structure of full length human AMPK in complex with a small molec... -

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基本情報

登録情報
データベース: PDB / ID: 4cfe
タイトルStructure of full length human AMPK in complex with a small molecule activator, a benzimidazole derivative (991)
要素
  • (5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ...) x 2
  • 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2
キーワードTRANSFERASE / NUCLEOTIDE-BINDING / STAUROSPORINE-BINDING / SERINE/THREONINE-PROTEIN KINASE / ACTIVATOR / CARBOHYDRATE BINDING MODULE (CBM)
機能・相同性
機能・相同性情報


nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / histone H2BS36 kinase activity / cAMP-dependent protein kinase regulator activity / AMP-activated protein kinase activity / lipid droplet disassembly / Lipophagy ...nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / histone H2BS36 kinase activity / cAMP-dependent protein kinase regulator activity / AMP-activated protein kinase activity / lipid droplet disassembly / Lipophagy / regulation of carbon utilization / import into nucleus / nucleotide-activated protein kinase complex / negative regulation of hepatocyte apoptotic process / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / protein kinase regulator activity / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / Nuclear events mediated by NFE2L2 / regulation of glycolytic process / cAMP-dependent protein kinase activity / protein localization to lipid droplet / negative regulation of tubulin deacetylation / AMP binding / Macroautophagy / cholesterol biosynthetic process / lipid biosynthetic process / response to muscle activity / positive regulation of protein kinase activity / positive regulation of macroautophagy / regulation of macroautophagy / fatty acid homeostasis / cellular response to nutrient levels / cellular response to glucose starvation / energy homeostasis / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / negative regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / positive regulation of autophagy / positive regulation of gluconeogenesis / cellular response to calcium ion / regulation of microtubule cytoskeleton organization / positive regulation of glycolytic process / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / regulation of circadian rhythm / ADP binding / autophagy / cellular response to xenobiotic stimulus / Wnt signaling pathway / cytoplasmic stress granule / fatty acid biosynthetic process / rhythmic process / cellular response to prostaglandin E stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / regulation of cell cycle / nuclear speck / ciliary basal body / negative regulation of gene expression / axon / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / dendrite / chromatin binding / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
類似検索 - 分子機能
PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / Kinase associated domain 1, KA1 / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain ...PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / Kinase associated domain 1, KA1 / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / KA1 domain/Ssp2, C-terminal / TATA-Binding Protein / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Immunoglobulin E-set / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-992 / ADENOSINE MONOPHOSPHATE / STAUROSPORINE / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-2 / 5'-AMP-activated protein kinase subunit beta-1
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: 3.023 Å
データ登録者Xiao, B. / Sanders, M.J. / Carmena, D. / Bright, N.J. / Haire, L.F. / Underwood, E. / Patel, B.R. / Heath, R.B. / Walker, P.A. / Hallen, S. ...Xiao, B. / Sanders, M.J. / Carmena, D. / Bright, N.J. / Haire, L.F. / Underwood, E. / Patel, B.R. / Heath, R.B. / Walker, P.A. / Hallen, S. / Giordanetto, F. / Martin, S.R. / Carling, D. / Gamblin, S.J.
引用ジャーナル: Nat.Commun. / 年: 2013
タイトル: Structural Basis of Ampk Regulation by Small Molecule Activators.
著者: Xiao, B. / Sanders, M.J. / Carmena, D. / Bright, N.J. / Haire, L.F. / Underwood, E. / Patel, B.R. / Heath, R.B. / Walker, P.A. / Hallen, S. / Giordanetto, F. / Martin, S.R. / Carling, D. / Gamblin, S.J.
履歴
登録2013年11月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02013年12月25日Provider: repository / タイプ: Initial release
改定 1.12014年1月8日Group: Database references
改定 1.22014年2月12日Group: Data collection / Refinement description
改定 1.32019年5月8日Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
カテゴリ: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
改定 1.42023年12月20日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.52024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
A: 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2
B: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
C: 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2
D: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
E: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
F: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)273,33216
ポリマ－269,4516
非ポリマー3,88010
水55831
1
C: 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2
D: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
F: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,6668
ポリマ－134,7263
非ポリマー1,9405
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15440 Å2
ΔGint-88.9 kcal/mol
Surface area39230 Å2
手法PISA
2
A: 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2
B: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
E: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,6668
ポリマ－134,7263
非ポリマー1,9405
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15770 Å2
ΔGint-90.7 kcal/mol
Surface area40700 Å2
手法PISA
単位格子
Length a, b, c (Å)76.030, 134.141, 140.558
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(0.988, 0.07, 0.135), (0.062, -0.996, 0.062), (0.139, -0.053, -0.989)-175.2662, -10.40475, 1953.21326
2given(0.992, 0.046, 0.12), (0.039, -0.997, 0.064), (0.123, -0.058, -0.991)-160.10246, 0.78274, 1964.40759
3given(0.992, 0.074, 0.098), (0.071, -0.997, 0.034), (0.1, -0.027, -0.995)-139.79034, 13.70968, 1978.54529
4given(0.51, 0.085, 0.856), (-0.147, -0.972, 0.184), (0.848, -0.22, -0.483)-646.41418, -20.43999, 1066.29578
5given(0.994, 0.066, 0.091), (0.062, -0.997, 0.043), (0.094, -0.037, -0.995)-132.96349, 10.07762, 1983.2821
6given(0.987, 0.029, 0.158), (0.017, -0.997, 0.079), (0.16, -0.075, -0.984)-196.08771, -4.3016, 1939.13306
7given(0.985, 0.069, 0.16), (0.053, -0.993, 0.102), (0.166, -0.092, -0.982)-199.09406, -46.87558, 1934.01746

