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- PDB-4yr8: Crystal structure of JNK in complex with a regulator protein -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 4yr8
タイトルCrystal structure of JNK in complex with a regulator protein
要素
  • Dual specificity protein phosphatase 16
  • Mitogen-activated protein kinase 8
キーワードTRANSFERASE/HYDROLASE / kinase domain / catalytic domain / TRANSFERASE-HYDROLASE complex
機能・相同性
機能・相同性情報


JUN phosphorylation / positive regulation of cell killing / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / basal dendrite / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / Suppression of autophagy / MAP kinase tyrosine/serine/threonine phosphatase activity / protein carrier chaperone ...JUN phosphorylation / positive regulation of cell killing / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / basal dendrite / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / Suppression of autophagy / MAP kinase tyrosine/serine/threonine phosphatase activity / protein carrier chaperone / positive regulation of establishment of protein localization to mitochondrion / JUN kinase activity / Activation of BIM and translocation to mitochondria / WNT5:FZD7-mediated leishmania damping / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / JUN kinase binding / positive regulation of cyclase activity / dephosphorylation / mitogen-activated protein kinase binding / histone deacetylase regulator activity / NRAGE signals death through JNK / mitogen-activated protein kinase p38 binding / protein-serine/threonine phosphatase / Activation of the AP-1 family of transcription factors / positive regulation of NLRP3 inflammasome complex assembly / Fc-epsilon receptor signaling pathway / protein serine/threonine phosphatase activity / positive regulation of protein metabolic process / phosphatase activity / energy homeostasis / phosphoprotein phosphatase activity / peptidyl-threonine phosphorylation / mitogen-activated protein kinase / regulation of macroautophagy / response to mechanical stimulus / negative regulation of protein binding / response to UV / stress-activated MAPK cascade / NRIF signals cell death from the nucleus / negative regulation of MAPK cascade / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / protein-tyrosine-phosphatase / protein serine/threonine kinase binding / cellular response to amino acid starvation / cellular response to reactive oxygen species / FCERI mediated MAPK activation / cellular response to mechanical stimulus / regulation of circadian rhythm / peptidyl-serine phosphorylation / Negative regulation of MAPK pathway / histone deacetylase binding / Signaling by ALK fusions and activated point mutants / cellular senescence / rhythmic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MAPK cascade / regulation of protein localization / cellular response to lipopolysaccharide / cellular response to oxidative stress / response to oxidative stress / Oxidative Stress Induced Senescence / cytoplasmic vesicle / protein phosphatase binding / protein phosphorylation / positive regulation of apoptotic process / axon / protein serine kinase activity / protein serine/threonine kinase activity / synapse / positive regulation of gene expression / negative regulation of apoptotic process / enzyme binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Mitogen-activated protein (MAP) kinase phosphatase / Mitogen-activated protein (MAP) kinase, JNK / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. ...Mitogen-activated protein (MAP) kinase phosphatase / Mitogen-activated protein (MAP) kinase, JNK / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Mitogen-activated protein kinase 8 / Dual specificity protein phosphatase 16
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: 2.4 Å
データ登録者Liu, X. / Wang, J. / Wu, J.W. / Wang, Z.X.
資金援助 中国, 4件
組織認可番号国
Ministry of Science and Technology2013CB530600 中国
Ministry of Science and Technology2011CB910800 中国
National Natural Science Foundation of China31270848 中国
National Natural Science Foundation of China31130062 中国
引用ジャーナル: Nat Commun / 年: 2016
タイトル: A conserved motif in JNK/p38-specific MAPK phosphatases as a determinant for JNK1 recognition and inactivation.
著者: Liu, X. / Zhang, C.S. / Lu, C. / Lin, S.C. / Wu, J.W. / Wang, Z.X.
履歴
登録2015年3月14日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02016年3月16日Provider: repository / タイプ: Initial release
改定 1.12016年3月30日Group: Database references
改定 1.22023年11月8日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
E: Mitogen-activated protein kinase 8
G: Dual specificity protein phosphatase 16
A: Mitogen-activated protein kinase 8
B: Dual specificity protein phosphatase 16
C: Mitogen-activated protein kinase 8
D: Dual specificity protein phosphatase 16
F: Mitogen-activated protein kinase 8
H: Dual specificity protein phosphatase 16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)247,13912
ポリマ－246,9978
非ポリマー1424
水6,413356
1
E: Mitogen-activated protein kinase 8
G: Dual specificity protein phosphatase 16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,7853
ポリマ－61,7492
非ポリマー351
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-18 kcal/mol
Surface area21640 Å2
手法PISA
2
A: Mitogen-activated protein kinase 8
B: Dual specificity protein phosphatase 16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,7853
ポリマ－61,7492
非ポリマー351
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-18 kcal/mol
Surface area21620 Å2
手法PISA
3
C: Mitogen-activated protein kinase 8
D: Dual specificity protein phosphatase 16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,7853
ポリマ－61,7492
非ポリマー351
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-19 kcal/mol
Surface area21790 Å2
手法PISA
4
F: Mitogen-activated protein kinase 8
H: Dual specificity protein phosphatase 16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,7853
ポリマ－61,7492
非ポリマー351
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-19 kcal/mol
Surface area21220 Å2
手法PISA
単位格子
Length a, b, c (Å)58.151, 74.850, 134.810
Angle α, β, γ (deg.)76.94, 84.32, 67.44
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Mitogen-activated protein kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase ...MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


