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- PDB-9eoy: Structure of Thr354Asn, Glu355Gln, Thr412Asn, Ile414Met, Ile464Hi... -

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基本情報

登録情報
データベース: PDB / ID: 9eoy
タイトルStructure of Thr354Asn, Glu355Gln, Thr412Asn, Ile414Met, Ile464His, and Phe467Met mutant human CaMKII alpha hub bound to PIPA
要素Calcium/calmodulin-dependent protein kinase type II subunit alpha
キーワードSIGNALING PROTEIN / CAMKII HUB / OLIGOMER
機能・相同性
機能・相同性情報


peptidyl-threonine autophosphorylation / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / Ca2+/calmodulin-dependent protein kinase / dendritic spine development / negative regulation of hydrolase activity / regulation of neurotransmitter secretion / Trafficking of AMPA receptors / regulation of neuron migration / positive regulation of calcium ion transport ...peptidyl-threonine autophosphorylation / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / Ca2+/calmodulin-dependent protein kinase / dendritic spine development / negative regulation of hydrolase activity / regulation of neurotransmitter secretion / Trafficking of AMPA receptors / regulation of neuron migration / positive regulation of calcium ion transport / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / regulation of mitochondrial membrane permeability involved in apoptotic process / CaMK IV-mediated phosphorylation of CREB / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Long-term potentiation / Regulation of MECP2 expression and activity / regulation of neuronal synaptic plasticity / HSF1-dependent transactivation / glutamate receptor binding / regulation of protein localization to plasma membrane / cellular response to interferon-beta / positive regulation of cardiac muscle cell apoptotic process / Ion homeostasis / Ras activation upon Ca2+ influx through NMDA receptor / response to ischemia / angiotensin-activated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / G1/S transition of mitotic cell cycle / positive regulation of NF-kappaB transcription factor activity / cellular response to type II interferon / long-term synaptic potentiation / endocytic vesicle membrane / Interferon gamma signaling / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium ion transport / Signaling by BRAF and RAF1 fusions / kinase activity / RAF/MAP kinase cascade / Ca2+ pathway / dendritic spine / calmodulin binding / neuron projection / protein phosphorylation / postsynaptic density / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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
類似検索 - ドメイン・相同性
: / ACETATE ION / Calcium/calmodulin-dependent protein kinase type II subunit alpha
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: 2.1 Å
データ登録者Narayanan, D. / Larsen, A.S.G. / Solbak, S.M.O. / Wellendorph, P. / Gee, C.L. / Kastrup, J.S.
資金援助 デンマーク, 米国, 4件
組織認可番号国
LundbeckfondenR277-2018-260 デンマーク
Novo Nordisk FoundationNNF17OC0028664 and NNF21OC0067835 デンマーク
Independent Research Fund Denmark - Technology and Production Sciences1026-00335B デンマーク
Howard Hughes Medical Institute (HHMI) 米国
引用ジャーナル: Protein Sci. / 年: 2024
タイトル: Ligand-induced CaMKII alpha hub Trp403 flip, hub domain stacking, and modulation of kinase activity.
著者: Narayanan, D. / Larsen, A.S.G. / Gauger, S.J. / Adafia, R. / Hammershoi, R.B. / Hamborg, L. / Bruus-Jensen, J. / Griem-Krey, N. / Gee, C.L. / Frolund, B. / Stratton, M.M. / Kuriyan, J. / ...著者: Narayanan, D. / Larsen, A.S.G. / Gauger, S.J. / Adafia, R. / Hammershoi, R.B. / Hamborg, L. / Bruus-Jensen, J. / Griem-Krey, N. / Gee, C.L. / Frolund, B. / Stratton, M.M. / Kuriyan, J. / Kastrup, J.S. / Langkilde, A.E. / Wellendorph, P. / Solbak, S.M.O.
履歴
登録2024年3月15日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年9月25日Provider: repository / タイプ: Initial release

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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: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha
G: Calcium/calmodulin-dependent protein kinase type II subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)109,98516
ポリマ－108,8617
非ポリマー1,1249
水1,838102
1
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha
G: Calcium/calmodulin-dependent protein kinase type II subunit alpha
ヘテロ分子

A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha
G: Calcium/calmodulin-dependent protein kinase type II subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)219,97032
ポリマ－217,72214
非ポリマー2,24818
水25214
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area34130 Å2
ΔGint-247 kcal/mol
Surface area76800 Å2
手法PISA
単位格子
Length a, b, c (Å)103.045, 182.918, 107.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDモデル要素
11A-606-

