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- PDB-7e1i: Crystal structure of Pr55Gag-matrix domain in complex with IP6 at... -

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基本情報

登録情報
データベース: PDB / ID: 7e1i
タイトルCrystal structure of Pr55Gag-matrix domain in complex with IP6 at ambient temperature in space group P1
要素Capsid protein p24カプシド
キーワードVIRAL PROTEIN (ウイルスタンパク質) / HIV-1 / Matrix protein (基質タンパク質) / Myo-inositol hexakisphosphate / Serial femtosecond X-ray crystallography / Ambient-temperature crystallography
機能・相同性
機能・相同性情報


viral process / viral nucleocapsid / host cell cytoplasm / structural molecule activity / RNA binding / 細胞質
類似検索 - 分子機能
gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal
類似検索 - ドメイン・相同性
フィチン酸 / Gag protein
類似検索 - 構成要素
生物種Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
手法X線回折 / 自由電子レーザー / フーリエ合成 / 解像度: 3.301 Å
データ登録者DeMirci, H. / Destan, E.
資金援助 米国, トルコ, 2件
組織認可番号国
National Science Foundation (NSF, United States)NSF-1231306 米国
Other government118C270 トルコ
引用ジャーナル: To Be Published
タイトル: Crystal structure of Pr55Gag-matrix domain in complex with IP6 at ambient temperature in space group P1
著者: DeMirci, H. / Destan, E.
履歴
登録2021年2月1日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年8月4日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)171,63124
ポリマ－163,71012
非ポリマー7,92012
水0
1
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,9086
ポリマ－40,9283
非ポリマー1,9803
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,5687
ポリマ－40,9283
非ポリマー2,6404
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,2485
ポリマ－40,9283
非ポリマー1,3202
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,9086
ポリマ－40,9283
非ポリマー1,9803
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)96.600, 96.600, 91.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Capsid protein p24 / カプシド / Matrix protein p17 / Nucleocapsid protein p7


分子量: 13642.536 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: gag / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: T2CJ20
#2: 化合物
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / フィチン酸 / フィチン酸


分子量: 660.035 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C6H18O24P6 / タイプ: SUBJECT OF INVESTIGATION
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: 4.5 Å3/Da / 溶媒含有率: 72.65 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 20% (w/v) polyethylene glycol 3350 (PEG 3350) as a precipitant and 100 mM MES-NaOH

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データ収集

回折平均測定温度: 293 K / Serial crystal experiment: N
放射光源由来: 自由電子レーザー / サイト: SLAC LCLS / ビームライン: CXI / 波長: 1 Å
検出器タイプ: CS-PAD CXI-1 / 検出器: PIXEL / 日付: 2018年12月1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: 1 Å / 相対比: 1
反射解像度: 3.3→25 Å / Num. obs: 35663 / % possible obs: 100 % / 冗長度: 62.3 % / CC1/2: 0.958 / Net I/σ(I): 2.67

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解析

ソフトウェア
名称バージョン分類
CrystFELデータ削減
PHENIXDEV-3318精密化
PDB_EXTRACT3.27データ抽出
CrystFELデータスケーリング
PHENIX位相決定
精密化構造決定の手法: フーリエ合成 / 解像度: 3.301→24.574 Å / SU ML: 0.78 / 交差検証法: THROUGHOUT / σ(F): 0.01 / 位相誤差: 52.71 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.4084 1159 3.25 %
