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- PDB-3sd0: Identification of a Glycogen Synthase Kinase-3b Inhibitor that At... -

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基本情報

登録情報
データベース: PDB / ID: 3sd0
タイトルIdentification of a Glycogen Synthase Kinase-3b Inhibitor that Attenuates Hyperactivity in CLOCK Mutant Mice
要素Glycogen synthase kinase-3 beta
キーワードTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
機能・相同性
機能・相同性情報


regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation ...regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / tau-protein kinase / CRMPs in Sema3A signaling / heart valve development / regulation of microtubule-based process / regulation of protein export from nucleus / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Maturation of nucleoprotein / cellular response to interleukin-3 / Wnt signalosome / negative regulation of protein localization to nucleus / negative regulation of TOR signaling / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of cell-matrix adhesion / regulation of axon extension / G protein-coupled dopamine receptor signaling pathway / negative regulation of phosphoprotein phosphatase activity / regulation of dendrite morphogenesis / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity / glycogen metabolic process / ER overload response / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / NF-kappaB binding / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cellular response to retinoic acid / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / excitatory postsynaptic potential / positive regulation of protein export from nucleus / positive regulation of GTPase activity / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / peptidyl-threonine phosphorylation / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / positive regulation of protein-containing complex assembly / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / tau protein binding / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / beta-catenin binding / circadian rhythm / positive regulation of protein catabolic process / cellular response to amyloid-beta / Regulation of RUNX2 expression and activity / neuron projection development / positive regulation of neuron apoptotic process / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / presynapse / insulin receptor signaling pathway / negative regulation of neuron projection development / kinase activity
類似検索 - 分子機能
Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Chem-TSK / Glycogen synthase kinase-3 beta
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: 2.7 Å
データ登録者Mesecar, A.M. / Walters, R.L.
引用ジャーナル: To be Published
タイトル: Identification of a Glycogen Synthase Kinase-3b Inhibitor that Attenuates Hyperactivity in CLOCK Mutant Mice
著者: Mesecar, A.M. / Walters, R.L.
履歴
登録2011年6月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02011年8月3日Provider: repository / タイプ: Initial release
改定 1.12024年2月28日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)81,1156
ポリマ－79,6062
非ポリマー1,5094
水5,116284
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Glycogen synthase kinase-3 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,5573
ポリマ－39,8031
非ポリマー7552
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
B: Glycogen synthase kinase-3 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,5573
ポリマ－39,8031
非ポリマー7552
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)88.505, 96.010, 124.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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要素

#1: タンパク質 Glycogen synthase kinase-3 beta / GSK-3 beta


分子量: 39802.793 Da / 分子数: 2 / 断片: UNP residues 35-384 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GSK3B
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P49841, tau-protein kinase
#2: 化合物 ChemComp-TSK / 3-(5-fluoro-6-iodo-1-methyl-1H-indol-3-yl)-4-(7-methoxy-1-benzofuran-3-yl)-1H-pyrrole-2,5-dione


分子量: 516.260 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C22H14FIN2O4
#3: 化合物 ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


分子量: 238.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H18N2O4S / コメント: pH緩衝剤*YM
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 284 / 由来タイプ: 天然 / 式: H2O

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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: 3.32 Å3/Da / 溶媒含有率: 62.9 %

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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: 22-ID
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD
放射モノクロメーター: double crystal Si (111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長相対比: 1
反射解像度: 2.7→50 Å / Num. all: 29833 / Num. obs: 29057 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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解析

