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- PDB-7zlx: Crystal Structure of the TSG101-UEV domain:space group P21 -

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基本情報

登録情報
データベース: PDB / ID: 7zlx
タイトルCrystal Structure of the TSG101-UEV domain:space group P21
要素Tumor susceptibility gene 101 protein
キーワードPROTEIN BINDING / UEV-domain
機能・相同性
機能・相同性情報


positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / positive regulation of exosomal secretion / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / virion binding / endosome to lysosome transport / viral budding via host ESCRT complex / negative regulation of epidermal growth factor receptor signaling pathway / viral release from host cell / autophagosome maturation / keratinocyte differentiation / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / ubiquitin binding / HCMV Late Events / macroautophagy / regulation of cell growth / Late endosomal microautophagy / Budding and maturation of HIV virion / protein modification process / calcium-dependent protein binding / late endosome membrane / transcription corepressor activity / late endosome / early endosome membrane / early endosome / regulation of cell cycle / endosome membrane / endosome / negative regulation of cell population proliferation / cell division / ubiquitin protein ligase binding / centrosome / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. / ESCRT assembly domain / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
類似検索 - ドメイン・相同性
Tumor susceptibility gene 101 protein
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: 2.25 Å
Model detailspH 7.0 P21 polymorph
データ登録者Camara-Artigas, A.
資金援助 スペイン, 1件
組織認可番号国
Ministerio de Ciencia e Innovacion (MCIN)BIO2016-78020-R スペイン
引用ジャーナル: To be published
タイトル: Crystal Structure of the TSG101-UEV domain:space group P21
著者: Camara-Artigas, A.
履歴
登録2022年4月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年6月22日Provider: repository / タイプ: Initial release
改定 1.12024年1月31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: Tumor susceptibility gene 101 protein
B: Tumor susceptibility gene 101 protein
C: Tumor susceptibility gene 101 protein
D: Tumor susceptibility gene 101 protein
E: Tumor susceptibility gene 101 protein
F: Tumor susceptibility gene 101 protein
G: Tumor susceptibility gene 101 protein
H: Tumor susceptibility gene 101 protein
I: Tumor susceptibility gene 101 protein
J: Tumor susceptibility gene 101 protein
K: Tumor susceptibility gene 101 protein
L: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)219,85522
ポリマ－218,89412
非ポリマー96110
水9,422523
1
A: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Tumor susceptibility gene 101 protein


分子量 (理論値)分子数
合計 (水以外)18,2411
ポリマ－18,2411
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
9
I: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
10
J: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
11
K: Tumor susceptibility gene 101 protein


分子量 (理論値)分子数
合計 (水以外)18,2411
ポリマ－18,2411
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
12
L: Tumor susceptibility gene 101 protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3372
ポリマ－18,2411
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)38.921, 168.223, 195.548
Angle α, β, γ (deg.)90.000, 92.910, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

#1: タンパク質
Tumor susceptibility gene 101 protein / ESCRT-I complex subunit TSG101 / TSG101


分子量: 18241.164 Da / 分子数: 12 / 断片: UEV domain, residues 1-145 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TSG101 / プラスミド: pET15 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q99816
#2: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 10 / 由来タイプ: 合成 / 式: SO4
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 523 / 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N

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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: 2.92 Å3/Da / 溶媒含有率: 57.89 % / Mosaicity: 0.23 °
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 25 % PEG 4000, 0.25 M Ammonium Sulfate, 0.1 proline, 0.1 M HEPES

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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: ESRF / ビームライン: ID23-2 / 波長: 0.8726 Å
検出器タイプ: DECTRIS PILATUS3 X 2M / 検出器: PIXEL / 日付: 2015年7月5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: 0.8726 Å / 相対比: 1
反射解像度: 2.25→39.06 Å / Num. obs: 107096 / % possible obs: 90.2 % / 冗長度: 4.4 % / Biso Wilson estimate: 34.19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.067 / Rrim(I) all: 0.15 / Net I/σ(I): 7.2 / Num. measured all: 474707 / Scaling rejects: 12
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.294.51.0242479054500.5580.5031.1491.390.8
12.32-39.064.80.04827285730.9980.0220.05320.877