Rwork0.3515 34504 -
obs0.3534 35663 83.43 %
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: 425.17 Å2 / Biso mean: 173.641 Å2 / Biso min: 0.3 Å2
精密化ステップサイクル: final / 解像度: 3.301→24.574 Å
タンパク質核酸リガンド溶媒全体
原子数11319 0 462 0 11781
Biso mean--98.58 --
残基数----1446
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 (%)
3.31-3.45070.5071070.4471298757
3.4507-3.63210.42881140.4333666
3.6321-3.85890.41071180.3752403077
3.8589-4.15550.38741360.3461431183
4.1555-4.57130.41921580.3363476292
4.5713-5.22720.37771880.3208493796
5.2272-6.56490.4111700.3754501497
6.5649-24.50.40981680.3328512799
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)
12.8147-0.651-3.74021.40431.35485.1742-0.5799-1.5927-0.19950.0493-0.3745-0.56330.84543.12890.41231.2732-0.0253-0.5411.6670.52962.640612.5595-9.856530.1346
28.4938-4.0879-2.26694.53184.65665.5299-1.08241.3302-0.8185-0.0634-0.59680.67681.60230.03060.1919-0.4756-0.39730.46011.6157-0.29950.76443.4069-19.146729.4811
30.68461.05970.37052.316-0.27371.28-0.1619-0.20220.3311-0.16330.3270.7254-0.89610.0311-0.23980.17470.76870.5930.6816-1.0069-0.0803-0.2909-3.17927.2047
42.7044-1.7210.75582.31721.16112.3705-0.4180.36031.08430.58981.1502-0.65680.65970.30890.03020.598-0.05010.13470.64490.21521.15381.48180.255839.423
51.96211.75862.62761.94891.81424.3417-0.4844-1.14860.29910.2916-0.69540.5586-0.2359-1.0104-0.52550.2163-0.2887-0.14611.16720.86352.903-2.5555-8.494537.8979
67.2756.34612.72625.83771.29864.83080.0787-0.0651-0.53830.6714-0.5225-0.48980.68070.1931-0.44271.2542-0.0693-0.69490.8659-0.37911.236410.3445-17.6239.7288
72.60420.0603-0.43866.1952-1.74821.2263-0.3455-0.33780.43490.42210.3106-0.1182-0.07730.27580.14421.0383-0.2396-0.88091.6067-1.94482.84152.3148-15.479144.923
88.2914-2.1235-5.08610.54821.30523.12240.977-2.51952.81353.54260.7173-1.9423-1.02261.7385-0.98314.5391-1.0092-1.63061.9854-0.78253.75885.2506-6.526960.8977
99.4899-1.7892-1.24595.4022-4.825.23180.1558-1.30611.56611.56930.59951.7374-1.2501-1.6436-0.4370.921-0.08350.06521.01730.15261.2722-12.681731.787130.2552
103.64492.1501-2.56424.44120.59343.1148-0.1238-0.0741-0.00710.5544-1.8992-0.86050.13031.96010.49420.6108-0.39850.54380.78321.45580.95290.144628.867529.9148
111.8791-1.4589-0.293.07251.53732.05090.48120.16850.01440.15030.4379-1.2593-0.37140.6766-0.35011.37220.0748-0.3005-0.09880.37840.1649-11.796417.283827.4156
124.9805-2.581-3.39293.03883.20433.598-1.73150.3319-1.06780.9092-0.151.0808-0.66460.61041.71470.96590.2902-0.30040.48710.19860.7046-15.877817.337939.4789
134.6244-1.81190.91043.6388-2.51479.4865-0.734-0.97462.30820.3877-0.21930.480.4377-1.18550.0460.60880.15790.2120.7152-0.82062.0145-6.440118.298437.8105
142.01570.80730.59640.86290.79241.3175-0.3352-0.35510.48210.011-0.80750.1092-0.1308-0.41110.36721.4066-0.8313-0.89420.7424-0.47311.0256-5.381533.776240.2154
150.85310.3182-0.50930.8909-0.72070.67150.0314-0.1798-0.18011.2337-0.38810.46350.4671-0.2934-0.35431.03770.57990.57621.8211-1.0639-0.2638-2.874925.761845.4225
161.03171.6843-0.04983.0368-0.61571.0798-0.3053-0.44520.59892.07320.36253.0596-0.5644-0.4316-0.47652.58191.3952-0.82050.0183-0.3633.0029-12.061923.998361.0539