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要素

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タンパク質 , 1種, 2分子 AC

#1: タンパク質 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2 / AMPK SUBUNIT ALPHA-2 / ACETYL-COA CARBOXYLASE KINASE / ACACA KINASE / HYDROXYMETHYLGLUTARYL-COA ...AMPK SUBUNIT ALPHA-2 / ACETYL-COA CARBOXYLASE KINASE / ACACA KINASE / HYDROXYMETHYLGLUTARYL-COA REDUCTASE KINASE / HMGCR KINASE


分子量: 64650.977 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: A 172 THR AND C 172 THR ARE PHOSPHORYLATED. / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌)
参照: UniProt: P54646, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase

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5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ... , 2種, 4分子 BDEF

#2: タンパク質 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1 / AMPK SUBUNIT BETA-1 / AMPKB


分子量: 32448.453 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: B 108 SER AND D 108 SER ARE PHOSPHORYLATED. / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: Q9Y478
#3: タンパク質 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1 / AMPK GAMMA1 / AMPK SUBUNIT GAMMA-1 / AMPKG


分子量: 37626.289 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P54619

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非ポリマー , 4種, 41分子

#4: 化合物 ChemComp-STU / STAUROSPORINE


分子量: 466.531 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C28H26N4O3 / コメント: 抗生剤*YM
#5: 化合物 ChemComp-992 / 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid


分子量: 431.871 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C24H18ClN3O3
#6: 化合物
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


分子量: 347.221 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H14N5O7P / コメント: AMP*YM
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 31 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY
配列の詳細THE 19 RESIDUES (MSHHHHHHSSGLEVLFQGP) AT THE N-TERMINAL OF ALPHA-2 ARE EXPRESSION TAG. THE 16 ...THE 19 RESIDUES (MSHHHHHHSSGLEVLFQGP) AT THE N-TERMINAL OF ALPHA-2 ARE EXPRESSION TAG. THE 16 RESIDUES (MGLNDIFEAQKIEWHE) AT THE N- TERMINAL OF BETA-1 ARE EXPRESSION TAG

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 2.7 Å3/Da / 溶媒含有率: 54 % / 解説: NONE
結晶化手法: 蒸気拡散法, ハンギングドロップ法
詳細: CRYSTALS WERE GROWN BY THE HANGING DROP METHOD WITH RESERVOIR SOLUTION CONTAINING 13% PEG3350, 0.1M MGCL2, 1% GLUCOSE, 0.15% CAPB IN 0.1M IMIDAZOLE AT PH 6.2.