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.4459精密化
XDSデータ削減
Aimless0.7.7データスケーリング
PHASER位相決定
PDB_EXTRACT3.27データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 2F0R

2f0r


解像度: 2.25→39.06 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 1.04 / 位相誤差: 27.42 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2445 5170 4.83 %
Rwork0.2255 101888 -
obs0.2264 107058 90.16 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 133.79 Å2 / Biso mean: 48.1535 Å2 / Biso min: 21.4 Å2
精密化ステップサイクル: final / 解像度: 2.25→39.06 Å
タンパク質核酸リガンド溶媒全体
原子数12855 0 50 523 13428
Biso mean--56.48 39.99 -
残基数----1721
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.280.35941600.33363483364391
2.28-2.30.31282020.32243442364491
2.3-2.330.31671630.31923387355093
2.33-2.360.36411810.32123429361092
2.36-2.390.31992000.30473457365792
2.39-2.420.34061760.30193494367091
2.42-2.460.3061990.29783409360893
2.46-2.490.29811920.28913425361792
2.5-2.530.29881650.28323437360292
2.53-2.580.32871850.27963503368891
2.58-2.620.33751650.27143488365393
2.62-2.670.33561530.27843429358292
2.67-2.720.33781940.27053459365392
2.72-2.770.28761630.25953463362690
2.77-2.830.28281600.25313357351790
2.83-2.90.30341810.25323399358091
2.9-2.970.29771640.25953480364491
2.97-3.050.31540.25523440359492
3.05-3.140.3041470.24773365351290
3.14-3.240.28291980.23283488368691
3.24-3.360.21671680.2213337350591
3.36-3.490.23191710.20923435360691
3.5-3.650.20541510.20393390354190
3.65-3.850.19011880.19553387357589
3.85-4.090.19262010.17553243344488
4.09-4.40.17661850.15913346353188
4.4-4.840.16331620.15463241340385
4.84-5.540.20651350.18183296343186
5.54-6.980.21481630.21893240340386
6.98-39.060.21011440.20733139328381
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)
11.0669-1.83930.9855.2324-2.75352.08730.18570.76910.0501-1.1024-0.3829-1.730.38730.7330.18380.61740.20320.24170.5559-0.03790.736648.80351.034443.0068
24.4718-1.197-2.29596.91081.81865.8225-0.19630.08-0.53250.0763-0.0176-0.65710.30250.32320.22150.2980.02750.02910.36620.03340.316643.859658.071552.4594
37.9665-3.9188-2.61387.06796.11257.7858-0.6863-0.2819-0.32971.60560.46660.48870.68170.18080.20340.47830.03590.07910.26280.08020.258238.522463.527562.6086
41.57970.2752-0.84362.47210.79579.0231-0.09270.0493-0.456-0.0493-0.0248-0.22431.01250.02130.13310.540.02990.01760.2353-0.03410.283434.540953.063958.4716
53.09392.02033.94049.55296.82039.218-0.17550.0343-0.1724-0.8388-0.12870.258-0.641-0.09360.29910.39880.0290.00850.21960.0110.218131.577960.595851.2912
66.2723.9536.00444.00914.355.9780.2780.06740.38620.3772-0.15560.30311.0293-0.4072-0.18870.3564-0.0331-0.01510.37740.07890.235333.346963.01471.3084
74.0440.35210.06056.1532-0.07455.6765-0.0015-0.1737-0.4877-0.7316-0.0140.43950.4084-0.54280.02610.4243-0.0697-0.07330.38280.06110.382529.6565-29.351746.7172
