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- PDB-4cdk: Structure of ZNRF3-RSPO1 -

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基本情報

登録情報
データベース: PDB / ID: 4cdk
タイトルStructure of ZNRF3-RSPO1
要素
  • E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
  • R-SPONDIN-1
キーワードLIGASE (リガーゼ) / WNT SIGNALING (Wntシグナル経路) / ADULT STEM CELLS / E3 LIGASE (ユビキチンリガーゼ) / PROTEASE-ASSOCIATED DOMAIN / ZINC RING FINGER / LGR5 / R-SPONDIN
機能・相同性
機能・相同性情報


regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / regulation of receptor internalization / frizzled binding / regulation of canonical Wnt signaling pathway / limb development / negative regulation of Wnt signaling pathway / positive regulation of Wnt signaling pathway ...regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / regulation of receptor internalization / frizzled binding / regulation of canonical Wnt signaling pathway / limb development / negative regulation of Wnt signaling pathway / positive regulation of Wnt signaling pathway / Regulation of FZD by ubiquitination / stem cell proliferation / G protein-coupled receptor binding / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Wntシグナル経路 / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / heparin binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of protein phosphorylation / signaling receptor binding / extracellular region / metal ion binding / 細胞核 / 細胞膜
類似検索 - 分子機能
E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Ring finger domain / Glucose Oxidase; domain 1 - #30 / Glucose Oxidase; domain 1 ...E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Ring finger domain / Glucose Oxidase; domain 1 - #30 / Glucose Oxidase; domain 1 / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Furin-like repeat / Furin-like repeats / 薬指 / Growth factor receptor cysteine-rich domain superfamily / Zinc finger RING-type profile. / 3-Layer(bba) Sandwich / Zinc finger, RING-type / リボン / Zinc finger, RING/FYVE/PHD-type / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
R-spondin-1 / E3 ubiquitin-protein ligase ZNRF3
類似検索 - 構成要素
生物種MUS MUSCULUS (ハツカネズミ)
HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Peng, W.C. / de Lau, W. / Madoori, P.K. / Forneris, F. / Granneman, J.C.M. / Clevers, H. / Gros, P.
引用ジャーナル: Plos One / 年: 2013
タイトル: Structures of Wnt-Antagonist Znrf3 and its Complex with R-Spondin 1 and Implications for Signaling.
著者: Peng, W.C. / De Lau, W. / Madoori, P.K. / Forneris, F. / Granneman, J.C.M. / Clevers, H. / Gros, P.
履歴
登録2013年11月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02014年1月8日Provider: repository / タイプ: Initial release
改定 1.12019年4月3日Group: Data collection / Other / Source and taxonomy
カテゴリ: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
B: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
C: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
D: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
E: R-SPONDIN-1
F: R-SPONDIN-1
G: R-SPONDIN-1
H: R-SPONDIN-1


分子量 (理論値)分子数
合計 (水以外)126,7728
ポリマ－126,7728
非ポリマー00
水99155
1
A: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
E: R-SPONDIN-1


分子量 (理論値)分子数
合計 (水以外)31,6932
ポリマ－31,6932
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-10.9 kcal/mol
Surface area14230 Å2
手法PISA
2
C: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
G: R-SPONDIN-1


分子量 (理論値)分子数
合計 (水以外)31,6932
ポリマ－31,6932
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-9.2 kcal/mol
Surface area14430 Å2
手法PISA
3
D: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
H: R-SPONDIN-1


分子量 (理論値)分子数
合計 (水以外)31,6932
ポリマ－31,6932
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-7.8 kcal/mol
Surface area14170 Å2
手法PISA
4
B: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
F: R-SPONDIN-1


分子量 (理論値)分子数
合計 (水以外)31,6932
ポリマ－31,6932
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-7.5 kcal/mol
Surface area14210 Å2
手法PISA
単位格子
Length a, b, c (Å)51.700, 80.160, 82.980
Angle α, β, γ (deg.)66.27, 81.36, 80.66
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
22
/ NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 / ZINC/RING FINGER PROTEIN 3


分子量: 17986.316 Da / 分子数: 4 / 断片: ECTODOMAIN, RESIDUES 53-205 / 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / 細胞株 (発現宿主): HEK293 / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q5SSZ7
#2: タンパク質
R-SPONDIN-1 / ROOF PLATE-SPECIFIC SPONDIN-1 / HRSPO1 / R-SPONDIN 1


分子量: 13706.780 Da / 分子数: 4 / 断片: FURIN-LIKE DOMAIN, RESIDUES 31-145 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q2MKA7
#3: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 55 / 由来タイプ: 天然 / 式: H2O
配列の詳細GS AT N-TERMINUS AND AAAHHHHHH AT C-TERMINUS ARE CLONING ARTIFACTS.