分子量: 42830.461 Da / 分子数: 4 / 断片: UNP RESIDUES 1-363 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C / プラスミド: PET21b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P45983, mitogen-activated protein kinase
#2: タンパク質
Dual specificity protein phosphatase 16 / Mitogen-activated protein kinase phosphatase 7 / MKP-7


分子量: 18918.904 Da / 分子数: 4 / 断片: UNP RESIDUES 156-301 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DUSP16, KIAA1700, MKP7 / プラスミド: PET15b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: Q9BY84, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#3: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 356 / 由来タイプ: 天然 / 式: H2O
配列の詳細SEQUENCE OF THE CHAINS A,C,E,F WAS BASED ON ISOFORM 4 OF DATABASE P45983

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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: 2.14 Å3/Da / 溶媒含有率: 42.44 %
結晶化温度: 294 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 0.1M HEPES, pH 7.0, 14% PEG 3350, 0.2M MgCl2, 6% 1,6-Hexanediol, 0.005M EDTA

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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: SSRF / ビームライン: BL17U / 波長: 0.9793 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2012年4月5日
放射モノクロメーター: double crystal / 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: 0.9793 Å / 相対比: 1
反射解像度: 2.4→40 Å / Num. obs: 78865 / % possible obs: 99.6 % / 冗長度: 3.5 % / Biso Wilson estimate: 28.04 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.1
反射 シェル解像度: 2.4→2.49 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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解析

ソフトウェア名称: PHENIX / バージョン: 1.8.4_1496 / 分類: 精密化
精密化構造決定の手法: 分子置換
開始モデル: 1UKH, 1ZZW

