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- PDB-6pxl: 3.74 Angstroms resolution structure of HlsU with an axial-channel plug -

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基本情報

登録情報
データベース: PDB / ID: 6pxl
タイトル3.74 Angstroms resolution structure of HlsU with an axial-channel plug
要素ATP-dependent protease ATPase subunit HslU
キーワードHYDROLASE / AAA+ ATPase / peptidase
機能・相同性
機能・相同性情報


protein denaturation / HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding ...protein denaturation / HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / identical protein binding / membrane / cytosol
類似検索 - 分子機能
Heat shock protein HslU / : / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease ATPase subunit HslU / ATP-dependent protease ATPase subunit HslU
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.741 Å
データ登録者Baytshtok, V. / Grant, R.A. / Sauer, R.T.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) 米国
引用ジャーナル: Cell Rep / 年: 2021
タイトル: Heat activates the AAA+ HslUV protease by melting an axial autoinhibitory plug.
著者: Baytshtok, V. / Fei, X. / Shih, T.T. / Grant, R.A. / Santos, J.C. / Baker, T.A. / Sauer, R.T.
履歴
登録2019年7月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月29日Provider: repository / タイプ: Initial release
改定 1.12021年2月10日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32023年11月15日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
改定 1.42024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: ATP-dependent protease ATPase subunit HslU
B: ATP-dependent protease ATPase subunit HslU
C: ATP-dependent protease ATPase subunit HslU
D: ATP-dependent protease ATPase subunit HslU
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
G: ATP-dependent protease ATPase subunit HslU
H: ATP-dependent protease ATPase subunit HslU
I: ATP-dependent protease ATPase subunit HslU
J: ATP-dependent protease ATPase subunit HslU
K: ATP-dependent protease ATPase subunit HslU
L: ATP-dependent protease ATPase subunit HslU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)616,99629
ポリマ－611,60412
非ポリマー5,39117
水00
1
A: ATP-dependent protease ATPase subunit HslU
B: ATP-dependent protease ATPase subunit HslU
C: ATP-dependent protease ATPase subunit HslU
D: ATP-dependent protease ATPase subunit HslU
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)308,48614
ポリマ－305,8026
非ポリマー2,6848
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area34250 Å2
ΔGint-136 kcal/mol
Surface area100150 Å2
手法PISA
2
G: ATP-dependent protease ATPase subunit HslU
H: ATP-dependent protease ATPase subunit HslU
I: ATP-dependent protease ATPase subunit HslU
J: ATP-dependent protease ATPase subunit HslU
K: ATP-dependent protease ATPase subunit HslU
L: ATP-dependent protease ATPase subunit HslU
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)308,51015
ポリマ－305,8026
非ポリマー2,7089
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area35330 Å2
ΔGint-140 kcal/mol
Surface area100380 Å2
手法PISA
単位格子
Length a, b, c (Å)414.594, 92.331, 200.849
Angle α, β, γ (deg.)90.000, 114.370, 90.000
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質
ATP-dependent protease ATPase subunit HslU / Heat shock protein HslU / Unfoldase HslU


分子量: 50967.012 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: hslU / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: C3SIX7, UniProt: P0A6H5*PLUS
#2: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM