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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: 2.73 Å3/Da / 溶媒含有率: 55 % / 解説: NONE
結晶化詳細: 0.2M SODIUM BROMIDE AND 20% W/V PEG 3350

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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: SLS / ビームライン: X06SA / 波長: 1
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL
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: 2.8→75.63 Å / Num. obs: 29157 / % possible obs: 95.4 % / Observed criterion σ(I): 3.2 / 冗長度: 2.2 % / Biso Wilson estimate: 54.27 Å2 / Rmerge(I) obs: 0.09
反射 シェル解像度: 2.8→75.63 Å

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解析

ソフトウェア名称: PHENIX / バージョン: (PHENIX.REFINE) / 分類: 精密化
精密化構造決定の手法: 分子置換 / 解像度: 2.8→44.706 Å / SU ML: 0.34 / σ(F): 1.97 / 位相誤差: 27.5 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2464 1437 5.1 %
Rwork0.2177 --
obs0.2192 28133 95.3 %
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: 83.8 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→44.706 Å
タンパク質核酸リガンド溶媒全体
原子数7896 0 0 55 7951
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0058111
X-RAY DIFFRACTIONf_angle_d1.20910912
X-RAY DIFFRACTIONf_dihedral_angle_d11.9673058
X-RAY DIFFRACTIONf_chiral_restr0.0481207
X-RAY DIFFRACTIONf_plane_restr0.0061442
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.90020.32891500.28742668X-RAY DIFFRACTION95
2.9002-3.01620.26061380.26112665X-RAY DIFFRACTION95
3.0162-3.15350.29041230.26282694X-RAY DIFFRACTION95
3.1535-3.31970.27521450.24322680X-RAY DIFFRACTION96
3.3197-3.52760.26171280.23642659X-RAY DIFFRACTION94
3.5276-3.79980.27031590.23572647X-RAY DIFFRACTION95
3.7998-4.1820.26461510.20582676X-RAY DIFFRACTION97
4.182-4.78650.16891350.17542677X-RAY DIFFRACTION95
4.7865-6.02820.23731580.20992660X-RAY DIFFRACTION95
6.0282-44.71210.24391500.20262670X-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)
10.57570.0601-0.47080.24990.01510.24370.18460.10720.31730.0792-0.4661-0.3397-0.15440.7159-0.01240.3310.0351-0.02410.41280.01780.34327.972619.437219.4723
20.2604-0.0124-0.0110.1353-0.1630.2882-0.1630.14440.2848-0.2217-0.18240.0669-0.10380.1487-0.04780.29090.0276-0.07720.2611-0.06850.21512.440614.4614.8379
30.01570.02110.00490.01860.0070.0072-0.1630.2111-0.38430.00080.17680.18270.0222-0.1081-0.00110.3993-0.0333-0.07580.3802-0.06910.4502-8.08841.40213.6863
40.8640.36370.15370.9996-0.13020.0085-0.1766-0.0941-0.3384-0.09930.179-0.0556-0.1473-0.5015-0.07160.3151-0.0005-0.08090.3507-0.00750.3085-1.63743.494718.8322
50.22330.1715-0.29270.5541-0.22150.68620.477-1.5829-1.5663-0.0143-0.3264-0.75520.1707-0.1124-1.02920.25030.17530.13760.4696-0.3152-0.80682.98357.05326.7637
60.2436-0.1162-0.22550.1906-0.02110.47950.452-0.20590.22720.08050.1871-0.144-0.1870.15770.29420.381-0.098-0.00580.3306-0.15590.41657.212618.41218.1923
70.34430.2320.2040.25630.05280.5024-0.1098-0.2145-0.1083-0.53270.00390.09930.65660.2596-0.10330.4473-0.0067-0.13760.3139-0.08550.350820.507911.19158.9282
80.0503-0.0442-0.12420.0555-0.09780.5006-0.1179-0.1881-0.2342-0.4529-0.21890.4850.24360.0289-0.07990.4264-0.0452-0.09910.3511-0.14220.708111.91873.67684.0195
90.10090.1125-0.20470.1493-0.26640.4475-0.3944-0.26950.2444-0.0469-0.139-0.43340.0357-0.0482-0.1180.2762-0.0665-0.0350.4026-0.08150.537524.646922.977715.6177
100.0139-0.0224-0.02720.08240.09990.09360.2751-0.05190.0298-0.23150.015-0.0984-0.3832-0.08810.28060.5251-0.1831-0.07330.385-0.22240.033515.701323.33850.265