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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: Diamond / ビームライン: I04-1 / 波長: 0.92
検出器タイプ: DECTRIS PIXEL / 検出器: PIXEL
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: 0.92 Å / 相対比: 1
反射解像度: 3.02→30 Å / Num. obs: 50545 / % possible obs: 93.4 % / Observed criterion σ(I): 2 / 冗長度: 2.7 % / Biso Wilson estimate: 96.99 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21
反射 シェル解像度: 3.02→3.21 Å / 冗長度: 2.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 95

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
DENZOデータ削減
SCALEPACKデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRIES 2Y94, 2F15

2y94
PDB 未公開エントリ

2f15


解像度: 3.023→19.914 Å / SU ML: 0.45 / σ(F): 1.35 / 位相誤差: 28.51 / 立体化学のターゲット値: ML
詳細: K SOL IS K_OVERALL B SOL IS B_OVERALL NCS RESIDUES D189-D194 AND B190-D193: INSUFFICIENT ELECTRON DENSITY TO BUILD SIDE CHAINS. PRESENT AS A GUIDE TO VISUALISE THE DIRECTION OF THE LOOP THAT ...詳細: K SOL IS K_OVERALL B SOL IS B_OVERALL NCS RESIDUES D189-D194 AND B190-D193: INSUFFICIENT ELECTRON DENSITY TO BUILD SIDE CHAINS. PRESENT AS A GUIDE TO VISUALISE THE DIRECTION OF THE LOOP THAT LINKS CBM TO REGULATORY FRAGMENT
Rfactor反射数%反射
Rfree0.2529 2550 5.1 %
Rwork0.2176 --
obs0.2194 50545 92 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 27.78 Å2 / ksol: 0.078 e/Å3
原子変位パラメータBiso mean: 78.14 Å2
精密化ステップサイクル: LAST / 解像度: 3.023→19.914 Å
タンパク質核酸リガンド溶媒全体
原子数14021 0 270 31 14322
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00214647
X-RAY DIFFRACTIONf_angle_d0.65319908
X-RAY DIFFRACTIONf_dihedral_angle_d11.5975381
X-RAY DIFFRACTIONf_chiral_restr0.0432255
X-RAY DIFFRACTIONf_plane_restr0.0032444
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0235-3.08140.35981070.36772008X-RAY DIFFRACTION70
3.0814-3.14410.37421590.33862721X-RAY DIFFRACTION95
3.1441-3.21220.31071400.32492803X-RAY DIFFRACTION97
3.2122-3.28660.34011460.31082780X-RAY DIFFRACTION96
3.2866-3.36840.31361450.29732747X-RAY DIFFRACTION97
3.3684-3.4590.32311270.28562867X-RAY DIFFRACTION97
3.459-3.56020.28371510.26252747X-RAY DIFFRACTION96
3.5602-3.67450.30051510.24462754X-RAY DIFFRACTION95
3.6745-3.80490.29231300.24242778X-RAY DIFFRACTION95
3.8049-3.95610.25041450.2252705X-RAY DIFFRACTION94
3.9561-4.13470.24841550.2072618X-RAY DIFFRACTION91
4.1347-4.35050.25091480.19072704X-RAY DIFFRACTION94
4.3505-4.61990.21271460.17962788X-RAY DIFFRACTION95
4.6199-4.97150.21541440.16692768X-RAY DIFFRACTION95
4.9715-5.46240.19281350.17392756X-RAY DIFFRACTION94
5.4624-6.23150.23181430.19332730X-RAY DIFFRACTION94
6.2315-7.77260.24971630.2082622X-RAY DIFFRACTION90
7.7726-19.91440.24531150.22392099X-RAY DIFFRACTION71
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)
13.465-0.41840.04228.93810.63373.9364-0.3024-0.17560.11280.14230.3635-0.2735-0.3834-0.1549-0.04340.41380.16750.05880.520.00590.394484.301433.6773987.0304
23.3131-0.5078-0.50254.00440.30652.7729-0.2402-0.4578-0.39830.41240.50580.66150.0632-0.7833-0.1810.43950.22380.05950.83020.20960.624477.811213.95351002.6531
34.6218-1.54171.38531.89560.94414.92380.11250.2330.3584-1.01810.12120.45550.1357-1.1926-0.20520.8080.0745-0.23140.929-0.03950.6629503.35075.7296995.1052
43.90651.9468-2.04124.76450.85588.6955-0.6049-1.04910.35680.88870.0281.3864-0.3761-0.69920.54140.65080.33530.07540.8167-0.14560.8666509.3225-5.91061025.8088
53.9734-2.3299-1.37833.70441.05710.6906-0.0176-0.4660.6380.62090.0209-0.255-1.189-0.5216-0.11281.3010.4522-0.23880.9484-0.29170.6091501.916128.12521028.2664