#3: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4
#4: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Mg
研究の焦点であるリガンドがあるかN
Has protein modificationY

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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: 2.86 Å3/Da / 溶媒含有率: 57.03 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.2 M ammonium sulfate, 18% PEG-3350, 0.1 M TRIS pH 7.5

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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: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2016年8月6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: 3.74→100 Å / Num. obs: 68296 / % possible obs: 94.62 % / 冗長度: 3.8 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.068 / Rrim(I) all: 0.14 / Net I/σ(I): 10.3
反射 シェル解像度: 3.74→3.81 Å / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 68296 / CC1/2: 0.691 / Rpim(I) all: 0.397 / Rrim(I) all: 0.694

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3211精密化
PDB_EXTRACT3.24データ抽出
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1DO0

1do0


解像度: 3.741→49.56 Å / SU ML: 0.52 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 29.03
Rfactor反射数%反射
Rfree0.2651 3465 5.07 %
Rwork0.2202 --
obs0.2225 68296 94.62 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 388.31 Å2 / Biso mean: 159.6123 Å2 / Biso min: 68.93 Å2
精密化ステップサイクル: final / 解像度: 3.741→49.56 Å
タンパク質核酸リガンド溶媒全体
原子数36674 0 337 0 37011
Biso mean--120.92 --
残基数----4667
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 (%)
3.741-3.79180.4057960.3347167261
3.7918-3.84590.35741430.3261214779
3.8459-3.90330.38191260.3167230286
3.9033-3.96430.37971350.2998249992
3.9643-4.02920.30891350.2848256893
4.0292-4.09870.31220.2876258495
4.0987-4.17320.31881310.2743263196
4.1732-4.25340.29691330.2703260196
4.2534-4.34020.29661280.2587262596
4.3402-4.43450.27451540.2436263296
4.4345-4.53760.28411370.2363259396
4.5376-4.65090.29771320.229261496
4.6509-4.77660.26081380.229260795
4.7766-4.9170.251420.2226268097
4.917-5.07560.28791280.2343265998
5.0756-5.25680.28581530.2379269799
5.2568-5.4670.29481490.2389272099
5.467-5.71550.28041490.2378270099
5.7155-6.01630.27571530.2456269899
6.0163-6.39260.27851740.2441269398
6.3926-6.88490.28191600.21792741100
6.8849-7.57560.23071380.2068276799
7.5756-8.66670.18631240.1646276199
8.6667-10.90.18471600.1584275299
10.9-49.560.27661250.1899288899
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)
10.1659-0.0533-0.19990.10720.2843-0.06050.18440.1212-0.0882-0.1601-0.1954-0.06970.2039-0.0907-01.25960.0516-0.02850.9743-0.06791.062-94.8047-10.070281.486
20.7587-0.68940.43430.28230.0704-0.53940.3848-0.0833-0.11940.0497-0.61790.33250.032-0.22301.1863-0.4043-0.16841.15370.02091.146-114.562-26.861890.202
31.66760.2272-1.444-0.437-0.01890.32040.01180.035-0.2699-0.20730.0785-0.1497-0.2541-0.1393-00.96080.0756-0.140.74830.03170.9889-106.2547-0.589790.2232
40.1298-0.062-0.03860.0238-0.0283-0.03020.13390.44470.23120.53450.16560.4689-0.7912-0.858501.01850.20550.07641.5040.20991.2107-129.92712.194983.9587
5-0.34120.91120.03970.12080.87360.93940.3233-0.2149-0.2290.37070.1367-0.0870.3716-0.2289-00.95580.0843-0.2951.1190.30571.3925-132.7358-14.4048104.5106
6-0.04270.0619-0.01950.0250.06580.23110.39720.4105-0.031-0.39890.3239-0.2510.46660.603502.28250.40610.12643.13950.58352.9709-124.3172-30.7693126.5324