HOH

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要素

#1: タンパク質
Calcium/calmodulin-dependent protein kinase type II subunit alpha / CaM kinase II subunit alpha / CaMK-II subunit alpha


分子量: 15551.578 Da / 分子数: 7 / 変異: T354N, E355Q, T412N, I414M, I464H, and F467M / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CAMK2A, CAMKA, KIAA0968 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C2H3O2
#3: 化合物 ChemComp-A1H6K / 2-[6-(4-chlorophenyl)imidazo[1,2-b]pyridazin-2-yl]ethanoic acid


分子量: 287.701 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C14H10ClN3O2 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 102 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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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: 2.38 Å3/Da / 溶媒含有率: 48.42 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8
詳細: 500 nL protein + 2.65 mM compound in 25 mM Tris, 150 mM KCl, 10 mM imidazole, 1 mM DTT, 10% glycerol, pH 8.5, 10% DMSO + 1000 nL well solution (11% w/v PEG3350, 300 mM potassium acetate, pH 8. ...詳細: 500 nL protein + 2.65 mM compound in 25 mM Tris, 150 mM KCl, 10 mM imidazole, 1 mM DTT, 10% glycerol, pH 8.5, 10% DMSO + 1000 nL well solution (11% w/v PEG3350, 300 mM potassium acetate, pH 8.0), equilibrated against 50 uL well solution.

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 8.2.2 / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS3 2M / 検出器: PIXEL / 日付: 2019年6月26日
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
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.1→46.48 Å / Num. obs: 59633 / % possible obs: 100 % / 冗長度: 14.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.029 / Rrim(I) all: 0.111 / Χ2: 1.01 / Net I/σ(I): 14.4 / Num. measured all: 885236
反射 シェル解像度: 2.1→2.16 Å / % possible obs: 100 % / 冗長度: 15 % / Rmerge(I) obs: 2.402 / Num. measured all: 68772 / Num. unique obs: 4582 / CC1/2: 0.576 / Rpim(I) all: 0.637 / Rrim(I) all: 2.486 / Χ2: 1.02 / Net I/σ(I) obs: 1.3