81.9387-0.640.26573.9651-1.22757.28230.115-0.073-0.1376-0.266-0.23660.0507-0.37110.39270.11030.4695-0.0726-0.01650.330.10750.325639.2696-28.730241.7627
93.60670.8259-0.77827.95563.61387.35230.519-0.16230.3281-0.05090.3732-1.0205-0.29360.9645-0.93280.2515-0.01340.03720.5867-0.08930.666157.1846-23.3075-5.3459
103.59390.82240.48293.94976.10832.11380.11310.1511-0.1672-0.2583-0.0121-0.6161-0.27020.4432-0.21610.361-0.0260.00830.2825-0.00030.246848.9568-25.6817-6.9885
113.9611-3.158-0.82792.8766-0.82095.5697-0.5432-0.7305-1.07640.12921.01610.31740.68580.2376-0.44030.3709-0.0334-0.03170.43330.08040.620649.2871-30.92154.8367
122.6212-0.6716-1.55975.4994.88426.7214-0.0507-0.354-0.18980.48680.2357-0.365-0.37720.4842-0.17220.4504-0.0519-0.0670.2390.03980.234343.6701-24.88814.9828
133.1130.07340.57012.42564.25277.6095-0.0462-0.3725-0.08910.8010.36320.04030.2070.2585-0.3260.8916-0.0443-0.08840.29570.0360.302243.6121-27.370913.8251
141.8287-0.619-0.34476.0572-0.16485.14140.1067-0.22-0.23520.66170.02220.48120.6123-0.4701-0.06880.3982-0.08-0.00890.22860.00710.36534.617-28.5425.7181
151.2751-0.81090.01433.51311.01575.6989-0.0792-0.4064-0.13421.2212-0.0740.20940.644-0.22790.07080.5524-0.08010.01630.30810.03590.265235.605-19.547511.0433
166.11185.28272.96796.543.71666.6663-0.21840.5087-0.1886-0.25790.8202-1.3883-0.06091.1811-0.62510.31950.00030.07640.3984-0.0850.544150.076-28.678189.4112
172.8831-0.9578-0.727.51317.74438.93980.06950.29120.0118-1.4309-0.1584-0.344-1.22980.52960.0230.4887-0.06340.04390.33730.03860.239643.6934-23.976488.8169
185.3147-3.6644-0.30867.8149-1.45815.7698-0.2159-0.7439-1.09940.40960.474-0.04090.25680.2276-0.27930.2402-0.1005-0.02060.50980.06550.525344.9748-32.5729100.7423
195.8291-4.3701-3.77335.77865.31989.6901-0.3052-0.06690.00090.91960.1558-0.42340.2030.11870.15250.397-0.0539-0.07280.2050.03720.237539.3792-23.1121104.6382
206.1362-1.822-0.36267.81493.23633.9880.19160.1931-0.6004-0.0771-0.17250.1269-0.2626-0.04490.01870.1789-0.02760.01010.1621-0.03740.289538.4308-34.739690.7855
216.22252.00923.25862.44654.13727.20790.0408-0.3724-0.39980.05160.1229-0.3506-0.04390.0938-0.15310.6603-0.0361-0.02110.25940.0450.280739.7985-28.6315109.8523
221.55170.36011.87711.9731.89854.60860.0266-0.3241-0.32870.4249-0.0030.19930.8408-0.5417-0.00060.4489-0.12110.03160.30010.0390.316130.4292-30.7147107.1181
233.4387-2.219-2.57176.64256.44366.9298-0.12180.0012-0.3046-0.0318-0.08550.5465-0.0415-0.30910.15370.2231-0.0130.01340.17130.03540.210730.7955-24.646995.279
246.72212.5975.82492.39184.51288.7305-0.5425-0.02060.60990.72710.1502-0.3036-1.9968-0.39930.36660.9156-0.0824-0.04250.34250.01080.258132.646-20.4333116.6848