67.0244-0.99651.19957.15990.22594.5288-0.5771-0.37790.5520.43520.4646-0.4427-0.5541-0.00490.12440.65160.04-0.11650.51660.13790.6343482.165854.586985.192
71.4359-0.099-0.38640.24470.16130.1793-0.019-0.03810.04080.131-0.03650.09950.0629-0.04050.10421.79210.3265-0.09080.967-0.7711.4686498.621343.23371030.0457
82.0582-0.8466-0.99382.61710.26770.507-0.1423-0.22310.17310.32510.32980.146-0.2395-0.5625-0.23320.75140.4347-0.14180.8047-0.0610.5052502.540313.27961021.1786
96.1543-1.795-1.81594.84341.30545.91580.46341.03150.1622-1.2686-0.37080.1945-1.4698-0.20860.04040.67790.1808-0.09430.58180.04390.4423517.17515.8291001.5163
101.0643-0.57651.02981.9407-2.49374.4746-0.5324-0.45040.23960.57180.1503-0.7067-0.67350.45850.30550.60880.2406-0.18120.73-0.1130.4671523.47747.37641031.9462
116.4380.6575-0.34378.49591.26435.81310.00570.21330.2542-0.1568-0.2068-0.2245-0.31860.45870.13970.41230.1188-0.09370.53070.00950.3822521.22836.39181007.8025
122.41171.42050.16993.43312.29054.40620.05450.4469-1.1148-0.9941-0.0720.14110.74121.1555-0.01270.9640.48630.00111.1437-0.280.898529.7182-13.8854999.9637
136.6625-1.9095-0.31244.7808-0.89474.73080.0368-0.5868-0.61490.29430.13360.2110.85920.0786-0.17470.69590.2728-0.16270.7180.08050.5059523.9025-13.5931028.3817
147.2861-1.2278-0.21586.68270.88194.0401-0.06550.3103-1.3991-0.4443-0.116-0.0571.42720.46640.22330.82180.2435-0.040.5692-0.10220.6039524.5201-14.77721007.9897
152.11750.47890.11458.1297-0.3184.37860.0639-0.3784-0.1685-0.01980.0569-0.4960.49240.2098-0.10980.4121-0.1333-0.1040.75440.05070.4671520.261353.9471047.1633
163.0965-0.3059-0.83764.1627-0.44553.29480.150.33120.2223-0.06340.04040.28070.0034-0.7341-0.14490.2715-0.0763-0.05720.71460.01690.6193514.834671.97391029.737
173.80793.85570.39135.5623-0.36160.37811.5067-0.46030.52291.427-0.21281.4631-1.5333-1.0629-1.07571.10950.26540.40770.86530.08751.1291537.943384.72291036.2363
185.33772.44142.20356.735-1.71126.15890.71321.14931.0193-0.5992-0.61761.6453-1.8587-1.1386-0.06530.79570.33740.06190.89420.06110.8728547.418593.70411013.6911
195.0521.0411.20922.75710.73273.4985-0.321.1209-1.4664-0.67390.1788-0.62910.9977-0.18010.13320.9883-0.19760.32640.7605-0.35521.1614543.077458.3831008.5432
206.17390.367-0.13217.40060.88713.9554-0.63460.1483-0.477-0.3372-0.036-0.93831.56420.73790.53671.16870.12740.24240.82420.27720.8052517.784732.96551051.4788
211.24490.4388-0.21040.7399-1.08311.7733-0.9693-0.28790.92880.25440.0334-0.9795-1.7309-0.09430.90492.01840.2083-0.24870.6573-0.30642.0697542.896842.87261009.7653
226.84023.23450.444.69810.97786.4409-0.15180.7314-0.0706-0.56590.27130.0496-0.0471-0.6559-0.11490.36460.02360.08690.52240.08850.6091541.742973.64061014.8864
238.13151.61811.17536.41840.60498.22360.2975-1.6652-0.25521.2711-0.57190.26651.61320.17290.35870.56530.12650.09180.63250.07280.4394553.694282.72161035.7604
242.60810.7828-0.33716.1162-2.43493.5376-0.65490.4128-0.9616-0.64290.2569-0.88350.40280.43210.34460.4014-0.00620.11650.5774-0.11620.6561563.009380.94351006.0947
254.96812.32780.24132.3296-1.72055.07720.1509-0.5326-0.64380.4566-0.2816-0.2013-0.31050.68080.24140.39760.133-0.02240.58470.11070.5879558.372782.35461029.9699
262.5855-2.7837-1.9544.01112.87724.92190.771-1.24161.23761.25630.37910.2983-1.12351.7141-1.02751.0599-0.36960.14590.998-0.26110.6408564.7731103.24581037.8403
277.02022.19080.68055.68760.91165.82560.03340.31050.94-0.25040.15830.3189-1.2262-0.1389-0.12510.61550.05570.13070.45130.03910.4745562.854101.65141008.6604