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487)精密化
XDSデータ削減
Aimless0.7.4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 / 解像度: 2.1→46.48 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.18 / 位相誤差: 32.25 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2509 3046 5.11 %5
Rwork0.2238 ---
obs0.2252 59590 99.96 %-
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
精密化ステップサイクル: LAST / 解像度: 2.1→46.48 Å
タンパク質核酸リガンド溶媒全体
原子数7501 0 77 102 7680
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0037810
X-RAY DIFFRACTIONf_angle_d0.6410554
X-RAY DIFFRACTIONf_dihedral_angle_d21.0452901
X-RAY DIFFRACTIONf_chiral_restr0.0441073
X-RAY DIFFRACTIONf_plane_restr0.0111391
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.43431260.36632533X-RAY DIFFRACTION100
2.13-2.170.37371290.35362540X-RAY DIFFRACTION100
2.17-2.210.34861480.37162546X-RAY DIFFRACTION100
2.21-2.250.40551620.36852538X-RAY DIFFRACTION100
2.25-2.290.40761010.38382570X-RAY DIFFRACTION100
2.29-2.340.31171300.34372566X-RAY DIFFRACTION100
2.34-2.390.34041380.322547X-RAY DIFFRACTION100
2.39-2.440.32581040.3122556X-RAY DIFFRACTION100
2.44-2.50.34431300.3212567X-RAY DIFFRACTION100
2.5-2.570.36331300.33082557X-RAY DIFFRACTION100
2.57-2.650.34031220.30072570X-RAY DIFFRACTION100
2.65-2.730.34151550.28812532X-RAY DIFFRACTION100
2.73-2.830.31521500.27932553X-RAY DIFFRACTION100
2.83-2.940.3281620.27372530X-RAY DIFFRACTION100
2.94-3.080.25261250.26682600X-RAY DIFFRACTION100
3.08-3.240.27231430.25512558X-RAY DIFFRACTION100
3.24-3.440.24051380.2322573X-RAY DIFFRACTION100
3.44-3.710.23691680.20292545X-RAY DIFFRACTION100
3.71-4.080.22491230.18662621X-RAY DIFFRACTION100
4.08-4.670.18081430.15592612X-RAY DIFFRACTION100
4.67-5.880.1911640.1642599X-RAY DIFFRACTION100
5.88-46.480.22131550.18032731X-RAY DIFFRACTION100
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)
13.1259-1.4682-0.92932.250.1910.3678-0.48670.92880.1656-0.5901-0.1285-1.50870.80770.3337-0.10741.2670.39460.86620.55540.0540.928-30.954-75.6785-29.357
23.73513.25410.74289.67034.60722.4468-0.90151.2381-0.4284-2.33030.8254-0.78460.82421.6393-0.00021.2395-0.14210.20050.95610.02571.0013-24.7643-64.4394-33.6266
32.90280.07252.24159.2331-0.11581.91-0.60630.0756-0.6137-0.05240.3214-0.4780.55110.83470.13320.82040.24220.34370.47640.11140.7008-28.4439-70.0859-21.7018
46.18250.31312.15574.09941.61644.0601-0.12580.3966-0.7158-0.04150.09280.19730.41790.27710.11950.99940.22670.40990.45510.07630.6207-32.5424-75.9396-24.8194
58.08560.49981.20981.00780.97546.5897-0.3316-0.7708-2.12931.4365-0.80931.22432.043-0.65571.03291.4932-0.12620.53950.77420.13031.0299-48.2479-84.3872-10.679
66.91123.06382.74387.4935-2.49847.08810.0893-1.6811-0.2691.6556-0.39150.06891.0924-0.77140.35231.41330.05870.32890.75910.12040.6331-41.9707-75.4215-0.194
71.94930.03212.19931.8872-1.01276.2347-0.7434-0.3554-0.25051.520.11880.20250.23290.07680.59430.83260.2110.15650.46820.10290.5362-36.7015-64.8727-10.9782
89.25992.1757-2.36027.59032.33575.79890.3936-1.05510.28021.3745-0.01380.16710.0062-0.1145-0.29391.32830.19620.30140.8336-0.02690.61-42.3722-65.0334-0.6937
96.2007-0.59511.18570.5078-0.09460.5873-0.1869-2.6220.28090.3445-0.19570.1786-0.1348-0.72550.11171.74380.04120.80991.3119-0.04941.0157-55.3436-64.628-1.449
102.6889-2.9766-1.75427.33885.06583.5595-0.3435-0.836-0.94981.2474-0.02970.9089-0.20280.06040.30291.5534-0.04590.52870.61070.20921.0969-56.0012-74.3777-14.4109
113.7713-1.95460.37024.03241.81073.41150.0644-0.4975-0.87030.7446-0.11380.14710.39260.01350.0690.99260.05560.45030.41860.04540.7237-46.2432-79.0642-16.6993
120.94080.23351.0660.60241.22112.8873-0.2157-0.30280.28990.12260.13230.0418-0.4502-0.34060.19351.57320.08821.04130.9072-0.55651.2914-64.6974-58.0203-11.2622