253.82841.5311-0.64543.74172.17681.99370.0431-0.07130.15480.4056-0.5401-1.55670.39030.77870.43260.3164-0.011-0.04310.55360.08610.655452.677541.411918.8069
264.92310.0557-1.07786.3363-1.11632.29940.15720.80770.2067-0.2344-0.1217-0.65040.1490.06610.00640.25190.0694-0.04350.3649-0.01150.34246.766236.756715.9567
275.22082.7898-1.14827.7245-3.27743.8179-0.18030.00030.1049-0.22-0.1105-0.73620.70890.62820.26380.36260.2030.0250.3772-0.040.296343.720129.007515.6357
282.33271.8265-2.84574.6521-6.04898.2108-0.35560.2012-0.0968-0.61930.179-0.25480.4701-0.2030.20080.29930.0388-0.0460.1978-0.00730.201839.666131.437915.6424
293.14360.5905-1.7186.82841.53773.8918-0.06290.3058-0.3207-0.11520.0310.27010.9652-0.00670.02280.4166-0.0012-0.05020.2346-0.02170.243235.387125.66319.4297
303.56630.2344-1.05115.2742-4.80096.7660.046-0.05830.2110.32210.31030.3614-0.5451-0.3163-0.34690.2610.03420.04240.2156-0.02530.189932.758835.147219.3026
315.6602-3.3828-6.32127.65522.65967.2773-0.2298-0.5621-0.27910.3169-0.1331.31631.6910.1760.38591.0187-0.021-0.02870.3229-0.06930.326633.62114.184214.3933
323.688-2.3015-1.47799.26472.732.5822-0.1411-0.269-0.09630.32310.00150.98040.4247-0.33130.13310.3083-0.0862-0.00030.32970.00780.32327.1902-53.46480.377
332.0771-1.6592-0.54913.2770.94122.7095-0.0165-0.165-0.08070.12610.0405-0.07140.44740.065-0.02760.3951-0.0586-0.00650.1902-0.01250.21237.9628-56.670884.1619
347.592-0.1027-1.25192.50351.90745.3820.07110.1513-0.38350.4561-0.14570.0646-0.345-0.27110.05180.4673-0.0717-0.0120.3279-0.00930.250421.401-11.1229-11.0004
354.9928-0.58542.34073.96162.97453.7878-0.06210.37221.0774-0.445-0.4029-0.4873-0.40850.76080.32370.4889-0.11760.09970.47980.03560.564426.0308-0.2192-9.0452
362.9356-0.15430.57892.22873.45095.3868-0.07510.04290.2690.1982-0.1980.0593-0.4811-0.39470.28420.5304-0.02890.02430.21590.01450.236930.0744-2.535-3.0598
372.1036-1.4092-0.89017.12792.99633.38080.0643-0.0970.2286-0.1512-0.0561-0.1971-0.40020.0065-0.00280.4227-0.03530.01080.21340.00390.208236.86380.0667-0.1466
387.06771.849-4.94712.1107-0.66073.66210.05750.96370.2620.47130.1180.2689-0.4334-1.0779-0.17340.59310.0130.00330.53750.05650.270712.7021-11.091384.4653
398.75351.074-8.15776.742-2.34832.0136-0.045-0.5794-0.96530.919-0.3278-0.21450.9798-0.13290.40890.4502-0.1042-0.03170.36820.0340.293121.2856-15.339987.6996
404.7444-0.2091.95923.91772.64893.09-0.09930.45690.7002-0.3228-0.21120.0064-0.62710.11680.21640.3904-0.01390.0280.24660.06070.376522.9183-1.838793.3119
411.67141.11730.30426.69964.27813.90810.08330.12660.2596-0.2027-0.01090.1399-0.6921-0.0612-0.08570.3770.00850.03870.21970.0570.242328.93370.534591.1131
425.5157-4.2293-1.11178.20594.3124.16740.54430.10220.8239-1.4841-0.2172-0.7194-1.24330.0825-0.30580.5948-0.06140.09390.2790.00030.28135.2884-0.447990.6774