110.0181-0.0042-0.00340.05-0.0970.02910.04750.2721-0.2710.1851-0.1660.1004-0.21670.0231-0.0010.43920.01120.00620.37050.04930.309811.72427.53281.0183
120.027-0.001-0.0131-0.00640.03080.02850.111-0.12230.0376-0.2462-0.3443-0.0530.18080.2005-0.00010.67320.08840.08810.54610.06340.540128.458633.5164-4.3409
130.1577-0.2176-0.10860.32140.06880.04140.2447-0.01960.1701-0.0825-0.31220.2992-0.4036-0.4275-0.25370.4250.02230.00850.2552-0.10650.403818.011128.71545.949
140.41790.16220.4040.07470.14880.32350.4042-0.2310.56380.0533-0.2226-0.6871-0.17540.01170.01010.2351-0.0480.05350.2394-0.03840.646727.596827.74089.2327
150.01660.0286-0.00390.06450.02630.03450.0407-0.1009-0.0451-0.6912-0.4144-0.17390.42440.2491-0.00140.45130.06940.07930.5236-0.06280.315423.881913.1734-2.9321
160.3009-0.1389-0.11820.14030.02050.051-0.5704-0.4058-0.10480.3242-0.0418-0.0540.29040.4142-0.13960.4698-0.1893-0.23630.061-0.748-0.302117.666513.27139.966
170.2692-0.075-0.13950.104-0.24210.23270.2041-0.1268-0.5124-0.0360.04590.1301-0.04970.07410.02890.3172-0.00640.03820.34560.01860.43615.273132.71130.9565
180.2785-0.01690.01190.5606-0.20810.52490.0852-0.079-0.031-0.15010.28620.62290.35710.01950.17210.1825-0.01120.07750.39160.09060.37283.675534.536932.5128
190.0439-0.0067-0.01860.5423-0.1750.0570.3033-0.0779-0.08530.510.02180.4602-0.0064-0.00080.04340.373-0.00210.01190.4574-0.0260.248514.465941.285139.3147
200.0235-0.01430.0235-0.02570.02340.02730.04-0.18280.1496-0.1641-0.0113-0.1492-0.08150.31290.00020.56280.11150.08580.7174-0.02210.716216.297750.646441.0739
211.3959-0.61610.1831.6145-0.19180.67420.0127-0.4215-0.26350.23420.13090.1561-0.18140.09540.38060.2972-0.01860.0840.45990.04620.280210.291736.108844.8393
220.0799-0.05310.04010.072-0.03830.09980.11520.021-0.26520.38820.38190.1019-0.5038-0.153100.3931-0.09980.04690.46710.05850.6946-6.748748.327534.605
230.0044-0.04720.03440.097-0.07780.09140.0111-0.1376-0.00630.32440.0018-0.0966-0.5066-0.0523-0.00090.62410.06910.01160.42210.0460.6621-1.311453.457238.0507
240.2376-0.26060.02570.2682-0.07450.1760.16620.1314-0.05030.04410.06440.15950.1374-0.2598-0.0480.3897-0.0588-0.14460.46870.1320.9461-11.669935.350426.202
250.9879-0.001-0.4940.1265-0.03190.32-0.1543-0.3864-0.3945-0.49710.0133-0.103-0.14270.3593-0.04730.51730.0047-0.0669-0.0627-0.1340.5797-3.295849.712819.9182
260.00630.00160.00860.03510.0650.02860.5231-0.15640.36160.0552-0.2010.11440.35670.03640.00020.32220.29190.05870.49120.11340.51853.584746.739414.2221
270.0358-0.052-0.17310.09210.21080.57340.045-0.0239-0.0718-0.19990.02170.0381-0.13720.28540.01220.321-0.1071-0.0790.1901-0.01340.3387-12.594551.022415.64
280.09230.04930.0057-0.0033-0.03510.1636-0.29160.163-0.4186-0.3242-0.49290.25140.3670.1498-0.25620.4488-0.1205-0.2770.3243-0.20090.6725-8.424542.533110.8659
290.1950.07810.14821.08140.44732.0030.41130.366-0.1058-0.31270.39810.76040.046-0.01010.68260.4202-0.0403-0.16970.26330.13110.6263-13.841745.032318.9978
300.17180.0075-0.10040.03060.05410.1969-0.07650.1635-0.3124-0.1032-0.37720.46430.0696-0.066-0.15710.29120.1193-0.18340.2599-0.04521.0726-11.064432.775519.0481
310.1090.1116-0.26320.3077-0.30030.39230.1162-0.1546-0.1116-0.52810.4523-0.0174-0.543-0.66520.46490.20090.01430.20010.34590.16990.7346-12.363352.75526.8565
320.1067-0.0795-0.23950.19490.21960.9337-0.5386-0.2135-0.07940.1702-0.01780.185-0.1008-0.06-0.53630.3516-0.00710.00230.2714-0.02250.7611-4.487847.174132.7612
330.72370.31260.0260.14410.08010.44970.0592-0.48710.0639-0.04450.1425-0.10420.0427-0.0955-0.64790.43380.33640.4471.1673-0.43450.9219-22.626411.315826.912
