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- PDB-7dv8: The crystal structure of rice immune receptor RGA5-HMA2. -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7dv8
タイトルThe crystal structure of rice immune receptor RGA5-HMA2.
要素Disease resistance protein RGA5
キーワードPLANT PROTEIN (植物) / Immune receptor
機能・相同性
機能・相同性情報


plant-type hypersensitive response / innate immune response-activating signaling pathway / ADP binding / : / defense response to bacterium / ATP binding / metal ion binding / 細胞質
類似検索 - 分子機能
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Disease resistance protein RGA5
類似検索 - 構成要素
生物種Oryza sativa subsp. japonica (イネ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.447 Å
データ登録者Zhang, X. / Liu, J.F.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)32030089 中国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2021
タイトル: A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors.
著者: Liu, Y. / Zhang, X. / Yuan, G. / Wang, D. / Zheng, Y. / Ma, M. / Guo, L. / Bhadauria, V. / Peng, Y.L. / Liu, J.
履歴
登録2021年1月12日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年10月20日Provider: repository / タイプ: Initial release
改定 1.12022年2月23日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
改定 1.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Disease resistance protein RGA5
B: Disease resistance protein RGA5
C: Disease resistance protein RGA5
D: Disease resistance protein RGA5
E: Disease resistance protein RGA5
F: Disease resistance protein RGA5
G: Disease resistance protein RGA5
H: Disease resistance protein RGA5
I: Disease resistance protein RGA5
J: Disease resistance protein RGA5
K: Disease resistance protein RGA5
L: Disease resistance protein RGA5
M: Disease resistance protein RGA5
N: Disease resistance protein RGA5


分子量 (理論値)分子数
合計 (水以外)110,71914
ポリマ－110,71914
非ポリマー00
水52229
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Disease resistance protein RGA5
B: Disease resistance protein RGA5
C: Disease resistance protein RGA5
D: Disease resistance protein RGA5
F: Disease resistance protein RGA5
G: Disease resistance protein RGA5
H: Disease resistance protein RGA5
I: Disease resistance protein RGA5
J: Disease resistance protein RGA5
K: Disease resistance protein RGA5
L: Disease resistance protein RGA5
M: Disease resistance protein RGA5
N: Disease resistance protein RGA5


分子量 (理論値)分子数
合計 (水以外)102,81113
ポリマ－102,81113
非ポリマー00
水19811
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-59 kcal/mol
Surface area46860 Å2
手法PISA
単位格子
Length a, b, c (Å)119.033, 78.230, 121.004
Angle α, β, γ (deg.)90.000, 90.540, 90.000
Int Tables number3
Space group name H-MP121

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要素

#1: タンパク質
Disease resistance protein RGA5 / / Os11gRGA5 / SasRGA5


分子量: 7908.507 Da / 分子数: 14 / 変異: G1009D, S1027V / 由来タイプ: 組換発現
由来: (組換発現) Oryza sativa subsp. japonica (イネ)
遺伝子: RGA5 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: F7J0N2
#2: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 29 / 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: 5.09 Å3/Da / 溶媒含有率: 75.83 %
結晶化温度: 291 K / 手法: 蒸気拡散法 / 詳細: PEG 3350, ammonium nitrate