ソフトウェア
名称バージョン分類NB
REFMAC5.2.0019精密化
PDB_EXTRACT3.1データ抽出
SERGUIデータ収集
精密化構造決定の手法: 分子置換 / 解像度: 2.7→44.95 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 22.235 / SU ML: 0.238 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.636 / ESU R Free: 0.328 / 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
Rfree0.254 1473 5.1 %RANDOM
Rwork0.1786 ---
obs0.1786 28995 97.36 %-
all-27522 --
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: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータBiso max: 147.24 Å2 / Biso mean: 57.1652 Å2 / Biso min: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.65 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→44.95 Å
タンパク質核酸リガンド溶媒全体
原子数5592 0 90 284 5966
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225833
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9977948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74323.02255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95415964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3811546
X-RAY DIFFRACTIONr_chiral_restr0.1040.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024428
X-RAY DIFFRACTIONr_nbd_refined0.2430.22878
X-RAY DIFFRACTIONr_nbtor_refined0.3240.23987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2322
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.210
X-RAY DIFFRACTIONr_mcbond_it0.6471.53533
X-RAY DIFFRACTIONr_mcangle_it1.1925741
X-RAY DIFFRACTIONr_scbond_it2.04132565
X-RAY DIFFRACTIONr_scangle_it3.0274.52207
LS精密化 シェル解像度: 2.7→2.769 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.337 89 -
Rwork0.261 1952 -
all-2041 -
obs--93.84 %
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)
117.3214-6.2725-0.588813.13336.65778.71280.12910.17930.67060.3033-0.4707-0.08430.0801-0.56920.34160.1817-0.09810.0037-0.04670.06720.03813.4126-56.2976-19.0094
22.42960.559-1.560524.05084.39824.87760.0929-0.437-0.1210.4376-0.0953-0.20550.4619-0.28690.00240.0879-0.1224-0.04230.33920.0074-0.10744.9384-55.2842-17.5266
310.18692.2779-1.4743.41421.62553.31440.5061-0.34550.43710.2665-0.04280.441-0.4345-0.2104-0.46330.0325-0.0120.00190.0887-0.12280.09046.7214-46.3566-16.036
44.97410.77722.14876.43830.27726.61360.15070.67920.3442-1.3077-0.0424-0.5364-0.19450.8465-0.10830.1296-0.03420.02850.06660.01020.138313.404-49.3347-29.4258
59.87226.7527-12.17384.6189-8.327115.01210.15320.4751-0.6182-0.57840.2731-0.46560.8578-0.1954-0.42640.084-0.0172-0.0750.0837-0.05230.172320.3782-54.3386-25.4619
64.7820.05032.70990.74850.56991.92760.2924-0.5932-0.59150.3405-0.1571-0.00570.1566-0.0385-0.13520.1133-0.0666-0.01960.11180.00980.130917.3332-54.877-15.0469
79.51332.8431-3.785512.5233-9.27719.4236-0.71911.57931.0955-0.69620.98830.776-0.5072-1.6411-0.26920.1628-0.0831-0.03940.20.07860.10725.4171-47.9768-34.2383
83.68653.60193.56663.77424.29136.00190.0133-0.60420.5348-0.0915-0.28010.5242-0.3876-0.37980.26690.0929-0.0053-0.00130.1208-0.12770.228114.7325-40.7608-12.9964
910.2508-17.655811.117842.6551-11.570916.7482-0.9801-0.27550.49380.640.57290.0399-1.2868-0.5810.40720.0168-0.12910.12720.153-0.08080.035224.2205-29.43770.2734