171.21141.85572.08732.83483.20463.62971.1136-1.0478-0.98510.32191.07840.28790.6052-0.53180.54351.21860.54830.66211.34810.65561.4903-36.1563-10.699930.2619
182.7302-0.41113.0462.5246-1.0113.50250.2526-0.91530.3509-0.9941-0.2473-0.12-0.4733-1.14870.20381.6041-0.5564-0.4141-0.0884-1.4809-1.3853-39.90562.168929.4692
195.0235-1.4314-4.18787.70811.61074.09360.4549-0.09480.8290.182-0.0564-0.01320.33670.3073-0.00980.9171-0.7572-0.45331.8569-0.06821.1991-24.0537-2.951527.3107
201.8282-0.6729-0.24772.1874-0.09952.8560.0937-0.93430.0677-0.2691-0.5167-0.95120.392-0.45140.22530.20550.82770.8299-0.5309-1.63750.1651-22.157-6.284939.4359
213.46843.21390.373.71560.09532.72820.0908-0.39050.71620.9378-1.1096-0.071-0.3252-0.0660.26051.0042-0.30160.37460.6544-0.05923.7955-27.69761.60537.623
225.69032.01050.85234.72653.21616.3944-1.3740.2250.97530.1957-1.0859-0.59330.7408-0.77151.13771.8495-0.3477-0.35911.72660.05571.0671-41.8192-5.237240.2917
233.6138-1.5949-0.67661.2606-0.15410.5144-0.5053-0.5057-1.0536-0.325-0.4911-0.3758-0.1311-0.28810.14840.9171-0.4932-0.3941-0.1355-0.14281.4501-36.00621.22345.2234
242.80320.9748-0.82390.77130.16440.7081-0.0968-0.8418-1.5805-0.1268-0.1499-0.95580.31480.45180.68050.50130.16541.12382.11691.80994.3938-29.7073-6.400961.6848
253.44511.2348-0.83180.6843-0.75651.11240.1663-0.57770.897-0.0965-0.30491.53040.7329-1.0464-0.15241.8328-0.52620.11141.0341-0.56783.2726-36.951417.4117-15.4138
266.0749-1.31332.78810.79391.12247.3242-0.22051.57211.3068-0.80171.33030.024-1.6855-0.8051-0.52110.9608-0.3937-0.2991.32320.69221.2451-27.20826.9933-15.9726
270.7372-0.85480.13551.24520.30820.6578-0.1176-0.45731.47090.52620.45480.16030.6116-0.14990.18381.24832.1513-0.42580.86980.5011.1028-23.840410.9253-18.1594
283.9797-1.0347-1.79272.2162.77875.0177-1.07050.5016-2.60970.2226-0.58440.68470.6873-0.35090.92360.7676-0.15470.00560.4463-0.120.8048-25.77737.2884-6.1897
298.50713.06662.21464.1375-1.15983.14190.4159-1.73080.02421.56420.33590.4166-0.15670.4355-0.98970.9324-0.01890.01661.2165-0.63223.4482-21.835615.9556-7.8112
300.2605-0.1832-0.17860.26280.24760.7801-0.5079-0.12120.34990.1438-0.58420.5081-0.2332-0.5217-1.45141.09330.3697-0.90661.2281-1.386-0.3247-34.916924.543-5.6309
310.9868-0.16870.34291.35910.38690.2655-0.84150.423-0.07870.60260.7639-0.8232-0.48240.6195-0.04821.312-0.29640.707-0.16570.25831.9236-26.220423.1625-0.4029
324.9507-0.72461.63871.02940.7151.526-0.73991.064-1.6380.67090.11520.79220.60220.7010.79960.73380.15672.20611.3345-0.31124.3645-29.464513.848715.7272
331.8605-3.4447-1.45266.38092.72991.13890.73910.42171.69160.08240.3866-1.733-0.10140.11260.43530.7620.0373-0.35510.7580.21352.774411.635618.3662-15.358
343.91293.1285-2.96535.0077-1.05592.9281-0.6856-0.6952-1.0404-1.2504-1.5143-0.82450.80952.36860.84662.12090.52790.3690.81870.5660.940715.59125.3799-15.953
350.0853-0.009-0.0083-0.00440.0194-0.00260.1568-0.3764-1.6040.6283-0.29160.1117-0.04310.23470.34140.6148-0.18420.13431.28550.1010.9809-0.140610.3033-18.2621
365.43862.12411.96182.36832.48933.6856-0.2176-0.57450.91480.1976-0.3661.5662-0.9106-0.06190.14780.8495-0.06540.20310.2870.2481.0104-2.298213.9228-6.3539