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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: SSRF / ビームライン: BL17U1 / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年5月29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: 2.44→44 Å / Num. obs: 79835 / % possible obs: 96.78 % / 冗長度: 6.4 % / Biso Wilson estimate: 62.03 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Net I/σ(I): 29.41
反射 シェル解像度: 2.45→2.53 Å / Num. unique obs: 4041 / CC1/2: 0.99

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
HKL-2000データスケーリング
PDB_EXTRACT3.27データ抽出
HKL-2000データ収集
PHENIX位相決定
HKL-2000データ削減
精密化構造決定の手法: 分子置換
開始モデル: 5ZNE

5zne


解像度: 2.447→43.994 Å / SU ML: 0.33 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 31.1 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2471 2004 2.51 %
Rwork0.2059 77743 -
obs0.2069 79747 96.75 %
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 max: 176.14 Å2 / Biso mean: 86.4765 Å2 / Biso min: 45.26 Å2
精密化ステップサイクル: final / 解像度: 2.447→43.994 Å
タンパク質核酸リガンド溶媒全体
原子数7672 0 0 29 7701
Biso mean---67.25 -
残基数----1022
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.447-2.50780.3451350.3156510890
2.5078-2.57560.3341480.29635696100
2.5756-2.65130.35791500.29225679100
2.6513-2.73690.32381400.28365724100
2.7369-2.83470.28841510.24025691100
2.8347-2.94820.27331410.23485731100
2.9482-3.08230.29011410.24915681100
3.0823-3.24480.27971470.24965750100
3.2448-3.4480.28821490.22365719100
3.448-3.71410.27141280.2173458980
3.7141-4.08760.2271290.2041503488
4.0876-4.67850.20261470.1687569899
4.6785-5.89220.21241490.1814576199
5.8922-43.9940.23141490.1774588299
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)
16.7816-1.99150.43666.0051-1.96316.7063-0.17270.3168-0.39980.75330.2404-0.0791-0.76060.88040.17431.2129-0.1368-0.17010.6155-0.06520.724926.1852-2.807-33.7921
27.3482-2.072-1.19526.3493-1.87785.1455-0.3608-0.5588-0.35761.1747-0.3559-0.391-0.03360.42280.12421.5084-0.0924-0.18240.7119-0.01330.725729.6625-1.596-27.4561
34.45524.1839-1.71766.2851-0.9626.34-0.1610.05630.53530.731-0.24871.2829-1.5483-0.53660.16771.32150.07040.03530.68-0.05741.005619.30285.5773-25.934
48.64213.8207-2.86552.7832-2.9837.6607-0.3587-0.8450.25840.787-0.270.21480.57770.33250.47081.2919-0.203-0.07490.6322-0.08750.856830.12254.3332-25.129
59.37445.51210.98314.59683.40174.63820.0865-1.21860.2350.9592-0.49940.15070.6872-0.08130.68011.1872-0.1214-0.04240.72380.04710.707236.0048-36.8934.8647
66.6965-2.84390.72518.04353.00624.8769-0.0491-0.23890.5551.5165-0.03290.42980.1166-0.0820.18031.2119-0.10340.21720.51560.03810.674531.6021-38.947830.4122
73.63530.74764.58356.8849-1.35419.2990.3985-0.6362-0.54851.3171-0.3134-0.17260.8827-0.2151-0.04121.415-0.11610.07750.5361-0.04220.673935.0082-45.966435.0711
82.7111-0.4146-0.48967.11831.48673.3510.4603-0.22310.36650.6922-0.16790.1977-1.37350.2096-0.43621.3021-0.16150.25740.59810.05650.74727.216413.37836.2869
97.2154.45774.49296.5796.37686.1330.44410.55060.94730.30130.18530.5851-2.3925-0.1498-0.06151.6179-0.06660.31650.48220.02860.69124.116817.166234.4813
105.5791-4.5733-4.03873.53472.83326.73830.5216-0.81130.0890.801-0.0597-0.6877-1.61011.1494-0.1771.1223-0.23030.07420.76430.08910.848836.594317.931636.3122