136.33820.64731.7462.2786-0.66073.38890.2127-0.536-0.3460.6419-0.490.02030.7933-0.057-0.06071.06420.01640.38140.46220.08570.5135-44.3383-76.1649-12.6354
147.73461.30123.04053.6893-2.86234.5206-0.649-1.256-0.77441.4590.93910.1350.1758-1.448-0.30331.16640.20560.39330.64640.14150.695-40.639-75.6265-10.0036
155.34151.3325-0.55594.9014-0.22961.6323-0.07881.0407-0.26510.35540.5561-1.91640.10651.7345-0.32440.53350.1671-0.16821.3238-0.13611.0903-9.0854-46.3582-18.6246
168.22132.94061.22054.555-2.12042.3919-0.70210.8069-1.0609-0.18150.9592-1.43241.08831.5303-0.22830.58460.19650.10090.8583-0.17790.8448-18.4793-55.884-24.378
175.4427-1.105-2.82718.46422.68723.2276-0.16961.2755-0.1781-1.3547-0.7621-1.27780.8736-0.25050.84231-0.0160.18720.90570.07560.8434-16.1283-39.3959-30.2354
184.4171-1.38980.47578.7723-2.11536.505-0.30190.0643-0.08630.1150.2176-1.14850.26831.19260.15980.5470.0917-0.26370.7375-0.06030.7727-14.8491-40.6566-15.7667
195.27541.4072-5.56536.7649-0.89957.83140.52690.3671-0.8018-0.73070.0092-1.19410.36561.0026-0.5760.83990.3349-0.20660.8545-0.15820.9356-13.2681-48.4678-16.0692
200.2661-0.14790.40241.962-1.96542.2733-0.1251-0.0245-0.53912.50720.0532-0.51131.42050.6056-0.2762.53380.4158-0.57480.54820.22020.6233-22.2687-50.79484.1192
212.00292.7105-3.47713.7616-5.13838.6881-0.1745-0.880.07032.59660.003-0.131-0.08940.91370.4711.67780.1383-0.04580.53640.17730.5681-28.3127-37.91231.897
221.45093.59622.57629.09976.59924.8281-1.0995-0.818-0.19930.6951-0.91772.22340.5629-0.02512.03632.025-0.24630.34371.6583-0.50550.9915-41.5246-48.04987.4096
231.1714-2.8638-1.95257.94312.83847.5045-0.6582-0.8664-0.30352.196-0.1820.7697-0.85290.17070.3981.83060.31420.05690.69940.07930.7301-31.8272-59.2583-1.8625
247.7117-1.17590.0474.15360.36961.6973-0.145-0.69530.07371.94240.0831-0.57420.57330.58430.15131.4750.6321-0.29420.44840.00960.8085-21.7562-56-4.2371
252.9206-0.37910.28946.86921.01494.0349-0.4221-0.2508-0.37171.5184-0.20340.59250.2337-0.04360.15881.46690.30870.02530.5250.11440.5702-30.5007-52.0939-3.7193
262.2190.0944-0.10594.5542-1.27424.8152-0.2907-1.2903-0.29071.71940.1352-0.3720.4028-0.0892-0.20931.60580.4266-0.26880.72190.15240.5368-20.706-47.71420.2746
271.79290.1968-0.03079.40272.37233.23650.1863-0.03030.144-1.50560.5057-0.9273-0.86350.9309-0.6270.548-0.24520.13280.6858-0.0040.6726-17.3633-14.9998-23.0818
287.81471.33390.44247.8046-7.82588.43160.17541.5935-0.0268-2.1126-0.5105-1.32290.19761.74560.03480.9458-0.1764-0.01851.14450.16960.6861-25.3437-15.2838-34.4949
295.83690.09860.71776.95622.09072.08320.07950.3064-0.2256-0.94370.0834-0.3506-1.68490.8524-0.00590.4431-0.2772-0.10970.50750.08020.3958-26.0695-10.8312-21.6337
309.07560.5753-0.94347.3611-2.14132.38210.04890.92740.538-0.9010.3722-0.8313-0.71641.2837-0.10460.1893-0.4603-0.09220.9103-0.00660.6858-18.9993-14.402-18.7412
311.8631-1.89970.59963.2769-1.2453.76630.1511-1.2805-0.64281.57150.1327-0.18860.46630.3737-0.27310.8065-0.0379-0.44310.76460.08740.5375-25.7508-16.51794.1702
322.329-2.1474-2.10745.49990.63496.34650.0619-0.11550.18530.53880.0670.28510.01690.0765-0.15730.366-0.0589-0.1790.32450.06130.4828-33.4004-11.335-7.6181
332.946-1.5061-2.33354.1179-3.92669.7651-0.1769-0.67080.0033-0.2465-0.54820.1541-0.78110.12420.32280.3515-0.0084-0.24250.5105-0.01910.4509-37.1782-10.4207-13.2649
349.8555-0.1331-0.96433.4079-3.34363.3964-0.23820.1110.0951-0.01780.30791.4718-0.5368-0.1306-0.07670.4659-0.0616-0.03970.58220.11160.5304-41.5977-12.4187-1.3803
352.8189-2.3738-3.35743.96863.39518.816-0.6312-1.8016-0.34221.49010.09791.19440.6553-0.4290.57461.1859-0.10990.04260.78170.20810.9262-36.6955-25.75053.2757
366.64-1.8869-1.42992.7553-2.59134.33670.5527-0.83110.4660.5759-0.155-0.8501-0.661.20980.50320.105-0.0738-0.52281.3277-0.33550.9361-14.5839-15.8206-5.5333