373.92410.0054-2.79635.4837-1.77656.81850.1999-0.379-0.05821.2443-0.0791-0.11640.3764-0.09660.08450.8776-0.9817-1.5402-0.7153-0.52192.61293.32566.2314-8.1282
384.3039-1.272.33630.4064-0.76241.4618-0.6202-0.33740.6345-0.2237-0.57270.3565-0.6074-0.37050.38620.2592-0.4489-1.14062.20260.03530.625917.058512.774-5.3724
390.16450.35780.35640.76120.70830.6739-0.5981-1.28420.82320.19990.78270.6596-0.6398-0.20390.09112.84140.31860.24431.1166-0.5691.614511.80486.3449-0.3114
403.97510.08270.71993.4860.17633.3887-0.3996-1.7690.39510.54120.13312.22970.1269-1.31820.75790.5620.5783-0.21121.151-0.24412.02245.81513.05514.785
414.07941.26791.47380.4990.21851.13021.1324-0.8851-1.71350.3990.4391-0.99730.5852-0.30380.7211.0533-0.2462-0.1291.4130.72383.1091-11.5314-24.3326-15.2895
422.961.61161.71123.84011.84275.29880.0630.68970.0934-0.3125-0.48531.4978-0.1347-0.27170.36820.34990.3094-0.61671.8261-1.31222.431-24.564-21.1712-15.8179
433.4303-2.6067-1.55822.07440.47756.24470.4053-0.1550.5190.57490.2778-0.20410.25190.12140.23131.38340.0771-0.6150.6134-0.7811.3429-12.2922-9.8311-18.1926
440.397-0.07630.05584.6665-2.38792.4874-0.11630.4606-0.43150.1294-0.4614-0.69130.37481.007-0.44010.5019-0.0238-0.14681.3493-0.60810.4895-8.3697-9.7453-6.0317
458.772-0.8165-2.02118.38161.53968.6775-0.4108-0.22710.270.2509-0.2986-0.9775-0.92890.2987-0.39050.8621-0.1264-0.21930.90940.27331.7512-18.0111-10.7555-7.7794
460.9619-2.01511.26374.6091-3.13263.6664-0.5711-0.26810.3734-0.59650.14250.24120.0818-0.46850.19851.4276-0.273-0.45011.02930.37451.2271-18.8777-26.0287-5.1667
478.59716.2456-0.04115.2204-0.8541.01611.2207-1.28461.07970.1413-0.4992-3.1871-0.25530.5299-0.26480.50820.551-0.2620.1142-0.01252.5221-21.8893-18.15040.1094
480.15350.3803-0.18261.9473-0.5540.21210.4823-1.3872-0.5081.3745-1.2226-1.7772-0.21110.5040.41261.3011-0.1809-1.25241.8311.87514.2484-12.2776-16.351315.956
490.4284-0.22251.1951.217-1.03013.2649-0.3319-2.01021.01530.22351.23870.6195-0.0125-1.2096-0.0240.76730.35330.71511.9117-0.20312.2156-85.154518.286462.8443
503.1825-0.5937-1.68890.21780.7812.8054-0.56960.4339-1.19680.1076-0.5647-0.24961.01971.24020.68561.1129-0.05681.20681.8168-0.64820.8867-75.68138.595563.5002
513.6831-0.98991.0133.36683.65915.39580.4385-0.68761.1338-0.49090.1177-0.899-1.03960.7511-0.27621.2463-0.1228-0.04650.85420.33321.8383-71.843324.63666.0189
522.30141.1986-3.62446.05410.25469.87761.75920.16760.9239-0.6966-0.46261.15320.0588-2.0962-0.88120.2198-0.16030.55911.71410.8593-0.239-74.039827.872853.4547
536.7102-1.0708-1.59718.3590.85780.62460.4613-0.99980.493-0.94490.2411-2.8429-0.17470.43530.66690.432-0.05110.55980.5680.29620.4488-70.107419.061355.0619
542.84612.1080.63322.23870.60451.58610.1979-0.5772-0.69140.2171-0.5057-0.45530.14660.1292-0.11170.58-0.1688-0.75671.281.26572.847-82.510210.6252.5775
550.14770.33290.24330.86710.86671.71330.21850.1425-0.1627-1.1533-0.12620.7953-0.2577-0.6306-0.08571.18370.5765-0.83454.1013.02583.0423-74.927312.290947.9441
561.26730.7460.90752.02932.78133.8408-0.20230.6356-0.1402-0.1536-0.3840.4050.5583-1.13120.7773.13380.56610.26662.3567-0.54110.895-77.818221.074731.7359
571.18670.20131.24710.09430.76135.3059-0.03740.1681-1.82431.02941.6667-0.10562.69620.2274-0.60381.64530.0777-0.05990.7299-0.24891.5948-36.406816.776862.8718