70.0185-0.0978-0.0022-0.02070.01740.029-0.0596-0.29690.3373-0.37680.27110.49680.21230.6295-02.8986-0.4274-0.80422.23670.22732.243-126.9541-34.7746122.1438
80.38750.0836-0.6158-0.02260.12811.2232-0.0377-0.1038-0.0866-0.07870.1664-0.2183-0.0832-0.389700.82250.03020.02071.2350.1711.1656-128.77411.2841108.3055
90.11110.03140.21890.0342-0.15650.05650.2640.1289-0.42240.5757-0.1738-0.4859-0.747-0.789-01.24130.22650.13751.56310.33811.4445-144.565711.1591128.6337
100.22820.0708-0.21530.02120.26590.25370.47180.3929-0.13450.2216-0.3739-0.2068-0.2009-0.263701.1082-0.00350.17211.6641-0.04111.4198-135.0641-3.987136.199
11-0.21480.0682-0.49860.1044-0.1321-0.1572-0.2504-0.05780.04380.33720.0941-0.4015-0.3162-0.718102.1595-0.14920.13661.64960.14471.2937-125.4497-40.1457147.0463
120.62620.38240.11770.4652-0.1830.94280.58790.16590.1223-0.234-0.16060.3066-0.0042-0.1494-01.39390.270.03161.40150.17061.0708-126.5052-2.4447137.3056
130.44780.52740.39540.01510.13320.14150.366-0.50230.2234-0.12-0.14740.2463-0.43870.375-01.4732-0.1080.281.5183-0.05251.0824-118.80096.1408164.4545
140.0895-0.1114-0.28980.04540.03320.40730.0156-0.5844-0.0118-0.2571-0.1116-0.01370.55570.18801.3273-0.07150.02172.07440.21850.9199-110.4993-11.2374162.3267
150.7676-0.09250.22830.09560.2765-0.4393-0.55960.0804-0.3211-0.1250.5039-1.27150.1012-0.144101.71930.05580.1431.3453-0.06111.4085-100.9716-32.679147.9317
16-0.0854-0.1432-0.00860.00760.0809-0.05120.24310.39690.45370.13281.17350.05220.71780.0253-02.53680.3695-0.41732.9492-0.12812.223-97.1167-33.0773128.9323
171.82090.187-0.0749-0.3186-0.0956-0.15090.3321-0.6022-0.0470.0845-0.31030.3679-0.06060.3627-01.3068-0.1153-0.01351.62360.36290.9995-91.8252-10.8362153.8439
180.0037-0.08450.06240.15820.0710.0847-0.2356-0.6661-0.3543-0.5819-0.2399-0.36030.2961-0.1557-00.85390.4308-0.16472.29380.81751.8749-67.7903-20.9697146.3547
19-0.0652-0.030.01610.02830.0180.034-0.1027-0.5438-0.05770.29610.4024-0.06160.19520.257401.2501-0.0247-0.06951.970.34011.3248-79.3062-17.3857149.1171
200.04760.03940.01670.0310.1090.1120.0540.2243-0.2017-0.6898-0.6724-0.17050.174-0.015801.363-0.4078-0.2241.40070.43291.8979-78.2823-14.5289132.9605
21-0.1939-0.1521-0.0072-0.06330.1238-0.30170.12040.1769-0.804-0.257-0.05040.03920.1949-0.00750-4.7042-4.6545-3.55080.1349-0.28130.1523-83.0723-27.1109130.1985
220.25950.01860.68150.21710.46880.62980.2922-0.4869-0.1047-0.14490.0026-0.180.1735-0.222-01.4418-0.1313-0.04341.48750.17211.2983-76.4278-17.6961134.3868
230.17510.03450.37580.1549-0.1210.2570.3056-0.344-0.0534-0.338-0.12250.1905-0.35750.7148-01.218-0.1287-0.03431.3693-0.09061.3854-53.5592-5.8879118.5661
240.2268-0.00590.15880.3485-0.15420.32730.3098-0.0706-0.266-0.1244-0.1243-0.0973-0.03390.111100.87910.0408-0.0930.93960.05341.4728-68.6169-16.4719107.3896
250.01090.2386-0.03470.10970.0567-0.1133-0.25280.46220.1943-0.2114-0.0388-0.19250.07640.2267-01.326-0.05340.10561.0749-0.23761.0787-89.3304-39.403893.797
26-0.026-0.0787-0.1071-0.0034-0.0135-0.05720.4339-1.4575-0.457-0.1886-0.46150.00560.59660.487402.21350.1689-0.36962.18670.22421.7843-101.8248-34.388999.4451
271.8392-0.3381-0.28980.24340.19460.79590.1074-0.00550.0225-0.0264-0.0197-0.2948-0.2279-0.01301.025-0.0147-0.02640.6844-0.07430.8616-77.2485-6.628697.1659
280.1151-0.114-0.23120.2579-0.36660.15020.10740.40850.32530.36290.20340.2183-0.2343-0.527901.4130.77540.00491.67890.46351.2859-114.585348.572621.4627