373.6957-0.3732-0.81578.31361.41014.563-0.629-1.0091-0.34880.94760.09740.51740.63470.6397-0.05410.39430.0074-0.22370.49960.11880.4673-29.4733-23.5945-3.8014
388.4453-4.0787-2.01935.10760.28268.6028-0.0138-0.59570.19631.0020.17430.03620.026-0.5313-0.1030.4175-0.1035-0.17880.51730.11780.3687-28.6106-14.2339-4.4715
393.26343.1132-4.19576.6531-1.43737.2420.3357-1.63071.04011.2798-0.6665-0.2549-1.56080.87340.33790.9839-0.1086-0.35350.8556-0.13240.8176-49.34715.342-11.8378
404.41041.725-0.56265.3938-1.6374.12450.3032-0.60840.49450.8089-0.22280.5245-0.5782-0.5029-0.15330.58590.109-0.19270.6115-0.16570.5895-63.7512-2.8439-17.5914
416.75932.2572-1.53498.7308-5.31917.504-0.2287-0.48020.66511.02150.25850.5054-1.3307-0.49490.08160.71480.02-0.17230.5348-0.08470.5893-50.5494-1.7532-13.1765
425.96511.4722-0.39046.8238-2.74125.7360.3052-0.9581-0.15480.058-0.59250.4296-0.4146-0.04980.26630.2945-0.0971-0.21230.5501-0.03010.5126-50.2584-5.519-15.2837
438.9158-1.039-1.59854.27824.48496.4161-0.274-0.68310.91651.09530.27750.067-0.6115-0.06980.20280.68550.0275-0.32810.4661-0.11220.6477-55.96152.328-19.9794
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 344 through 401 )
2X-RAY DIFFRACTION2chain 'A' and (resid 402 through 415 )
3X-RAY DIFFRACTION3chain 'A' and (resid 416 through 458 )
4X-RAY DIFFRACTION4chain 'A' and (resid 459 through 475 )
5X-RAY DIFFRACTION5chain 'B' and (resid 342 through 363 )
6X-RAY DIFFRACTION6chain 'B' and (resid 364 through 377 )
7X-RAY DIFFRACTION7chain 'B' and (resid 378 through 390 )
8X-RAY DIFFRACTION8chain 'B' and (resid 391 through 401 )
9X-RAY DIFFRACTION9chain 'B' and (resid 402 through 409 )
10X-RAY DIFFRACTION10chain 'B' and (resid 410 through 415 )
11X-RAY DIFFRACTION11chain 'B' and (resid 416 through 438 )
12X-RAY DIFFRACTION12chain 'B' and (resid 439 through 443 )
13X-RAY DIFFRACTION13chain 'B' and (resid 444 through 458 )
14X-RAY DIFFRACTION14chain 'B' and (resid 459 through 474 )
15X-RAY DIFFRACTION15chain 'C' and (resid 344 through 384 )
16X-RAY DIFFRACTION16chain 'C' and (resid 385 through 401 )
17X-RAY DIFFRACTION17chain 'C' and (resid 402 through 415 )
18X-RAY DIFFRACTION18chain 'C' and (resid 416 through 458 )
19X-RAY DIFFRACTION19chain 'C' and (resid 459 through 475 )
20X-RAY DIFFRACTION20chain 'D' and (resid 344 through 384 )
21X-RAY DIFFRACTION21chain 'D' and (resid 385 through 401 )
22X-RAY DIFFRACTION22chain 'D' and (resid 402 through 410 )
23X-RAY DIFFRACTION23chain 'D' and (resid 411 through 415 )
24X-RAY DIFFRACTION24chain 'D' and (resid 416 through 438 )
25X-RAY DIFFRACTION25chain 'D' and (resid 439 through 457 )
26X-RAY DIFFRACTION26chain 'D' and (resid 458 through 475 )
27X-RAY DIFFRACTION27chain 'E' and (resid 342 through 401 )
28X-RAY DIFFRACTION28chain 'E' and (resid 402 through 415 )
29X-RAY DIFFRACTION29chain 'E' and (resid 416 through 458 )
30X-RAY DIFFRACTION30chain 'E' and (resid 459 through 474 )
31X-RAY DIFFRACTION31chain 'F' and (resid 344 through 372 )
32X-RAY DIFFRACTION32chain 'F' and (resid 373 through 384 )
33X-RAY DIFFRACTION33chain 'F' and (resid 385 through 390 )
34X-RAY DIFFRACTION34chain 'F' and (resid 391 through 401 )
35X-RAY DIFFRACTION35chain 'F' and (resid 402 through 415 )
36X-RAY DIFFRACTION36chain 'F' and (resid 416 through 425 )
37X-RAY DIFFRACTION37chain 'F' and (resid 426 through 458 )
38X-RAY DIFFRACTION38chain 'F' and (resid 459 through 475 )
39X-RAY DIFFRACTION39chain 'G' and (resid 344 through 363 )
40X-RAY DIFFRACTION40chain 'G' and (resid 364 through 401 )
41X-RAY DIFFRACTION41chain 'G' and (resid 402 through 425 )
42X-RAY DIFFRACTION42chain 'G' and (resid 426 through 458 )
43X-RAY DIFFRACTION43chain 'G' and (resid 459 through 473 )

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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