580.12980.30140.29570.61080.64720.66960.8038-0.08161.2656-0.2037-0.5122-0.7771-1.9561.2642-1.49520.8547-0.13741.09591.9791.18210.4778-33.023729.986563.5539
594.2303-1.552-2.32723.4429-0.04523.79380.3444-0.63740.0139-0.23990.07490.6485-0.17230.07680.31980.19460.0924-0.20322.0332-0.643.5214-48.423525.339165.776
603.4933-2.67880.85442.0657-0.81393.6905-0.3215-0.9798-0.8891-0.12560.97541.68622.4139-0.6437-1.05231.63620.3703-0.7360.8870.09321.3696-50.320921.657453.6122
614.3562-3.3195-0.11178.11841.49852.54010.3785-0.06040.5345-0.21160.75960.8820.21660.7419-0.43860.8169-0.24120.47480.96620.43531.2191-44.836129.477555.236
620.5928-0.3322-0.03280.1982-0.0660.3922-0.5429-0.5003-0.55380.3191-0.1075-0.3584-0.11930.0891-0.57930.50662.48480.07921.1082-0.55371.8015-30.764222.776553.1478
633.05880.04321.28960.86880.38040.67120.90031.3378-0.888-0.1661-0.002-0.60640.42680.7866-0.53141.1522-0.0852-0.81311.2389-1.08352.7163-36.330628.727647.7452
643.01541.194-1.3625.7948-1.3421.1984-0.78050.158-0.0639-2.74240.4125-0.09621.0906-1.19550.22172.5189-0.6121-0.1963.81261.65852.0484-42.171621.926231.6498
656.52053.058-4.40512.4806-1.478.39580.3521-0.97611.7561-0.88050.7894-0.4375-1.87320.4703-0.82251.1645-0.41260.54341.20380.57312.6229-59.796759.855262.7768
661.1373-1.30532.90954.8619-5.088.2692-0.7257-0.08580.6125-0.37320.72562.2519-0.9661-3.5052-0.24591.12561.0692-1.00361.86850.14180.4985-72.797956.283363.5834
672.24470.7420.95774.0102-1.96921.75970.1431-1.15940.58721.32760.23610.08410.22510.3977-0.60831.2986-0.3382-0.15630.98490.03131.8673-60.571945.266465.7753
682.4422-0.12881.69531.60121.33992.39941.16420.907-1.1236-0.94050.2238-0.3506-0.5358-0.1127-0.35831.3114-0.69060.61131.0258-0.16951.9536-57.033445.443653.4235
697.47472.47110.52925.93662.33840.9239-0.2869-0.0324-2.7495-0.78430.39450.26270.6887-1.5803-0.35030.7495-0.1061-0.10631.77620.0420.7107-66.510746.360355.2891
703.6585-2.64422.82454.44281.33816.68460.8572-0.7980.24940.6039-1.66970.8712.0278-0.59090.65691.2320.35070.2260.9090.42841.5912-67.714261.366552.8712
711.1571-0.6883-0.49430.8566-0.68022.30490.31950.68720.8221-0.2288-0.26250.251-0.61520.3452-0.21181.3352-0.74762.19251.4608-0.4161.5424-70.081354.050547.6985
727.56220.50712.43631.81831.64995.1676-0.4973.290.1636-1.56090.33550.2178-0.59591.67180.02791.7893-1.217-0.75872.3084-0.55350.9449-61.103552.344931.8855
730.15350.68730.04334.92461.38830.8026-0.11650.04830.36330.81460.01011.5662-0.6783-0.95470.09381.8830.0488-0.16870.1683-0.31442.7513-36.188274.163417.0722
742.52740.62621.29020.18630.10521.75570.6525-0.6308-0.88220.0847-0.33730.20051.4584-2.008-0.40120.2237-0.8509-1.2740.8962-1.40781.7828-39.748461.08417.9771
751.7460.2130.48231.20691.51863.06440.0814-0.28830.5444-0.1370.6257-0.84980.0410.5011-0.02510.89970.0748-0.29631.12780.673.6103-23.86265.916820.2347
761.98122.5371-4.54145.78193.52975.9035-0.30841.23820.5907-0.5250.2948-1.4985-0.924-1.88240.03031.65480.31390.26840.69760.1961.4428-22.225669.46287.8877
779.2390.6977-1.57292.00730.87063.06890.28240.8178-2.2127-1.1733-0.6619-2.34691.8206-0.2814-0.35611.4509-0.0469-0.24310.7320.09910.287-27.833561.54769.3845