116.1113-6.1336-5.22299.26294.77627.80070.67870.61841.13020.31630.1041-0.4275-0.9347-0.2816-0.48331.2413-0.18280.1510.58160.11260.758526.455923.361432.3023
125.9522-5.30072.9664.6962-3.6574.91910.7748-0.1277-0.810.21810.33610.10131.9226-0.336-0.77771.4711-0.0927-0.3850.5897-0.07660.908132.93820.4023-27.879
138.83353.6564-1.71058.9672-5.16023.4789-0.66290.30880.15461.38290.26410.01940.8892-0.67620.28771.1203-0.0779-0.10740.6593-0.1870.726829.556429.2986-24.1432
145.44444.6794-3.40289.8088-7.77829.56060.5417-0.3368-0.1090.8012-0.3715-0.12260.69530.4564-0.20211.3447-0.0137-0.16290.4819-0.14150.730136.082923.4949-25.1765
153.92844.0116-4.20755.0107-4.76964.54950.2895-0.2081-0.3976-0.2335-0.22110.13721.91580.6381-0.0221.7467-0.1293-0.30720.6320.00160.808234.414316.907-21.3361
166.0786-4.43164.70133.4596-3.05143.95080.4935-1.0747-0.05340.4424-0.07430.83382.1114-1.5612-0.28351.0999-0.2290.01590.7983-0.08320.794823.134419.2442-24.2387
177.2612-5.32935.11275.9132-4.96257.77470.76680.0815-0.406-0.31940.08920.06811.1735-0.1256-0.70971.3204-0.1967-0.160.6451-0.11490.81533.198213.827-28.2089
183.81811.13531.20851.79941.01182.8579-0.16721.05740.2012-0.53510.3155-0.2230.01210.0001-0.09370.8139-0.0246-0.1251.42760.1220.721211.6199-4.07960.4266
192.45672.5717-2.13562.9917-2.63842.04510.2810.23040.038-1.36460.44590.10580.80120.1273-0.51910.98790.0917-0.03071.29010.07160.828118.64021.53235.043
203.9692-1.2167-3.05674.38230.88587.2979-0.03850.3091-0.4857-0.53230.0027-0.16260.0874-0.02020.11650.80750.1477-0.01271.404-0.00070.757214.1773-6.40923.9713
215.54760.56-0.81784.1147-1.77554.2155-0.3370.1793-0.7110.2328-0.0570.0159-0.0457-0.40340.14790.75160.2072-0.0071.1924-0.00520.74536.8748-4.767.0318
225.97732.1826-1.40975.9547-3.09114.6349-0.01410.38630.265-0.1335-0.2899-0.036-0.3629-0.61460.14760.89160.0587-0.13821.2604-0.01060.7926.07070.27920.8878
234.39660.5281-1.54522.3824-1.51173.3085-0.69131.22380.4452-0.85720.03090.5816-0.1173-0.37450.41910.8288-0.06640.06311.4974-0.20610.774548.3645-36.9271-60.0738
241.60941.4531.34382.91963.04573.1864-0.01760.6482-1.1038-1.21891.09260.1743-1.4141-0.1038-0.56050.8430.14880.08331.2741-0.05550.936340.7293-42.4876-56.2231
256.1385-0.05481.95183.26041.84056.1630.70710.85470.1334-0.3485-0.37110.1012-0.09380.4968-0.18430.78790.15690.00221.22420.01030.785248.011-36.3009-51.0248
267.9027-1.13096.01574.7729-1.12577.7890.22380.80890.2747-0.7867-0.43460.48720.49040.40250.09310.90490.1477-0.10611.29370.06560.793749.222-34.6837-58.053
272.28050.78410.33012.22480.49162.53660.53630.1812-1.3139-0.7001-0.77390.00721.36491.60450.45130.89710.1210.10031.2265-0.03890.913652.7429-46.3014-58.4717
287.02173.98234.13223.60364.92477.5479-0.5475-0.6008-0.32-1.34150.268-0.6742-0.79260.80580.41411.01290.03710.1651.41020.08050.864155.4573-35.2262-61.0518
297.2192-6.9682-5.40457.95896.57356.3084-0.4797-0.1411-0.57841.56110.39650.74331.2086-0.12970.07360.6171-0.06610.16680.57780.09210.559432.9632-24.054820.8779
300.1198-0.6118-0.67155.0323-0.07391.9743-00.36420.14440.2788-0.3772-0.77251.16820.5330.27420.80170.0034-0.00970.73660.02340.721140.8496-35.935717.9977
316.60841.54071.39256.57394.41373.51340.2635-0.6449-0.18341.1194-0.06780.1517-0.0508-0.7811-0.15950.9467-0.0272-0.00810.52620.05420.64235.1183-29.72526.7205