433.32051.31411.09898.64524.94468.81530.12340.14610.06520.0079-0.13790.01440.98240.17010.0460.40390.0128-0.03660.19430.02440.191133.1341-10.474592.8445
444.6261-4.2176-1.80527.91076.13326.5112-0.2276-0.1537-0.27920.7583-0.03320.0074-0.4181-0.22260.2610.82340.03930.0870.2476-0.02860.40430.62415.1073107.3409
454.2799-0.2891.91164.6739-1.00414.9083-0.2429-0.32190.3109-0.38120.1894-0.2598-0.83940.19810.05790.5698-0.07480.07010.4728-0.02570.277242.1382-8.298963.7472
462.4795-0.7255-0.50614.1055-0.7932.5247-0.05650.16650.1741-0.73490.07470.0899-0.294-0.1162-0.0230.6229-0.0642-0.0070.40640.05930.23431.8479-3.032558.0895
479.1807-0.6594-4.42397.29083.68545.32720.00280.7905-0.1557-0.36340.00290.8077-0.0378-1.2366-0.04270.3956-0.0599-0.08920.63990.04150.292826.5095-97.336924.7896
484.8118-0.920.83456.9505-0.30372.769-0.1270.60910.3007-0.67360.2045-0.2749-0.2166-0.317-0.11040.37040.00510.02420.3816-0.0070.231631.04-95.784932.2252
495.7844-1.28034.19074.7125-0.84327.7373-0.0473-0.42440.37720.4221-0.0532-0.1624-0.8201-0.40370.11720.3635-0.04030.08440.2474-0.02090.262136.0533-90.272242.9054
504.73990.4851-0.675.06121.53336.11540.08360.02490.5631-0.07560.1205-0.0408-1.01350.4962-0.20410.4536-0.06830.06810.2990.00740.239741.1929-86.149235.3347
516.8810.19860.13853.4274.52556.23030.12790.0852-0.0423-0.1521-0.3314-0.17690.75770.51630.19210.48950.01590.00750.33630.03490.224344.7158-96.530136.1433
526.5746-4.3508-4.38076.99775.52435.96840.338-1.00550.26651.40330.749-0.8566-0.6320.4058-1.07960.88140.0621-0.00690.4666-0.1080.371342.4749-82.082351.6607
534.17554.12734.58794.07464.5215.0249-0.8855-1.5745-0.22970.7641-0.34880.49440.5591-1.01961.2211.2747-0.06390.26580.6143-0.13110.65377.350330.500432.88
543.4723.31483.26483.6362.51763.94760.121-0.53681.41670.1248-0.55620.8659-0.334-1.03220.44440.42250.1668-0.01880.4018-0.17290.641818.78143.795338.752
559.09854.72782.10019.22746.04714.1363-0.08350.1610.1458-0.4468-0.09240.00540.1049-0.10760.16380.50260.1016-0.06610.3064-0.04630.234223.163438.295731.5989
564.3225-1.9852-1.37235.7751-0.31062.7089-0.1237-1.10580.070.67450.41630.00760.04610.2906-0.27610.37490.0001-0.02640.5060.01490.279223.774429.750342.3652
572.40292.3251-0.2136.46143.38663.2946-0.2905-0.2557-0.25730.41820.0141-0.01651.1207-0.06940.21460.75910.13080.05320.32580.04730.271327.304820.130737.4819
582.72661.60380.70685.71610.75814.3419-0.2774-0.71930.99430.4950.05950.13250.1402-0.33290.25090.29620.112-0.01020.3645-0.12760.348330.417141.358941.1337
594.94055.1185-1.56452.013-5.53666.38130.2189-0.284-0.20631.02530.67570.87280.4013-0.4247-0.90770.76330.10320.08690.39550.05970.46126.999522.416345.8708
601.97450.2091-0.39666.77850.5274.1437-0.0055-0.3723-0.2430.35940.0506-0.11960.55590.2362-0.05490.43510.0672-0.01960.3482-0.0060.222535.442825.783939.2407