1ukh

1zzw


解像度: 2.4→38.02 Å / SU ML: 0.29 / σ(F): 1.97 / 位相誤差: 27.3 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.239 3405 5.09 %
Rwork0.217 --
obs0.218 66889 83.8 %
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
原子変位パラメータBiso mean: 46.81 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→38.02 Å
タンパク質核酸リガンド溶媒全体
原子数14615 0 4 356 14975
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01514948
X-RAY DIFFRACTIONf_angle_d1.56420185
X-RAY DIFFRACTIONf_dihedral_angle_d16.725675
X-RAY DIFFRACTIONf_chiral_restr0.1162240
X-RAY DIFFRACTIONf_plane_restr0.0082566
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4012-2.43550.311890.2151181X-RAY DIFFRACTION6
2.4355-2.47190.269220.2223399X-RAY DIFFRACTION13
2.4719-2.51050.2844440.2699932X-RAY DIFFRACTION29
2.5105-2.55170.2774660.26961563X-RAY DIFFRACTION49
2.5517-2.59570.31841310.29172262X-RAY DIFFRACTION72
2.5957-2.64280.2951410.28362508X-RAY DIFFRACTION80
2.6428-2.69370.28161250.2712746X-RAY DIFFRACTION87
2.6937-2.74860.2931410.2692881X-RAY DIFFRACTION91
2.7486-2.80840.31151640.2833049X-RAY DIFFRACTION96
2.8084-2.87370.25661600.26893144X-RAY DIFFRACTION98
2.8737-2.94550.31781730.27453105X-RAY DIFFRACTION99
2.9455-3.02510.26441530.25783167X-RAY DIFFRACTION100
3.0251-3.11410.2751730.25533138X-RAY DIFFRACTION100
3.1141-3.21460.28031810.24083163X-RAY DIFFRACTION100
3.2146-3.32940.27591610.23543102X-RAY DIFFRACTION100
3.3294-3.46260.25041590.22453185X-RAY DIFFRACTION100
3.4626-3.62010.22011780.19783139X-RAY DIFFRACTION100
3.6201-3.81080.20991850.18883114X-RAY DIFFRACTION99
3.8108-4.04930.211710.18353117X-RAY DIFFRACTION99
4.0493-4.36150.19951530.17563170X-RAY DIFFRACTION99
4.3615-4.79970.19021850.16863108X-RAY DIFFRACTION99
4.7997-5.49240.2251950.18733099X-RAY DIFFRACTION100
5.4924-6.91310.23671630.21493182X-RAY DIFFRACTION100
6.9131-38.02170.19671720.18943030X-RAY DIFFRACTION96
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)
16.02024.7003-1.95534.063-0.26075.0492-0.2063-0.1546-0.0976-0.0745-0.0123-0.71750.10410.18630.14930.35780.2148-0.00780.37410.00950.332-23.253452.264590.1022
22.84271.48791.01552.05910.61252.3177-0.20930.12610.0942-0.27070.1294-0.20810.2350.13110.03910.4650.1681-0.02930.3269-0.03540.3421-34.499750.295282.8564
30.88010.39731.38954.65620.43232.2236-0.07610.22910.3805-0.5590.1429-0.6471-0.14630.1541-0.1790.42420.1672-0.06840.3056-0.04570.3595-28.741950.101782.5422
41.07580.1576-0.14971.34320.74990.8804-0.2796-0.15370.0679-0.19380.0490.032-0.16370.07830.07860.38120.3213-0.07760.37960.03090.218-53.380945.067385.6406
51.35841.26070.63562.37041.26550.7803-0.23580.3160.0079-0.28510.3415-0.5453-0.14770.28190.05370.48510.1205-0.00920.3405-0.02040.254-48.2732.181776.5068
61.48570.57880.20461.45860.36370.6162-0.22620.02580.0794-0.16240.06730.2476-0.1761-0.17220.06950.40250.1896-0.05060.29460.00610.1439-58.901332.948580.7786
74.86040.08610.91712.1470.0612.7181-0.2133-0.0897-0.16110.359-0.0923-1.0493-0.08451.66510.2270.38050.0361-0.02911.00530.15540.6016-24.099614.232585.364
83.7822-0.90751.36952.4623-0.19381.9474-0.11930.4209-0.2431-0.2356-0.2146-0.97180.2321.73430.1180.35060.16190.09661.09620.08370.5166-27.13511.186472.7788