328.50670.22330.39465.53612.91049.1174-0.30610.17430.21860.2829-0.01970.6876-0.1952-0.05960.06910.8035-0.11430.05110.5861-0.05160.729633.3486-27.789319.8089
336.549-3.8348-5.86998.12340.84277.79230.5154-0.2950.38430.3729-0.2505-0.684-0.63730.6584-0.26260.6365-0.153-0.02790.6275-0.03160.685439.7806-22.951318.4624
347.4778-6.90984.28648.3151-6.92516.761-0.9021-0.21090.65741.35840.4662-0.7362-0.78-0.32790.57360.6773-0.0367-0.14480.4626-0.0770.533226.8631-16.9432-39.7155
351.4818-0.75871.64023.52111.29142.76380.11910.17630.0273-0.2908-0.34130.7278-0.0325-0.11810.51290.7018-0.02870.01230.7116-0.0630.6719.115-5.0923-42.5983
365.43961.7496-2.64757.5714-6.84329.85690.1883-0.3060.22771.79070.3449-0.1947-0.45640.4523-0.57961.0489-0.01520.0320.5178-0.07770.646224.7282-11.307-33.823
374.43720.6069-1.23162.455-2.53393.3690.2060.10340.24080.5249-0.0974-0.2005-0.2527-0.1079-0.35760.9185-0.1529-0.04330.70630.03090.700326.4579-13.0866-40.8087
384.0091-3.37263.18542.9281-2.57582.65050.26990.103-0.75760.7059-0.16222.2631.431-2.24950.19450.7821-0.21070.03890.86620.02190.847815.17-16.6405-41.3272
394.6042-5.75874.43549.5492-6.06253.96730.3163-0.59230.40570.6477-0.2377-0.2325-0.1143-0.1747-0.15710.6266-0.053-0.12310.6546-0.0670.661726.0534-19.7479-43.0318
408.8626-1.53694.85933.8157-1.54133.6011-0.5968-0.00581.08380.1799-0.04-0.5079-0.2958-0.0560.65880.3790.0119-0.00440.71450.04650.571513.2145-7.9672-61.488
418.96795.9134.40346.68882.60812.7859-0.54470.5865-0.70690.25870.2725-0.1875-1.16960.8279-0.03070.3891-0.02480.15610.73820.05030.588922.2989-8.8233-65.422
423.88142.19281.71471.9684-0.29877.24560.42260.1208-0.164-0.1702-0.4498-0.429-0.1938-0.98450.10520.5052-0.04530.09230.78760.06530.615412.9997-7.3306-70.7682
434.52884.32411.60324.28950.99012.5191-0.5420.05210.8562.03650.6979-0.134-1.9847-0.63520.76791.14460.0117-0.10740.81330.12140.823916.7741-0.0081-55.921
445.08133.4775.87497.15394.14967.32530.33430.2127-0.1233-0.3668-0.6646-0.17280.3299-0.52890.15480.6743-0.04740.06760.76250.00730.62318.8614-9.5355-67.8752
454.4951-2.76774.50118.1337-3.27624.87020.5030.8242-1.4115-0.5625-0.3645-1.04572.03760.2841-0.16150.76120.04110.02530.7104-0.02570.843314.2672-18.5025-63.1803
467.6468-2.9915.18537.6075-1.86123.4446-0.3060.85720.07440.3098-0.0114-0.6106-0.11980.44950.1820.5681-0.0207-0.01360.8071-0.00310.5997.8704-10.558-60.35
479.8069-1.1869-5.56893.25920.62214.2015-0.18540.2608-1.0332-0.0023-0.25780.6168-0.3122-0.10390.34220.38260.0019-0.03020.6709-0.07910.605846.8784-32.758-0.9538
484.74594.1001-5.96255.187-3.02487.8335-0.4092-0.2860.7892-0.03390.12260.29620.1391-0.31650.1140.41330.0387-0.22330.8067-0.08340.733738.2853-31.6094-5.5938
496.14412.7844-4.77538.8393-3.41634.1808-0.2574-0.0202-0.0703-0.1403-0.04220.19031.06720.64160.54180.6012-0.0376-0.08250.7359-0.12860.618946.1237-36.3606-4.9563
505.50031.8046-3.0518.9094-2.1997.17610.16320.3146-0.288-0.1248-0.5008-0.787-0.4472-0.30260.14120.6581-0.0361-0.09850.6775-0.03630.66751.6844-31.1405-7.3083
512.2282-2.6375-2.81233.02323.12443.4304-0.47880.83930.63420.11050.08770.709-1.0003-0.63130.30840.6540.0051-0.10560.6509-0.04080.841645.2692-22.7836-2.4348