290.04340.051-0.16830.0071-0.07240.01580.00330.80370.2244-0.0270.2972-0.3952-0.1949-0.236201.27820.28290.03621.42070.3531.3701-100.424241.75516.3234
30-0.0980.0075-0.10760.009-0.0101-0.03780.0980.53660.53-0.07270.0916-0.3656-0.51060.026601.60880.0242-0.27781.09220.55681.6042-92.777652.939120.319
31-0.0981-0.2362-0.33370.16610.1226-0.27130.0830.19530.72250.01050.11370.50360.9133-0.0903-02.1180.21850.25022.26630.37132.6784-74.013266.225713.7351
320.1344-0.13250.15280.1288-0.11390.01160.40060.25340.52720.65780.0629-0.73360.28120.465801.46170.20810.19771.6525-0.30332.1218-83.059363.52517.5854
330.14620.12840.06150.01290.0140.08930.45920.5043-0.4578-0.1690.1587-0.02920.09130.371601.35740.295-0.04911.28970.1641.3532-101.229329.960824.3764
340.41790.0383-0.31960.4194-0.20960.457-0.05390.2155-0.00610.1355-0.1472-0.0719-0.1131-0.2996-01.11160.189-0.07721.51220.29291.0908-107.179741.561410.9992
350.2071-0.1670.24650.1360.1070.09180.12620.70190.17540.1061-0.18450.13210.6889-0.3826-01.424-0.3775-0.23312.31950.30081.3314-105.986236.547-12.6761
360.0504-0.09420.13010.01930.06180.0524-0.52940.58260.161-0.50490.3544-0.3936-0.2025-0.948301.2180.16-0.22291.48350.37051.3414-86.066544.822-15.387
37-0.02190.0467-0.14280.0541-0.0195-0.1262-0.3601-0.0264-0.5860.06550.3393-0.758-0.8516-0.362201.56380.3461-0.18961.67170.03610.5897-92.728744.429-4.791
380.2844-0.2601-0.02750.17380.23670.09510.13710.50610.32120.4193-0.22060.54920.25330.1926-01.4466-0.0149-0.0321.5376-0.17661.2668-76.428940.7031.0744
390.03480.08930.22660.0436-0.0680.02670.1560.2122-0.4281-0.3560.08810.0108-0.4566-0.5664-01.42-0.1639-0.01381.73610.12721.3587-51.298672.4702-5.3671
40-0.04920.0647-0.15640.2674-0.07690.20610.3213-0.3552-0.0194-0.1032-0.2751-0.30130.0233-0.176701.08250.1350.0631.3351-0.11111.4236-62.984554.09433.4342
410.6436-0.50670.32610.21080.07810.1023-0.50120.11590.19460.22070.37590.31160.24260.5688-01.19310.00660.01431.9057-0.0431.11-87.774433.2834-2.0874
420.1705-0.18610.01690.11950.26360.2422-0.04290.11180.2782-0.3571-0.1562-0.32970.2812-0.300401.5959-0.05030.17341.6311-0.05391.1582-62.354423.3001-20.7705
430.0469-0.01090.03710.02890.01510.02340.4521-0.052-0.007-0.23460.102-0.3806-0.0250.207-01.8774-0.07850.26351.5207-0.09471.318-64.33911.1893-17.9473
440.18060.05880.24910.15360.18820.37570.42390.30130.115-0.4939-0.5104-0.1660.27720.383401.05330.10320.25911.40390.27951.3506-52.016127.3182-7.511
450.0356-0.11440.2663-0.0295-0.06530.10680.0603-0.33280.3499-0.2711-0.20920.04520.5280.356301.0630.00280.05281.1143-0.08721.3894-55.482331.07249.3258
46-0.1154-0.2092-0.23820.2163-0.2303-0.1139-0.3921-0.4677-0.89140.09710.2824-0.42470.23760.3674-02.02360.13890.05312.67170.01562.0935-54.810447.955626.9251
470.432-0.11050.59920.5838-0.55241.509-0.17430.0222-0.0599-0.30070.0833-0.02790.14410.1458-00.90950.03170.15640.87230.03641.1091-50.112517.01589.8322
4800.03770.02050.02060.01030.0637-0.2956-0.50280.2420.1405-0.0899-0.41250.15530.475500.929-0.0664-0.26661.36490.07381.3266-37.354513.101939.5838
490.00920.04640.02470.0101-0.00190.03830.5647-0.66890.16850.09550.5581-0.03990.1430.1291-01.10790.1405-0.09671.21860.01491.3542-37.679615.729829.4326
500.2938-0.3013-0.02120.2935-0.07350.05630.369-0.18740.6144-0.1681-0.297-0.47640.1738-0.427501.33130.31890.23031.10690.32291.2235-50.589417.232930.1069