340.718-0.6853-0.0660.59840.05810.0441-0.3002-0.2110.4815-0.1940.3048-0.23220.0708-0.40940.03590.3617-0.0829-0.060.52690.04230.2663-16.5197.833718.9929
350.1424-0.16140.02960.0596-0.01520.04610.03230.1887-0.0959-0.3630.1664-0.28610.30750.11340.19470.66920.0058-0.12120.3049-0.10190.3588-20.6988-1.011910.7804
360.01960.02610.01370.03110.01720.01320.2076-0.16620.250.0501-0.0437-0.1642-0.03790.04910.00020.53390.05660.14380.41810.06560.5615-14.41212.37292.8026
370.10250.03990.05710.10230.09620.1164-0.25820.00640.0765-0.2524-0.23090.13630.2004-0.4673-0.00140.89560.20290.13870.77160.0860.4347-16.4571-2.5485-6.4985
380.2503-0.40550.01160.66560.04060.07130.00230.0811-0.1554-0.046-0.0787-0.2150.02950.0094-0.06191.18110.33420.5220.65151.2699-0.3618-11.2376-2.9302-18.0506
390.10530.0020.10290.0258-0.01020.10010.2071-0.0376-0.3083-0.05960.0884-0.17150.2859-0.01930.02591.1868-0.35280.02881.1822-0.0370.9566-17.7511-9.5321-17.4654
400.0642-0.0475-0.01290.0840.13210.14830.0032-0.18880.0908-0.8907-0.0817-0.18920.252-0.02230.00050.8660.04310.09540.4770.03450.356519.485827.5681-14.4703
410.0635-0.1089-0.0936-0.00330.0695-0.06920.1015-0.15680.40490.10860.01130.4675-0.0112-0.1215-01.02950.0533-0.0411.45970.11241.2026-2.978538.1049-16.1261
420.6585-0.20730.00640.1279-0.18950.6104-0.6171-0.0798-0.18320.762-0.8545-0.63970.3407-0.0963-1.15490.38820.0777-0.15840.48570.95530.511932.33235.79145.6925
430.22180.03840.27020.38230.3790.8365-0.14840.10030.1084-0.0228-0.444-0.6499-0.20480.2304-0.75290.4151-0.0619-0.13050.72240.24740.616926.91842.033138.4224
44-0.005-0.0361-0.02370.03230.03360.01390.1259-0.15180.18080.5221-0.2571-0.462-0.2341-0.0186-0.00060.7594-0.0577-0.02190.71710.14210.548232.902150.947746.4565
450.034-0.0062-0.03660.01440.00650.0420.2963-0.33020.2706-0.2277-0.06160.2160.10310.00450.00680.61250.09780.03740.6982-0.04730.64226.391157.237539.2554
460.0274-0.0662-0.05660.15490.18020.2337-0.2952-0.1322-0.32880.10470.5828-0.3924-0.1768-0.0727-0.01780.76830.1413-0.03810.91630.12450.710328.326762.312443.4018
470.03190.03180.0070.0489-0.00390.0195-0.03910.0911-0.2468-0.05580.1433-0.3095-0.2875-0.19970.00130.72790.10760.07120.61690.19410.57329.27370.356438.2523
480.2859-0.1951-0.09110.13470.06010.0268-0.0264-0.19930.1660.0253-0.09810.0512-0.0677-0.0502-0.00230.77950.16390.10411.07170.30640.613723.472978.100435.9572
490.08560.0042-0.01640.009-0.00510.0001-0.0438-0.00850.01950.00390.03250.0266-0.0251-0.0609-01.57720.0787-0.04240.8589-0.15761.511626.498582.787141.4983
500.1211-0.0802-0.06380.20110.10.06960.0192-0.19790.0240.2678-0.0923-0.0299-0.1736-0.13220.04731.22640.0254-0.76141.25150.25551.217431.747578.77242.6939
510.12840.0575-0.0130.2044-0.09430.28150.54760.1944-0.0298-0.0121-0.2362-0.1058-0.45110.36730.00360.6458-0.06-0.02930.28180.02040.4718-6.815861.42279.6525
521.2526-0.08650.03050.0053-0.01050.25580.330.5656-0.8308-0.5759-0.30610.08270.5870.18620.00671.1302-0.0856-0.00110.9366-0.11861.3021.095356.5571-0.1309
530.02910.03810.02270.0747-0.03850.061-0.05350.0261-0.206-0.09630.0145-0.05670.13430.0251-0.02081.55840.39160.00592.00720.32151.841214.856555.83262.1505
54-0.0134-0.00490.0038-0.00180.0003-0.00270.0435-0.1143-0.04190.04020.0376-0.0176-0.00040.1382-01.39810.04730.18441.86550.1341.9320.346357.6768-0.8439
550.0036-0.0004-0.0029-0.0039-0.0008-0.00490.27790.01980.1867-0.0449-0.03060.01910.1065-0.06480.00041.7754-0.03010.68162.21290.23572.51529.22561.9827-4.2262