528.222-1.9533-6.37965.56751.74295.2928-0.31310.4078-0.22870.38890.09850.3360.0999-0.29160.0720.4628-0.0419-0.04410.72730.03720.545253.4544-30.49030.2014
538.3656-3.5132-0.01089.1727-4.91753.57921.01760.09720.1306-0.7248-0.86480.3864-0.07160.4137-0.14020.88620.10930.08370.5811-0.05230.4992-18.1931-0.1853-40.1549
541.372-2.09172.52193.8756-4.12484.79730.793-0.6682-0.46710.5884-0.06580.7976-0.55470.2353-0.64450.5896-0.07050.06480.6925-0.060.6642-17.0796-10.0837-42.2117
552.9992-1.44522.95895.3453-3.83728.77360.78370.38930.03630.038-0.33810.0475-0.58330.6336-0.00520.6340.06360.11270.76-0.09560.6384-18.3204-1.8299-49.0878
567.3949-1.3783.86748.0218-3.87543.67490.0012-0.31970.72490.2151-0.6236-0.2455-0.31670.15770.26820.7310.10840.11960.8055-0.00710.6156-16.85771.5121-42.6386
574.3426-3.5260.10253.5266-1.39062.78250.61330.3384-0.4745-0.1472-0.59190.6690.6626-0.5442-0.01280.8052-0.01110.15180.69770.01350.8385-27.3837-4.1523-39.5369
583.3447-0.9829-0.46975.6018-2.53667.6351.04480.36110.3138-0.6005-0.41180.3082-1.68090.7338-0.39771.10190.07630.25310.5806-0.01420.6501-21.21335.8794-39.8312
596.57393.3137-1.97165.7409-3.48017.19810.69950.1487-0.2091.1382-0.3712-0.1351-0.15290.456-0.14660.6677-0.0739-0.14060.4487-0.03720.506441.6634-40.5774-20.4321
605.61195.4667-5.60885.2515-5.45275.82380.07750.4975-0.1636-0.9488-0.14510.51090.4168-0.1384-0.07640.61620.0075-0.0920.7521-0.04690.672842.112-30.9318-18.3632
613.9514-0.2757-2.27874.2662-1.5317.8860.7397-0.0069-0.55450.0978-0.51050.03050.73040.19410.09540.7084-0.0335-0.14270.7256-0.12110.65940.8682-39.045-11.4523
622.44340.57960.37883.2696-2.99843.1569-0.99571.0896-0.4826-0.8005-0.7904-1.3206-1.11480.24490.2311.04540.1974-0.16211.24290.14281.021550.6889-39.8553-25.8812
633.00820.6502-4.51343.4732-2.39868.8681-0.2334-0.93051.36630.8864-0.0075-0.28151.15290.85930.50520.7042-0.0893-0.15810.75770.0060.642938.2487-43.5388-13.6531
643.96314.0358-1.56595.6183-4.06584.2871-0.17810.42890.8019-0.00950.54461.247-0.614-1.5232-0.19680.8380.0756-0.08070.705-0.0040.806531.92-36.7429-21.1702
654.52252.9102-1.56638.7966-6.29657.3890.2676-0.5226-0.16960.81780.1795-0.10910.8741-0.4026-0.06980.8605-0.054-0.1980.5771-0.0620.626838.2837-46.7433-20.8702
669.4681-5.3165-2.0834.2983.95345.32870.38620.734-0.0598-0.8645-0.58960.5997-1.3468-0.8270.52540.78040.0367-0.00240.62-0.00420.570520.4426-8.064619.5512
675.4572-0.1099-4.77557.34080.94334.6910.12740.5283-0.19140.5718-0.29920.44780.24-0.69040.03740.75180.09790.04850.73740.04360.704415.52210.409217.5944
689.1831-1.2426-3.88075.82272.41039.58980.40610.34990.0964-0.6611-0.0309-0.115-0.0579-0.2297-0.05650.79230.0102-0.06391.01270.09110.673920.5224-6.278610.5334
694.97151.1124-4.55196.25511.25425.3233-0.0306-0.0077-0.55380.2019-0.33530.05310.2411-0.46030.39340.5515-0.06130.0311.0001-0.02850.723620.6588-10.074116.9665
703.2491-4.3332-1.41119.6415.45726.56130.15040.20350.32870.2520.0038-0.4221-0.2950.25-0.1430.6084-0.09510.07620.58840.05440.618527.1717-5.513819.816
714.8299-4.28444.23786.3895-2.14534.83150.4460.57080.1516-0.6381-0.2618-0.6880.95190.26480.09770.63350.0403-0.00910.7188-0.00940.580340.3156-33.6735-40.9084