618.3339-4.99056.31813.8689-3.13434.9078-0.00291.08410.7511-0.5593-0.3725-0.69230.14220.78170.38510.4559-0.1120.04870.44960.10590.395658.0149-48.302960.7675
626.0048-2.69041.75022.0165-7.26595.19390.1886-0.4608-0.27761.3653-0.1559-0.1076-0.62990.0559-0.01490.6505-0.0888-0.10230.35070.03450.371849.9166-49.579366.0873
634.79361.4998-1.37997.3334-2.50144.9417-0.22760.6467-0.1469-0.7030.2171-0.32110.8050.18770.01220.47920.01980.03570.4081-0.06630.260148.3954-61.721758.3794
643.4770.0104-0.11943.38470.5553.0316-0.03220.6187-0.2141-0.71570.03310.13030.2568-0.07920.00440.565-0.0479-0.0240.36420.00430.203540.1951-59.236553.7558
653.3963-0.9483-0.30196.3051-2.5448.92640.15910.0920.0171.0651-0.00130.45710.0083-0.1537-0.17150.3799-0.02310.05120.26220.00550.21837.8627-56.231564.175
666.436-5.5702-0.79396.43053.34237.1019-0.9451-0.95050.12050.61940.01790.93651.1539-0.49170.94611.12850.0977-0.06340.4602-0.20280.512739.8171-75.718956.3356
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'K' and (resid 6 through 17 )K6 - 17
2X-RAY DIFFRACTION2chain 'K' and (resid 18 through 63 )K18 - 63
3X-RAY DIFFRACTION3chain 'K' and (resid 64 through 75 )K64 - 75
4X-RAY DIFFRACTION4chain 'K' and (resid 76 through 115 )K76 - 115
5X-RAY DIFFRACTION5chain 'K' and (resid 116 through 137 )K116 - 137
6X-RAY DIFFRACTION6chain 'K' and (resid 138 through 145 )K138 - 145
7X-RAY DIFFRACTION7chain 'L' and (resid 6 through 75 )L6 - 75
8X-RAY DIFFRACTION8chain 'L' and (resid 76 through 145 )L76 - 145
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 11 )A2 - 11
10X-RAY DIFFRACTION10chain 'A' and (resid 12 through 31 )A12 - 31
11X-RAY DIFFRACTION11chain 'A' and (resid 32 through 48 )A32 - 48
12X-RAY DIFFRACTION12chain 'A' and (resid 49 through 85 )A49 - 85
13X-RAY DIFFRACTION13chain 'A' and (resid 86 through 94 )A86 - 94
14X-RAY DIFFRACTION14chain 'A' and (resid 95 through 123 )A95 - 123
15X-RAY DIFFRACTION15chain 'A' and (resid 124 through 145 )A124 - 145
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 17 )B1 - 17
17X-RAY DIFFRACTION17chain 'B' and (resid 18 through 31 )B18 - 31
18X-RAY DIFFRACTION18chain 'B' and (resid 32 through 48 )B32 - 48
19X-RAY DIFFRACTION19chain 'B' and (resid 49 through 75 )B49 - 75
20X-RAY DIFFRACTION20chain 'B' and (resid 76 through 85 )B76 - 85
21X-RAY DIFFRACTION21chain 'B' and (resid 86 through 94 )B86 - 94
22X-RAY DIFFRACTION22chain 'B' and (resid 95 through 115 )B95 - 115
23X-RAY DIFFRACTION23chain 'B' and (resid 116 through 137 )B116 - 137
24X-RAY DIFFRACTION24chain 'B' and (resid 138 through 145 )B138 - 145
25X-RAY DIFFRACTION25chain 'C' and (resid 0 through 17 )C0 - 17
26X-RAY DIFFRACTION26chain 'C' and (resid 18 through 48 )C18 - 48
27X-RAY DIFFRACTION27chain 'C' and (resid 49 through 63 )C49 - 63