282.36741.7183-0.02586.43653.09375.62640.6111-0.74480.9328-0.1302-0.40560.4237-1.3616-0.0103-0.29480.948-0.13350.21320.7025-0.17240.6836560.2954103.61841029.3625
298.24214.28670.07969.8078-7.12596.78250.10530.05011.55332.27350.08380.3249-0.87090.1586-0.11750.88450.30950.01920.7227-0.11510.704526.0024-4.59991018.1393
308.54923.2684.9045.05032.03645.68110.63261.1957-1.7974-0.9229-0.4815-0.45970.3378-1.2923-0.12450.95330.00370.15010.9911-0.27180.9137563.292593.64041019.7403
311.5594-0.5911-1.80921.58141.50552.5932-0.10620.3958-0.15240.0291-0.0701-0.2108-0.212-0.28740.14740.2360.14120.0090.5140.05580.7213476.375427.2711989.1739
325.4833-0.3214-1.58828.67484.8713.1789-0.5194-0.86031.23750.5123-0.57360.50450.5037-1.02661.08790.38050.0001-0.00650.573-0.0980.4952512.299959.58791043.8502
334.8889-0.80336.793.015-1.72489.59870.03320.34570.44930.508-0.91721.4613-0.2937-1.06530.81640.7640.29260.29110.79340.20580.9558477.039442.3623987.9151
343.3966-0.0031-2.0222.1587-0.49832.69320.0520.6291-0.56780.5515-0.76080.0205-0.1783-0.39080.70660.9074-0.3604-0.24421.11390.17470.7728513.081244.65371046.4099
35-0.03430.02140.01020.08660.05810.02270.11970.08640.1994-0.26520.141-0.0949-0.2109-0.00611.2086-0.22860.2068-0.0918-0.314-0.0747-0.1898504.163647.61121011.2281
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 8:100)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 101:276)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 277:346)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 363:376)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 396:551)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 78:173)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 190:193)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 203:270)
9X-RAY DIFFRACTION9(CHAIN E AND RESID 27:47)
10X-RAY DIFFRACTION10(CHAIN E AND RESID 48:122)
11X-RAY DIFFRACTION11(CHAIN E AND RESID 128:183)
12X-RAY DIFFRACTION12(CHAIN E AND RESID 184:203)
13X-RAY DIFFRACTION13(CHAIN E AND RESID 204:274)
14X-RAY DIFFRACTION14(CHAIN E AND RESID 275:325)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 10:100)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 101:276)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 277:346)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 363:373)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 396:551)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 78:170)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 189:194)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 203:270)
23X-RAY DIFFRACTION23(CHAIN F AND RESID 27:47)
24X-RAY DIFFRACTION24(CHAIN F AND RESID 48:121)
25X-RAY DIFFRACTION25(CHAIN F AND RESID 128:183)
26X-RAY DIFFRACTION26(CHAIN F AND RESID 184:203)
27X-RAY DIFFRACTION27(CHAIN F AND RESID 204:274)
28X-RAY DIFFRACTION28(CHAIN F AND RESID 275:325)
29X-RAY DIFFRACTION29(CHAIN E AND RESID 1326:1328)
30X-RAY DIFFRACTION30(CHAIN F AND RESID 1326:1328)
31X-RAY DIFFRACTION31(CHAIN A AND RESID 1552)
32X-RAY DIFFRACTION32(CHAIN C AND RESID 1552)
33X-RAY DIFFRACTION33(CHAIN A AND RESID 1553)
34X-RAY DIFFRACTION34(CHAIN C AND RESID 1553)
35X-RAY DIFFRACTION35((CHAIN A AND RESID 2001:2013) OR (CHAIN B AND RESID 2001:2006) OR (CHAIN C AND RESID 2001:2006) OR (CHAIN D AND RESID 2001) OR (CHAIN E AND RESID 2001:2002) OR (CHAIN F AND RESID 2001:2003)

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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