722.9448-0.74172.26588.2548-1.34973.30370.56480.8534-1.14651.1884-0.0815-0.0409-0.72671.0802-0.70720.80860.0943-0.02230.8035-0.02070.738243.4685-41.5057-43.3085
736.75070.00822.33958.884-1.4959.43510.18530.182-0.5805-0.73610.2458-0.66080.10670.1936-0.43180.73290.0342-0.04370.9036-0.06190.719539.4283-34.7105-50.0449
748.41240.7474.51515.4233-0.4229.5315-0.0213-0.15360.75230.2374-0.4114-0.0426-0.49080.09630.07020.5844-0.031-0.09910.85190.07050.738439.1665-30.8832-43.7448
754.0891-5.38592.02699.6082-5.87278.49070.0966-0.2522-0.3302-0.81440.50021.20280.5606-0.5857-0.44660.7513-0.1968-0.08540.659-0.06260.722331.4899-40.5826-41.2258
761.7757-2.60330.62792.962-0.09663.80330.0015-0.0163-0.14770.33270.2627-0.02490.4288-0.1743-0.29410.6273-0.0143-0.11640.5919-0.01870.646733.9224-30.4997-40.5199
773.7864.0701-3.2465.6497-5.42435.3345-0.98240.2669-1.1540.7810.0613-1.3352-0.3036-1.32861.07951.2889-0.20090.01510.792-0.11710.752227.5541-1.5662-24.9017
785.4912-0.24010.00696.2915-5.62495.1598-0.2727-0.6799-0.5254-0.6702-0.22520.22221.06850.325-0.64371.3588-0.04550.15210.8148-0.04310.920319.5435-7.2191-26.5569
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'I' and (resid 1021 through 1031 )I0
2X-RAY DIFFRACTION2chain 'I' and (resid 1032 through 1046 )I0
3X-RAY DIFFRACTION3chain 'I' and (resid 1047 through 1057 )I0
4X-RAY DIFFRACTION4chain 'I' and (resid 1058 through 1069 )I0
5X-RAY DIFFRACTION5chain 'J' and (resid 997 through 1020 )J997 - 1020
6X-RAY DIFFRACTION6chain 'J' and (resid 1021 through 1046 )J0
7X-RAY DIFFRACTION7chain 'J' and (resid 1047 through 1069 )J0
8X-RAY DIFFRACTION8chain 'K' and (resid 997 through 1031 )K997 - 1031
9X-RAY DIFFRACTION9chain 'K' and (resid 1032 through 1046 )K0
10X-RAY DIFFRACTION10chain 'K' and (resid 1047 through 1058 )K0
11X-RAY DIFFRACTION11chain 'K' and (resid 1059 through 1069 )K0
12X-RAY DIFFRACTION12chain 'L' and (resid 997 through 1008 )L997 - 1008
13X-RAY DIFFRACTION13chain 'L' and (resid 1009 through 1021 )L0
14X-RAY DIFFRACTION14chain 'L' and (resid 1022 through 1036 )L0
15X-RAY DIFFRACTION15chain 'L' and (resid 1037 through 1046 )L0
16X-RAY DIFFRACTION16chain 'L' and (resid 1047 through 1058 )L0
17X-RAY DIFFRACTION17chain 'L' and (resid 1059 through 1069 )L0
18X-RAY DIFFRACTION18chain 'M' and (resid 997 through 1008 )M997 - 1008
19X-RAY DIFFRACTION19chain 'M' and (resid 1009 through 1021 )M0
20X-RAY DIFFRACTION20chain 'M' and (resid 1022 through 1036 )M0
21X-RAY DIFFRACTION21chain 'M' and (resid 1037 through 1046 )M0
22X-RAY DIFFRACTION22chain 'M' and (resid 1047 through 1069 )M0
23X-RAY DIFFRACTION23chain 'N' and (resid 997 through 1008 )N997 - 1008
24X-RAY DIFFRACTION24chain 'N' and (resid 1009 through 1020 )N0
25X-RAY DIFFRACTION25chain 'N' and (resid 1021 through 1031 )N0
26X-RAY DIFFRACTION26chain 'N' and (resid 1032 through 1046 )N0
27X-RAY DIFFRACTION27chain 'N' and (resid 1047 through 1058 )N0
28X-RAY DIFFRACTION28chain 'N' and (resid 1059 through 1069 )N0
29X-RAY DIFFRACTION29chain 'A' and (resid 997 through 1004 )A997 - 1004
30X-RAY DIFFRACTION30chain 'A' and (resid 1005 through 1020 )A0
31X-RAY DIFFRACTION31chain 'A' and (resid 1021 through 1031 )A0
32X-RAY DIFFRACTION32chain 'A' and (resid 1032 through 1046 )A0
33X-RAY DIFFRACTION33chain 'A' and (resid 1047 through 1069 )A0