101.01840.41251.04841.52550.47571.08130.0733-0.1939-0.06470.287-0.1228-0.16510.1531-0.14540.04950.1415-0.0398-0.00630.13470.00230.066529.9474-47.4815-11.0187
113.94940.0928-1.96792.81820.57317.76770.1182-0.18790.03160.2016-0.10920.22090.0589-0.4908-0.0090.0888-0.0408-0.03170.1164-0.03830.087824.1261-44.432-14.632
127.36050.55632.68162.8621-2.03523.8164-0.1369-0.209-0.2793-0.12190.01920.3360.06260.12750.11760.13720.008-0.01610.08140.00780.056131.58-40.7989-28.6751
131.38321.122.28880.27234.12090.09480.139-0.0334-0.0715-0.0325-0.405-0.10420.219-0.06230.1427-0.0002-0.02160.1148-0.02520.066736.0982-36.4417-24.6521
141.0270.4895-0.15910.2352-0.01551.93740.056-0.04220.12880.0681-0.115-0.0272-0.2876-0.10760.0590.11370.0148-0.01270.1111-0.0390.089834.553-31.2686-15.8117
152.05180.21910.39881.31543.37978.6970.0118-0.0134-0.0419-0.1124-0.0642-0.3512-0.16080.29710.05230.09290.01370.01540.09310.0090.139848.0881-32.9673-25.5994
165.5764-0.108-4.67030.1172.482753.69450.13720.15930.1455-0.0445-0.0727-0.1071-2.36552.0431-0.06450.194-0.1072-0.0454-0.01880.07080.094847.13-24.5969-16.1914
171.83460.2515-0.59651.33070.78194.22750.0773-0.15260.07480.3108-0.1758-0.05960.0365-0.14980.09850.1141-0.0215-0.07440.1386-0.00630.089639.9331-37.9705-5.3975
183.0948-3.3936-5.4816.4784.200210.8956-0.224-0.5658-0.55010.48490.20120.70280.0543-0.93690.02280.212-0.30970.12710.24360.09750.046825.2201-45.96528.3444
191.81691.05-3.50940.9513-1.25028.53470.2753-0.7386-0.7866-0.1459-0.4679-0.15490.43150.6270.19260.1201-0.0509-0.0260.08640.05930.10835.5983-56.4803-3.9075
2039.932234.505313.29441.2306-6.039631.33791.4107-2.1397-5.0442.1757-0.145-1.66160.2495-0.3572-1.26570.3693-0.221-0.13310.26280.30940.103933.7304-58.54428.6708
216.41711.6238-1.04817.4199-0.280815.8216-0.0033-0.20440.59890.4455-0.33360.67520.2305-0.9610.3369-0.0817-0.02080.08080.0451-0.00090.346843.22094.7369-23.2858
2218.35543.7238-13.11486.40670.42218.1084-0.17560.86760.5501-0.6791-0.0660.3625-0.1194-0.59630.24160.085-0.0677-0.0677-0.02190.02830.321244.98675.904-26.8247
235.98780.49310.526312.54223.00393.05960.4436-0.61550.33951.1245-0.88840.6117-0.0169-0.48660.4448-0.0031-0.11450.13990.1987-0.22020.221934.075-1.5946-20.9981
2410.9755-4.28933.91514.6757-3.69865.84360.53010.5015-0.80850.1535-0.5358-0.51640.82390.90470.00570.1302-0.0264-0.03320.0253-0.02390.051144.9179-9.6907-24.6492
251.58183.96412.50423.39620.14166.75870.44320.4694-0.0626-0.0179-0.4679-1.2010.01440.48940.02470.05510.01860.07980.0380.03780.102945.2271-10.5916-33.8654
265.83982.21683.76631.12970.56185.0432-0.30960.36840.232-0.36380.17080.0506-0.68740.11740.13880.1179-0.01440.0879-0.01320.00690.238138.1006-2.5122-35.288
274.9206-5.44910.964819.9914-18.35327.1970.4496-2.0262-0.3372.2584-0.1258-0.8843-0.4203-0.3438-0.32370.258-0.1581-0.04770.38440.04810.134249.2694-7.8376-15.7612
2822.30683.38543.59280.53820.54310.57890.5795-1.01090.76830.176-0.51740.2245-0.1745-0.4766-0.06210.04490.01620.06340.1669-0.07490.311932.5292-3.6318-27.4426
2931.4549-6.0964-13.0189.3355-3.33899.6019-0.0343-0.787-0.87210.7874-0.03740.4691-0.5952-0.25160.07170.14540.0229-0.03330.0947-0.05250.07113.7293-12.885-26.5118