51-0.07420.06460.0583-0.02270.0271-0.01430.3924-0.42271.0351-0.2849-0.3198-1.9625-0.34520.2159-02.12810.40410.3315-0.41760.0672.2198-53.049330.953737.5866
52-0.04160.04050.07950.0065-0.08350.0143-0.417-0.33320.5831-0.2399-0.1152-0.510.26530.2027-02.7173-0.29250.68491.2143-0.03812.2548-45.834241.92240.0012
530.146-0.1778-0.10630.14640.0670.14320.2252-0.00990.1404-0.1639-0.11420.28-0.88-0.6893-01.24140.26420.14311.2310.26391.05-60.877813.832623.4098
540.0056-0.16750.0710.02310.0240.18260.27660.4855-0.2457-0.31340.0489-0.4071-0.5611-0.6273-01.45990.29620.22220.86020.3671.1733-54.5120.964425.9155
550.0365-0.025-0.03270.01570.05120.04530.3834-0.63040.1232-0.2340.11960.0895-0.29930.113101.64460.27040.25971.2455-0.22441.3984-51.83126.062824.4289
560.1106-0.1804-0.07990.483-0.09090.32970.0079-0.3774-0.3790.01740.037-0.00540.26150.187901.25150.1511-0.03881.10760.13811.3079-55.8112.469958.941
570.19080.07150.1850.46920.41430.2839-0.1329-0.562-0.0333-0.19220.01070.1319-0.32560.517-01.13550.06970.00540.9540.06580.9517-64.27318.814163.1778
58-1.2561-0.4901-0.3085-0.03670.7853-0.91060.5799-2.7118-0.2894-0.6951-0.10530.2529-0.57340.9609-00.56460.91120.0556-2.12210.0260.3071-73.39346.034358.3368
590.08280.2570.04890.03450.09780.0455-0.39370.14860.5083-0.3436-0.24480.49010.50810.017802.43910.2115-0.19162.17760.0552.0649-77.380953.410842.326
60-0.2086-0.1888-0.0191-0.03870.0792-0.03780.2255-0.24090.17880.2243-0.4176-0.5267-0.3403-0.6126-02.04370.05550.08661.7227-0.21121.5102-71.098450.167754.5606
610.8682-0.5380.25310.47510.10030.25150.04990.0721-0.11590.1389-0.00250.0759-0.0331-0.042101.1880.08450.03650.75120.08111.0427-86.544118.185558.5918
620.157-0.005-0.05940.3026-0.28550.27490.0404-0.10410.2211-0.0912-0.07080.3733-0.3020.2359-01.20760.25930.02351.06840.11460.9074-100.617335.945152.8107
63-0.3977-0.5357-0.2890.0948-0.1765-0.0542.3382-4.12475.01521.08170.2268-1.5346-1.30931.095400.23841.4282-1.9169-1.50282.4574-2.9105-92.865172.231543.2431
640.3188-0.32690.78570.4746-0.2210.56230.18050.4873-0.0350.0894-0.12670.0548-0.28570.217901.17240.21190.031.2010.24911.0972-100.510433.310244.4623
650.1298-0.04720.10230.00030.24740.1439-0.76520.8892-0.21120.17430.6369-0.07850.3452-0.893900.85230.3237-0.06162.00560.27151.0956-125.857535.179829.5193
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 62 )A1 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 235 )A63 - 235
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 408 )A236 - 408
4X-RAY DIFFRACTION4chain 'A' and (resid 409 through 443 )A409 - 443
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 165 )B0 - 165
6X-RAY DIFFRACTION6chain 'B' and (resid 166 through 195 )B166 - 195
7X-RAY DIFFRACTION7chain 'B' and (resid 196 through 232 )B196 - 232
8X-RAY DIFFRACTION8chain 'B' and (resid 233 through 386 )B233 - 386
9X-RAY DIFFRACTION9chain 'B' and (resid 387 through 443 )B387 - 443
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 95 )C1 - 95
11X-RAY DIFFRACTION11chain 'C' and (resid 96 through 232 )C96 - 232
12X-RAY DIFFRACTION12chain 'C' and (resid 233 through 369 )C233 - 369
13X-RAY DIFFRACTION13chain 'C' and (resid 370 through 443 )C370 - 443
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 62 )D1 - 62
15X-RAY DIFFRACTION15chain 'D' and (resid 63 through 165 )D63 - 165
16X-RAY DIFFRACTION16chain 'D' and (resid 166 through 206 )D166 - 206
17X-RAY DIFFRACTION17chain 'D' and (resid 217 through 443 )D217 - 443