93.91752.2047-0.10082.6051-0.96611.939-0.07740.0858-0.4738-0.05870.0393-0.18850.35320.7060.07030.29070.11120.02510.3681-0.04580.2933-35.800610.717977.7333
103.9747-0.55961.3135.2948-0.35775.1807-0.0916-0.2688-0.7030.31280.13070.0170.38710.27430.10190.22490.09450.01450.2570.06020.2497-41.882310.100784.0837
114.5236-0.34340.2796.5676-0.55064.9154-0.00890.5915-0.8026-0.6511-0.0260.09150.60380.410.07620.33570.0590.00220.3194-0.06760.2299-45.15018.5171.4721
122.9025-1.3388-0.59281.88510.22030.56610.0198-0.24-0.16140.14290.0949-0.14450.08790.1288-0.0060.2701-0.2195-0.00220.24420.03770.2604-51.9174-13.526840.2827
131.6406-0.8482-0.17261.91310.41260.946-0.0985-0.2674-0.07020.20450.08370.18250.1427-0.137-0.04550.2836-0.18950.06070.270.010.1798-69.51471.884645.109
143.56070.61920.29032.4524-1.28163.7661-0.15510.45030.208-0.34570.1671-0.75390.24871.51020.14770.3033-0.04380.04560.7524-0.010.376-37.183621.949440.0633
154.94410.6617-0.11761.30610.02561.5255-0.0878-0.1589-0.17090.0204-0.2392-0.9398-0.02421.53990.15980.3015-0.0105-0.0190.95070.04950.3709-33.670320.218451.8282
163.36250.4479-0.04422.69950.11382.8852-0.08620.04960.47650.27410.0475-0.3404-0.40440.79770.03140.2341-0.1143-0.0520.3256-0.03790.2558-45.971525.352850.3241
173.76640.3855-0.27574.955-0.57455.762-0.00560.40740.7183-0.43810.17710.2534-0.4382-0.0377-0.02120.1318-0.0516-0.01440.1980.06640.1839-55.189724.876440.5988
185.10140.75820.69837.7851-0.56896.65090.0118-0.520.85660.67810.06930.3837-0.7174-0.3199-0.03710.24280.00140.0320.2352-0.06020.243-58.258526.491453.2133
191.9266-0.5017-0.78311.58140.5293.83180.31460.5554-0.3815-0.3396-0.17480.070.62770.28360.06140.60050.0239-0.11410.4858-0.00240.4236-42.811827.05813.943
202.36920.1184-0.64071.7532-0.00592.08570.08410.176-0.0039-0.1979-0.05820.12550.0262-0.0154-0.03140.3238-0.1453-0.07670.15920.07140.2803-58.100637.9722.6825
215.9732-0.5487-1.84518.3273-1.33054.19780.4111.7201-0.614-0.41790.1491-0.0641.38990.3444-0.28810.71360.0998-0.26271.1693-0.00640.4827-49.048332.5078-10.3079
225.74812.03410.79826.02462.11563.51110.03640.103-0.5746-0.10180.19980.17580.9332-0.0909-0.20790.7013-0.1956-0.03410.2809-0.05890.286-71.97222.351319.1525
233.5078-0.04571.01333.9991.91454.68090.01230.6772-0.7924-0.60580.3758-0.52171.20970.6532-0.3921.18090.09130.0130.5799-0.22360.4575-64.7458-1.52129.0596
242.15020.73320.93412.95050.68563.0241-0.24030.6427-0.0302-1.15760.23690.69550.7172-0.1793-0.04690.8471-0.3179-0.16920.50960.04880.3682-76.998.13079.9298
256.07-1.2530.05646.25280.15775.4967-0.139-0.38020.10560.49590.23320.82640.4499-0.3548-0.03080.4355-0.15560.06320.2555-0.0380.247-74.829614.023626.5046
263.1078-0.01691.19375.43040.25424.8383-0.33440.19760.3816-0.53210.10490.9353-0.0479-0.51760.10570.413-0.1677-0.12360.32930.05830.3517-77.629119.929318.3365
273.12340.70821.04661.2451-0.18752.69730.3332-0.52310.45330.3788-0.3185-0.0447-0.41480.29210.04160.55230.04790.04410.4194-0.05120.3361-32.22095.9334116.8767
280.7110.4383-0.00440.92890.26030.58890.2718-0.0921-0.02270.242-0.1190.04010.1343-0.0090.07810.40940.36690.00490.20210.02450.2681-43.7124-3.5081104.8284