301.18970.17731.4452.5840.49751.78620.0947-0.08890.4625-0.1764-0.0440.48460.0311-0.1777-0.05070.08110.0497-0.01210.0630.03060.174219.6495-10.1696-41.1093
315.7235-3.6241-0.89514.40630.03262.1703-0.0530.06890.3727-0.03580.051-0.0619-0.0828-0.19260.0020.0777-0.0043-0.00530.07390.00270.159228.9234-10.8893-36.256
3212.2371-11.6109-7.036411.55247.620510.72430.5110.84950.4294-0.4381-0.4323-0.46780.5158-0.0846-0.07870.12030.00780.04350.11520.05660.143641.1737-19.9199-39.2612
331.17150.03550.69472.0168-0.25430.44960.0653-0.0314-0.0543-0.0442-0.03910.04980.0975-0.062-0.02620.14730.0382-0.00540.1267-0.01460.089326.1689-27.278-35.2212
347.4982-3.9031.85915.16840.54765.69680.34120.8073-0.4188-0.6172-0.3120.14990.510.291-0.02920.15990.0317-0.04230.0607-0.08910.07228.0731-39.3001-43.5478
3511.3449-7.89163.755810.6553-1.72574.15020.2782-0.0366-1.0848-0.5421-0.05532.04110.3015-0.7228-0.22290.0002-0.0608-0.04180.04170.01950.213813.1667-33.5017-40.6743
3630.6891-0.6949-2.10566.09940.46010.17240.93090.0745-0.2159-1.0501-0.62110.5451-0.0872-0.0806-0.30980.13910.1054-0.06810.1839-0.01730.026614.4902-21.0808-47.1534
370.13410.3877-0.39077.09430.1121.3966-0.0520.37180.2532-0.8720.2584-0.00720.0843-0.2535-0.20640.16450.0603-0.03750.1393-0.01870.026826.4235-25.4753-47.6304
3813.6516-1.8097-0.74557.09653.69441.92620.21191.17130.8821-0.922-0.37030.0691-0.1081-0.11080.15840.18560.0689-0.0720.09140.14350.086318.7618-13.9002-50.6706
397.8436-2.637-3.47923.09432.67133.77840.25650.61061.1424-0.6903-0.0923-0.1243-0.2353-0.1205-0.16420.14130.0851-0.00240.02060.20060.108622.1042-3.9489-50.0582
4025.02617.8624-13.390613.51941.481310.0931-0.30241.69023.4069-2.10132.30340.2787-1.98270.1651-2.0010.50390.32540.02670.19260.46010.173821.818-1.0739-57.1564
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 46
2X-RAY DIFFRACTION2A47 - 62
3X-RAY DIFFRACTION3A63 - 81
4X-RAY DIFFRACTION4A82 - 93
5X-RAY DIFFRACTION5A94 - 102
6X-RAY DIFFRACTION6A103 - 116
7X-RAY DIFFRACTION7A117 - 126
8X-RAY DIFFRACTION8A127 - 145
9X-RAY DIFFRACTION9A146 - 157
10X-RAY DIFFRACTION10A158 - 180
11X-RAY DIFFRACTION11A181 - 209
12X-RAY DIFFRACTION12A210 - 220
13X-RAY DIFFRACTION13A221 - 234
14X-RAY DIFFRACTION14A235 - 270
15X-RAY DIFFRACTION15A271 - 291
16X-RAY DIFFRACTION16A292 - 302
17X-RAY DIFFRACTION17A303 - 343
18X-RAY DIFFRACTION18A344 - 358
19X-RAY DIFFRACTION19A359 - 379
20X-RAY DIFFRACTION20A380 - 384
21X-RAY DIFFRACTION21B35 - 46
22X-RAY DIFFRACTION22B47 - 58
23X-RAY DIFFRACTION23B59 - 80
24X-RAY DIFFRACTION24B81 - 93
25X-RAY DIFFRACTION25B94 - 102
26X-RAY DIFFRACTION26B103 - 116
27X-RAY DIFFRACTION27B117 - 127
28X-RAY DIFFRACTION28B128 - 138
29X-RAY DIFFRACTION29B139 - 150
30X-RAY DIFFRACTION30B151 - 171
31X-RAY DIFFRACTION31B172 - 199
32X-RAY DIFFRACTION32B200 - 211
33X-RAY DIFFRACTION33B212 - 270
34X-RAY DIFFRACTION34B271 - 290
35X-RAY DIFFRACTION35B291 - 308
36X-RAY DIFFRACTION36B309 - 320
37X-RAY DIFFRACTION37B321 - 332
38X-RAY DIFFRACTION38B333 - 341
39X-RAY DIFFRACTION39B342 - 376
40X-RAY DIFFRACTION40B377 - 383

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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://pdbjlvh1.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