780.18790.33850.32950.60550.58440.56340.57370.4767-0.87370.00860.01970.17940.18960.09730.19721.85011.8170.56381.80531.13192.0946-41.57868.07277.3836
790.2735-0.0406-0.04890.0166-0.00490.08530.11650.56530.1621-0.126-0.2530.10360.0108-0.00960.31192.9136-0.76032.4951.25462.04053.3353-36.326762.4052.103
800.4585-0.15470.34740.0446-0.12090.2638-0.23870.00740.0998-0.65680.1313-0.0118-0.69910.36080.00963.5675-1.48861.11411.6965-0.30580.7813-30.164369.1081-13.9259
814.89523.54671.41973.1755-0.26193.27270.3658-0.5261-2.2288-0.69850.4233-0.19691.4953-1.44770.03210.5287-0.31890.27621.1676-0.26312.5497-13.049231.464217.4551
821.46580.6805-3.82980.3031-1.71479.9737-0.7397-0.5889-0.82890.11430.3253-2.78160.90342.34730.34231.2740.09760.45641.2955-0.56963.65570.488634.505318.0424
834.1021-2.47342.23683.0343-0.68441.51160.0843-0.1838-0.98550.74070.90520.22670.16960.5312-0.07180.80610.1310.61661.0787-0.35092.1606-11.762646.075520.0812
847.67225.4468-4.26923.9115-3.18454.95320.50740.3751.50590.44630.59181.23510.3075-1.2803-0.57640.7211-0.1835-0.27640.77090.5030.6062-15.759145.95777.7094
852.28761.0258-3.8098.4781-5.66898.3055-0.84070.50881.2143-1.09040.08141.32370.87451.1213-0.07640.50180.08420.08461.20620.34411.5094-6.260345.1439.4422
861.0048-0.50970.0891.0464-0.37790.22790.0364-0.09810.11160.10290.26370.135-0.0132-0.1492-0.09671.62080.5801-1.90590.76010.09812.0034-4.911629.59717.4132
870.4812-0.2361-0.1290.17130.00660.30480.41330.147-0.6201-0.2881-0.11680.09340.24190.4007-0.13481.8701-1.6415-2.02561.77040.7152.5705-2.763937.09192.3444
884.0078-0.0711-4.15415.8785-0.64714.398-0.19360.6119-0.0688-1.00360.1018-0.0311-0.0567-0.90730.00011.8291-0.4669-0.46191.99741.41260.4082-11.548639.4253-13.5188
892.4841-2.42130.22112.3915-0.51454.3546-0.0661-0.31441.07320.3611-1.3515-0.4-0.7132.00540.62920.7107-0.0768-0.03071.837-0.62962.541112.584172.998417.0325
904.3369-3.29453.34682.5947-2.60462.61370.4870.41461.88010.7065-0.72361.3403-3.4-0.85390.2152.26680.3440.34171.31430.67811.96172.953882.843917.592
910.00820.0385-0.31830.0458-0.45874.7828-0.5720.2934-2.36390.2593-0.28880.17061.53161.24820.13740.78920.11350.43640.95090.24332.6215-0.781466.457919.963
924.16160.6225-3.35450.9961-0.20583.84251.0192.0049-1.173-0.3160.640.3493-0.27651.8288-0.50510.8226-0.38250.24811.92-0.35691.02921.541163.25497.8171
932.104-0.188-0.51222.4521-0.42293.54210.02940.529-0.32570.13890.0512-0.34021.35531.3966-1.30130.3155-0.30280.60350.7231.3517-1.2067-2.488472.08879.6311
943.170.45150.231.31920.42994.41170.93030.0823-0.7339-0.1545-0.0048-0.00080.8130.0572-0.24940.60360.06520.29231.2033-0.44331.284310.08980.66457.2043
950.1198-0.1102-0.09190.07790.070.74140.04120.05860.2092-0.00080.3953-0.3496-0.12690.11080.2460.9614-0.03950.61942.1625-3.7382.78632.192579.16342.1185
966.96923.57581.90845.0604-0.31871.0504-0.2477-0.2081-0.1431-0.70690.74370.5444-0.17450.0896-0.40621.7883-1.03180.74452.6936-0.88393.18015.093970.4175-13.6131
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )A2 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 30 )A18 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 42 )A31 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 64 )A43 - 64