34X-RAY DIFFRACTION34chain 'B' and (resid 997 through 1004 )B997 - 1004
35X-RAY DIFFRACTION35chain 'B' and (resid 1005 through 1020 )B0
36X-RAY DIFFRACTION36chain 'B' and (resid 1021 through 1031 )B0
37X-RAY DIFFRACTION37chain 'B' and (resid 1032 through 1046 )B0
38X-RAY DIFFRACTION38chain 'B' and (resid 1047 through 1058 )B0
39X-RAY DIFFRACTION39chain 'B' and (resid 1059 through 1069 )B0
40X-RAY DIFFRACTION40chain 'C' and (resid 997 through 1008 )C997 - 1008
41X-RAY DIFFRACTION41chain 'C' and (resid 1009 through 1020 )C0
42X-RAY DIFFRACTION42chain 'C' and (resid 1021 through 1031 )C0
43X-RAY DIFFRACTION43chain 'C' and (resid 1032 through 1036 )C0
44X-RAY DIFFRACTION44chain 'C' and (resid 1037 through 1046 )C0
45X-RAY DIFFRACTION45chain 'C' and (resid 1047 through 1057 )C0
46X-RAY DIFFRACTION46chain 'C' and (resid 1058 through 1069 )C0
47X-RAY DIFFRACTION47chain 'D' and (resid 997 through 1008 )D997 - 1008
48X-RAY DIFFRACTION48chain 'D' and (resid 1009 through 1021 )D0
49X-RAY DIFFRACTION49chain 'D' and (resid 1022 through 1036 )D0
50X-RAY DIFFRACTION50chain 'D' and (resid 1037 through 1046 )D0
51X-RAY DIFFRACTION51chain 'D' and (resid 1047 through 1058 )D0
52X-RAY DIFFRACTION52chain 'D' and (resid 1059 through 1069 )D0
53X-RAY DIFFRACTION53chain 'E' and (resid 997 through 1008 )E997 - 1008
54X-RAY DIFFRACTION54chain 'E' and (resid 1009 through 1020 )E0
55X-RAY DIFFRACTION55chain 'E' and (resid 1021 through 1031 )E0
56X-RAY DIFFRACTION56chain 'E' and (resid 1032 through 1046 )E0
57X-RAY DIFFRACTION57chain 'E' and (resid 1047 through 1058 )E0
58X-RAY DIFFRACTION58chain 'E' and (resid 1059 through 1069 )E0
59X-RAY DIFFRACTION59chain 'F' and (resid 997 through 1008 )F997 - 1008
60X-RAY DIFFRACTION60chain 'F' and (resid 1009 through 1020 )F0
61X-RAY DIFFRACTION61chain 'F' and (resid 1021 through 1031 )F0
62X-RAY DIFFRACTION62chain 'F' and (resid 1032 through 1036 )F0
63X-RAY DIFFRACTION63chain 'F' and (resid 1037 through 1046 )F0
64X-RAY DIFFRACTION64chain 'F' and (resid 1047 through 1058 )F0
65X-RAY DIFFRACTION65chain 'F' and (resid 1059 through 1069 )F0
66X-RAY DIFFRACTION66chain 'G' and (resid 997 through 1008 )G997 - 1008
67X-RAY DIFFRACTION67chain 'G' and (resid 1009 through 1020 )G0
68X-RAY DIFFRACTION68chain 'G' and (resid 1021 through 1031 )G0
69X-RAY DIFFRACTION69chain 'G' and (resid 1032 through 1046 )G0
70X-RAY DIFFRACTION70chain 'G' and (resid 1047 through 1069 )G0
71X-RAY DIFFRACTION71chain 'H' and (resid 997 through 1009 )H997 - 1009
72X-RAY DIFFRACTION72chain 'H' and (resid 1010 through 1020 )H0
73X-RAY DIFFRACTION73chain 'H' and (resid 1021 through 1031 )H0
74X-RAY DIFFRACTION74chain 'H' and (resid 1032 through 1046 )H0
75X-RAY DIFFRACTION75chain 'H' and (resid 1047 through 1057 )H0
76X-RAY DIFFRACTION76chain 'H' and (resid 1058 through 1069 )H0
77X-RAY DIFFRACTION77chain 'I' and (resid 997 through 1008 )I997 - 1008
78X-RAY DIFFRACTION78chain 'I' and (resid 1009 through 1020 )I0

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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

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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