294.5419-1.0397-0.23272.29831.28346.55540.0303-0.0250.36450.14070.14660.0309-1.3727-0.0136-0.03970.79390.175-0.00060.3438-0.01040.1051-58.70832.6856105.8307
301.51950.99290.18090.71270.12690.02280.1646-0.61240.45730.19690.0944-0.0204-0.42010.431-0.23491.1231-0.0066-0.110.5503-0.20340.3692-51.7636.5734115.8968
311.6371-0.4372-1.21982.00870.44132.795-0.1139-0.51750.17540.75540.21020.2404-0.5896-0.093-0.04371.12040.43730.25540.5739-0.06190.2471-63.89827.9808117.2488
322.44491.23772.68292.43031.24594.12710.2067-0.08360.09210.0427-0.13860.4307-0.0769-0.2616-0.1390.4880.2420.0480.3849-0.00990.2496-62.077722.8227108.9192
336.26751.1967-0.3966.2726-0.34065.1924-0.20390.51250.0227-0.57440.14530.6262-0.2993-0.3690.04170.51810.1351-0.06630.28590.01110.1974-62.040421.376998.4282
344.4388-0.2053-0.76095.2585-0.02614.5805-0.3034-0.1821-0.41530.31720.17030.89810.0796-0.50430.15010.42020.20710.09740.31690.05610.316-64.716915.0261106.4843
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'E' AND (RESID 7 THROUGH 23 )
2X-RAY DIFFRACTION2CHAIN 'E' AND (RESID 24 THROUGH 92 )
3X-RAY DIFFRACTION3CHAIN 'E' AND (RESID 93 THROUGH 114 )
4X-RAY DIFFRACTION4CHAIN 'E' AND (RESID 115 THROUGH 167 )
5X-RAY DIFFRACTION5CHAIN 'E' AND (RESID 168 THROUGH 203 )
6X-RAY DIFFRACTION6CHAIN 'E' AND (RESID 204 THROUGH 362 )
7X-RAY DIFFRACTION7CHAIN 'G' AND (RESID 158 THROUGH 183 )
8X-RAY DIFFRACTION8CHAIN 'G' AND (RESID 184 THROUGH 243 )
9X-RAY DIFFRACTION9CHAIN 'G' AND (RESID 244 THROUGH 262 )
10X-RAY DIFFRACTION10CHAIN 'G' AND (RESID 263 THROUGH 284 )
11X-RAY DIFFRACTION11CHAIN 'G' AND (RESID 285 THROUGH 298 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 8 THROUGH 167 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 168 THROUGH 362 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 158 THROUGH 190 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 191 THROUGH 208 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 209 THROUGH 262 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 263 THROUGH 284 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 285 THROUGH 298 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 10 THROUGH 167 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 168 THROUGH 330 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 331 THROUGH 362 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 158 THROUGH 169 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 170 THROUGH 182 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 183 THROUGH 263 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 264 THROUGH 277 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 278 THROUGH 299 )
27X-RAY DIFFRACTION27CHAIN 'F' AND (RESID 10 THROUGH 220 )
28X-RAY DIFFRACTION28CHAIN 'F' AND (RESID 221 THROUGH 362 )
29X-RAY DIFFRACTION29CHAIN 'H' AND (RESID 158 THROUGH 169 )
30X-RAY DIFFRACTION30CHAIN 'H' AND (RESID 170 THROUGH 182 )
31X-RAY DIFFRACTION31CHAIN 'H' AND (RESID 183 THROUGH 243 )
32X-RAY DIFFRACTION32CHAIN 'H' AND (RESID 244 THROUGH 262 )
33X-RAY DIFFRACTION33CHAIN 'H' AND (RESID 263 THROUGH 277 )
34X-RAY DIFFRACTION34CHAIN 'H' AND (RESID 278 THROUGH 300 )

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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