5X-RAY DIFFRACTION5chain 'A' and (resid 65 through 89 )A65 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 95 )A90 - 95
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 106 )A96 - 106
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 122 )A107 - 122
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 17 )B2 - 17
10X-RAY DIFFRACTION10chain 'B' and (resid 18 through 30 )B18 - 30
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 42 )B31 - 42
12X-RAY DIFFRACTION12chain 'B' and (resid 43 through 64 )B43 - 64
13X-RAY DIFFRACTION13chain 'B' and (resid 65 through 89 )B65 - 89
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 95 )B90 - 95
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 106 )B96 - 106
16X-RAY DIFFRACTION16chain 'B' and (resid 107 through 122 )B107 - 122
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 17 )C2 - 17
18X-RAY DIFFRACTION18chain 'C' and (resid 18 through 30 )C18 - 30
19X-RAY DIFFRACTION19chain 'C' and (resid 31 through 42 )C31 - 42
20X-RAY DIFFRACTION20chain 'C' and (resid 43 through 64 )C43 - 64
21X-RAY DIFFRACTION21chain 'C' and (resid 65 through 89 )C65 - 89
22X-RAY DIFFRACTION22chain 'C' and (resid 90 through 95 )C90 - 95
23X-RAY DIFFRACTION23chain 'C' and (resid 96 through 106 )C96 - 106
24X-RAY DIFFRACTION24chain 'C' and (resid 107 through 122 )C107 - 122
25X-RAY DIFFRACTION25chain 'D' and (resid 2 through 17 )D2 - 17
26X-RAY DIFFRACTION26chain 'D' and (resid 18 through 30 )D18 - 30
27X-RAY DIFFRACTION27chain 'D' and (resid 31 through 42 )D31 - 42
28X-RAY DIFFRACTION28chain 'D' and (resid 43 through 64 )D43 - 64
29X-RAY DIFFRACTION29chain 'D' and (resid 65 through 89 )D65 - 89
30X-RAY DIFFRACTION30chain 'D' and (resid 90 through 95 )D90 - 95
31X-RAY DIFFRACTION31chain 'D' and (resid 96 through 106 )D96 - 106
32X-RAY DIFFRACTION32chain 'D' and (resid 107 through 122 )D107 - 122
33X-RAY DIFFRACTION33chain 'E' and (resid 2 through 17 )E2 - 17
34X-RAY DIFFRACTION34chain 'E' and (resid 18 through 30 )E18 - 30
35X-RAY DIFFRACTION35chain 'E' and (resid 31 through 42 )E31 - 42
36X-RAY DIFFRACTION36chain 'E' and (resid 43 through 64 )E43 - 64
37X-RAY DIFFRACTION37chain 'E' and (resid 65 through 89 )E65 - 89
38X-RAY DIFFRACTION38chain 'E' and (resid 90 through 95 )E90 - 95
39X-RAY DIFFRACTION39chain 'E' and (resid 96 through 106 )E96 - 106
40X-RAY DIFFRACTION40chain 'E' and (resid 107 through 120 )E107 - 122
41X-RAY DIFFRACTION41chain 'F' and (resid 2 through 17 )F2 - 17
42X-RAY DIFFRACTION42chain 'F' and (resid 18 through 30 )F18 - 30
43X-RAY DIFFRACTION43chain 'F' and (resid 31 through 42 )F31 - 42
44X-RAY DIFFRACTION44chain 'F' and (resid 43 through 64 )F43 - 64
45X-RAY DIFFRACTION45chain 'F' and (resid 65 through 89 )F65 - 89
46X-RAY DIFFRACTION46chain 'F' and (resid 90 through 95 )F90 - 95
47X-RAY DIFFRACTION47chain 'F' and (resid 96 through 106 )F96 - 106
48X-RAY DIFFRACTION48chain 'F' and (resid 107 through 122 )F107 - 122
49X-RAY DIFFRACTION49chain 'G' and (resid 2 through 17 )G2 - 17
50X-RAY DIFFRACTION50chain 'G' and (resid 18 through 30 )G18 - 30
51X-RAY DIFFRACTION51chain 'G' and (resid 31 through 42 )G31 - 42