18X-RAY DIFFRACTION18chain 'E' and (resid 3 through 38 )E3 - 38
19X-RAY DIFFRACTION19chain 'E' and (resid 39 through 62 )E39 - 62
20X-RAY DIFFRACTION20chain 'E' and (resid 63 through 95 )E63 - 95
21X-RAY DIFFRACTION21chain 'E' and (resid 96 through 118 )E96 - 118
22X-RAY DIFFRACTION22chain 'E' and (resid 119 through 369 )E119 - 369
23X-RAY DIFFRACTION23chain 'E' and (resid 370 through 443 )E370 - 443
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 95 )F1 - 95
25X-RAY DIFFRACTION25chain 'F' and (resid 96 through 165 )F96 - 165
26X-RAY DIFFRACTION26chain 'F' and (resid 166 through 232 )F166 - 232
27X-RAY DIFFRACTION27chain 'F' and (resid 233 through 443 )F233 - 443
28X-RAY DIFFRACTION28chain 'G' and (resid 2 through 62 )G2 - 62
29X-RAY DIFFRACTION29chain 'G' and (resid 63 through 95 )G63 - 95
30X-RAY DIFFRACTION30chain 'G' and (resid 96 through 118 )G96 - 118
31X-RAY DIFFRACTION31chain 'G' and (resid 119 through 211 )G119 - 211
32X-RAY DIFFRACTION32chain 'G' and (resid 212 through 250 )G212 - 250
33X-RAY DIFFRACTION33chain 'G' and (resid 251 through 286 )G251 - 286
34X-RAY DIFFRACTION34chain 'G' and (resid 287 through 369 )G287 - 369
35X-RAY DIFFRACTION35chain 'G' and (resid 370 through 443 )G370 - 443
36X-RAY DIFFRACTION36chain 'H' and (resid 2 through 38 )H2 - 38
37X-RAY DIFFRACTION37chain 'H' and (resid 39 through 62 )H39 - 62
38X-RAY DIFFRACTION38chain 'H' and (resid 63 through 118 )H63 - 118
39X-RAY DIFFRACTION39chain 'H' and (resid 119 through 165 )H119 - 165
40X-RAY DIFFRACTION40chain 'H' and (resid 166 through 268 )H166 - 268
41X-RAY DIFFRACTION41chain 'H' and (resid 269 through 350 )H269 - 350
42X-RAY DIFFRACTION42chain 'H' and (resid 351 through 421 )H351 - 421
43X-RAY DIFFRACTION43chain 'H' and (resid 422 through 443 )H422 - 443
44X-RAY DIFFRACTION44chain 'I' and (resid 1 through 62 )I1 - 62
45X-RAY DIFFRACTION45chain 'I' and (resid 63 through 118 )I63 - 118
46X-RAY DIFFRACTION46chain 'I' and (resid 119 through 210 )I119 - 210
47X-RAY DIFFRACTION47chain 'I' and (resid 224 through 443 )I224 - 443
48X-RAY DIFFRACTION48chain 'J' and (resid 0 through 20 )J0 - 20
49X-RAY DIFFRACTION49chain 'J' and (resid 21 through 39 )J21 - 39
50X-RAY DIFFRACTION50chain 'J' and (resid 40 through 95 )J40 - 95
51X-RAY DIFFRACTION51chain 'J' and (resid 96 through 118 )J96 - 118
52X-RAY DIFFRACTION52chain 'J' and (resid 119 through 249 )J119 - 249
53X-RAY DIFFRACTION53chain 'J' and (resid 250 through 286 )J250 - 286
54X-RAY DIFFRACTION54chain 'J' and (resid 287 through 314 )J287 - 314
55X-RAY DIFFRACTION55chain 'J' and (resid 315 through 336 )J315 - 336
56X-RAY DIFFRACTION56chain 'J' and (resid 337 through 443 )J337 - 443
57X-RAY DIFFRACTION57chain 'K' and (resid 0 through 62 )K0 - 62
58X-RAY DIFFRACTION58chain 'K' and (resid 63 through 165 )K63 - 165
59X-RAY DIFFRACTION59chain 'K' and (resid 166 through 211 )K166 - 211
60X-RAY DIFFRACTION60chain 'K' and (resid 212 through 250 )K212 - 250
61X-RAY DIFFRACTION61chain 'K' and (resid 251 through 443 )K251 - 443
62X-RAY DIFFRACTION62chain 'L' and (resid 0 through 95 )L0 - 95
63X-RAY DIFFRACTION63chain 'L' and (resid 96 through 232 )L96 - 232
64X-RAY DIFFRACTION64chain 'L' and (resid 233 through 369 )L233 - 369
65X-RAY DIFFRACTION65chain 'L' and (resid 370 through 443 )L370 - 443

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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