28X-RAY DIFFRACTION28chain 'C' and (resid 64 through 85 )C64 - 85
29X-RAY DIFFRACTION29chain 'C' and (resid 86 through 115 )C86 - 115
30X-RAY DIFFRACTION30chain 'C' and (resid 116 through 137 )C116 - 137
31X-RAY DIFFRACTION31chain 'C' and (resid 138 through 145 )C138 - 145
32X-RAY DIFFRACTION32chain 'D' and (resid 0 through 75 )D0 - 75
33X-RAY DIFFRACTION33chain 'D' and (resid 76 through 145 )D76 - 145
34X-RAY DIFFRACTION34chain 'E' and (resid -1 through 29 )E-1 - 29
35X-RAY DIFFRACTION35chain 'E' and (resid 30 through 48 )E30 - 48
36X-RAY DIFFRACTION36chain 'E' and (resid 49 through 85 )E49 - 85
37X-RAY DIFFRACTION37chain 'E' and (resid 86 through 145 )E86 - 145
38X-RAY DIFFRACTION38chain 'F' and (resid -2 through 17 )F-2 - 17
39X-RAY DIFFRACTION39chain 'F' and (resid 18 through 31 )F18 - 31
40X-RAY DIFFRACTION40chain 'F' and (resid 32 through 75 )F32 - 75
41X-RAY DIFFRACTION41chain 'F' and (resid 76 through 104 )F76 - 104
42X-RAY DIFFRACTION42chain 'F' and (resid 105 through 115 )F105 - 115
43X-RAY DIFFRACTION43chain 'F' and (resid 116 through 137 )F116 - 137
44X-RAY DIFFRACTION44chain 'F' and (resid 138 through 145 )F138 - 145
45X-RAY DIFFRACTION45chain 'G' and (resid 6 through 63 )G6 - 63
46X-RAY DIFFRACTION46chain 'G' and (resid 64 through 145 )G64 - 145
47X-RAY DIFFRACTION47chain 'H' and (resid 4 through 17 )H4 - 17
48X-RAY DIFFRACTION48chain 'H' and (resid 18 through 49 )H18 - 49
49X-RAY DIFFRACTION49chain 'H' and (resid 50 through 75 )H50 - 75
50X-RAY DIFFRACTION50chain 'H' and (resid 76 through 115 )H76 - 115
51X-RAY DIFFRACTION51chain 'H' and (resid 116 through 137 )H116 - 137
52X-RAY DIFFRACTION52chain 'H' and (resid 138 through 145 )H138 - 145
53X-RAY DIFFRACTION53chain 'I' and (resid -2 through 4 )I-2 - 4
54X-RAY DIFFRACTION54chain 'I' and (resid 5 through 17 )I5 - 17
55X-RAY DIFFRACTION55chain 'I' and (resid 18 through 31 )I18 - 31
56X-RAY DIFFRACTION56chain 'I' and (resid 32 through 63 )I32 - 63
57X-RAY DIFFRACTION57chain 'I' and (resid 64 through 75 )I64 - 75
58X-RAY DIFFRACTION58chain 'I' and (resid 76 through 85 )I76 - 85
59X-RAY DIFFRACTION59chain 'I' and (resid 86 through 94 )I86 - 94
60X-RAY DIFFRACTION60chain 'I' and (resid 95 through 145 )I95 - 145
61X-RAY DIFFRACTION61chain 'J' and (resid -2 through 17 )J-2 - 17
62X-RAY DIFFRACTION62chain 'J' and (resid 18 through 31 )J18 - 31
63X-RAY DIFFRACTION63chain 'J' and (resid 32 through 75 )J32 - 75
64X-RAY DIFFRACTION64chain 'J' and (resid 76 through 115 )J76 - 115
65X-RAY DIFFRACTION65chain 'J' and (resid 116 through 137 )J116 - 137
66X-RAY DIFFRACTION66chain 'J' and (resid 138 through 145 )J138 - 145

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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