52X-RAY DIFFRACTION52chain 'G' and (resid 43 through 64 )G43 - 64
53X-RAY DIFFRACTION53chain 'G' and (resid 65 through 89 )G65 - 89
54X-RAY DIFFRACTION54chain 'G' and (resid 90 through 95 )G90 - 95
55X-RAY DIFFRACTION55chain 'G' and (resid 96 through 106 )G96 - 106
56X-RAY DIFFRACTION56chain 'G' and (resid 107 through 122 )G107 - 122
57X-RAY DIFFRACTION57chain 'H' and (resid 2 through 17 )H2 - 17
58X-RAY DIFFRACTION58chain 'H' and (resid 18 through 30 )H18 - 30
59X-RAY DIFFRACTION59chain 'H' and (resid 31 through 42 )H31 - 42
60X-RAY DIFFRACTION60chain 'H' and (resid 43 through 64 )H43 - 64
61X-RAY DIFFRACTION61chain 'H' and (resid 65 through 89 )H65 - 89
62X-RAY DIFFRACTION62chain 'H' and (resid 90 through 95 )H90 - 95
63X-RAY DIFFRACTION63chain 'H' and (resid 96 through 106 )H96 - 106
64X-RAY DIFFRACTION64chain 'H' and (resid 107 through 122 )H107 - 122
65X-RAY DIFFRACTION65chain 'I' and (resid 2 through 17 )I2 - 17
66X-RAY DIFFRACTION66chain 'I' and (resid 18 through 30 )I18 - 30
67X-RAY DIFFRACTION67chain 'I' and (resid 31 through 42 )I31 - 42
68X-RAY DIFFRACTION68chain 'I' and (resid 43 through 64 )I43 - 64
69X-RAY DIFFRACTION69chain 'I' and (resid 65 through 89 )I65 - 89
70X-RAY DIFFRACTION70chain 'I' and (resid 90 through 95 )I90 - 95
71X-RAY DIFFRACTION71chain 'I' and (resid 96 through 106 )I96 - 106
72X-RAY DIFFRACTION72chain 'I' and (resid 107 through 122 )I107 - 122
73X-RAY DIFFRACTION73chain 'J' and (resid 2 through 17 )J2 - 17
74X-RAY DIFFRACTION74chain 'J' and (resid 18 through 30 )J18 - 30
75X-RAY DIFFRACTION75chain 'J' and (resid 31 through 42 )J31 - 42
76X-RAY DIFFRACTION76chain 'J' and (resid 43 through 64 )J43 - 64
77X-RAY DIFFRACTION77chain 'J' and (resid 65 through 89 )J65 - 89
78X-RAY DIFFRACTION78chain 'J' and (resid 90 through 95 )J90 - 95
79X-RAY DIFFRACTION79chain 'J' and (resid 96 through 106 )J96 - 106
80X-RAY DIFFRACTION80chain 'J' and (resid 107 through 122 )J107 - 122
81X-RAY DIFFRACTION81chain 'K' and (resid 2 through 17 )K2 - 17
82X-RAY DIFFRACTION82chain 'K' and (resid 18 through 30 )K18 - 30
83X-RAY DIFFRACTION83chain 'K' and (resid 31 through 42 )K31 - 42
84X-RAY DIFFRACTION84chain 'K' and (resid 43 through 64 )K43 - 64
85X-RAY DIFFRACTION85chain 'K' and (resid 65 through 89 )K65 - 89
86X-RAY DIFFRACTION86chain 'K' and (resid 90 through 95 )K90 - 95
87X-RAY DIFFRACTION87chain 'K' and (resid 96 through 106 )K96 - 106
88X-RAY DIFFRACTION88chain 'K' and (resid 107 through 122 )K107 - 122
89X-RAY DIFFRACTION89chain 'L' and (resid 2 through 17 )L2 - 17
90X-RAY DIFFRACTION90chain 'L' and (resid 18 through 30 )L18 - 30
91X-RAY DIFFRACTION91chain 'L' and (resid 31 through 42 )L31 - 42
92X-RAY DIFFRACTION92chain 'L' and (resid 43 through 64 )L43 - 64
93X-RAY DIFFRACTION93chain 'L' and (resid 65 through 89 )L65 - 89
94X-RAY DIFFRACTION94chain 'L' and (resid 90 through 95 )L90 - 95
95X-RAY DIFFRACTION95chain 'L' and (resid 96 through 106 )L96 - 106
96X-RAY DIFFRACTION96chain 'L' and (resid 107 through 122 )L107 - 122

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万見について

-
お知らせ

-
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

-
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