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 57 THROUGH 93 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 94 THROUGH 100 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 101 THROUGH 113 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 114 THROUGH 157 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 158 THROUGH 197 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 198 THROUGH 208 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 54 THROUGH 68 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 69 THROUGH 83 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 84 THROUGH 93 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 94 THROUGH 106 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 107 THROUGH 125 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 126 THROUGH 138 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 139 THROUGH 157 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 158 THROUGH 184 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 185 THROUGH 197 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 198 THROUGH 211 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 57 THROUGH 68 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 69 THROUGH 93 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 94 THROUGH 106 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 107 THROUGH 119 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 120 THROUGH 211 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 56 THROUGH 68 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 69 THROUGH 84 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 85 THROUGH 93 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 94 THROUGH 106 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 107 THROUGH 119 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 120 THROUGH 132 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 133 THROUGH 148 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 149 THROUGH 168 )
30X-RAY DIFFRACTION30CHAIN D AND (RESID 169 THROUGH 178 )
31X-RAY DIFFRACTION31CHAIN D AND (RESID 179 THROUGH 197 )
32X-RAY DIFFRACTION32CHAIN D AND (RESID 198 THROUGH 209 )
33X-RAY DIFFRACTION33CHAIN E AND (RESID 36 THROUGH 45 )
34X-RAY DIFFRACTION34CHAIN E AND (RESID 46 THROUGH 76 )
35X-RAY DIFFRACTION35CHAIN E AND (RESID 77 THROUGH 92 )
36X-RAY DIFFRACTION36CHAIN E AND (RESID 93 THROUGH 101 )
37X-RAY DIFFRACTION37CHAIN E AND (RESID 102 THROUGH 126 )
38X-RAY DIFFRACTION38CHAIN E AND (RESID 127 THROUGH 131 )
39X-RAY DIFFRACTION39CHAIN E AND (RESID 132 THROUGH 145 )
40X-RAY DIFFRACTION40CHAIN F AND (RESID 40 THROUGH 76 )
41X-RAY DIFFRACTION41CHAIN F AND (RESID 77 THROUGH 142 )
42X-RAY DIFFRACTION42CHAIN G AND (RESID 39 THROUGH 60 )
43X-RAY DIFFRACTION43CHAIN G AND (RESID 61 THROUGH 76 )
44X-RAY DIFFRACTION44CHAIN G AND (RESID 77 THROUGH 92 )
45X-RAY DIFFRACTION45CHAIN G AND (RESID 93 THROUGH 101 )
46X-RAY DIFFRACTION46CHAIN G AND (RESID 102 THROUGH 111 )
47X-RAY DIFFRACTION47CHAIN G AND (RESID 112 THROUGH 126 )
48X-RAY DIFFRACTION48CHAIN G AND (RESID 127 THROUGH 131 )
49X-RAY DIFFRACTION49CHAIN G AND (RESID 132 THROUGH 136 )
50X-RAY DIFFRACTION50CHAIN G AND (RESID 137 THROUGH 145 )
51X-RAY DIFFRACTION51CHAIN H AND (RESID 39 THROUGH 76 )
52X-RAY DIFFRACTION52CHAIN H AND (RESID 77 THROUGH 96 )
53X-RAY DIFFRACTION53CHAIN H AND (RESID 97 THROUGH 106 )
54X-RAY DIFFRACTION54CHAIN H AND (RESID 107 THROUGH 126 )
55X-RAY DIFFRACTION55CHAIN H AND (RESID 127 THROUGH 143 )

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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