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- PDB-8vk8: Structure of UbV.d2.1 in complex with Ube2d2 -

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IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 8vk8
タイトルStructure of UbV.d2.1 in complex with Ube2d2
要素
  • Ubiquitin variant D2.1
  • Ubiquitin-conjugating enzyme E2 D2
キーワードTRANSFERASE / Ubiquitin conjugating enzyme / Ubiquitin variant / E2 enzyme / inhibitor
機能・相同性
機能・相同性情報


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol
類似検索 - 分子機能
Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
類似検索 - ドメイン・相同性
Ubiquitin-conjugating enzyme E2 D2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.99 Å
データ登録者Middleton, A.J.
資金援助 ニュージーランド, 1件
組織認可番号国
Health Research Council (HRC) ニュージーランド
引用ジャーナル: Febs J. / 年: 2024
タイトル: Structural and biophysical characterisation of ubiquitin variants that inhibit the ubiquitin conjugating enzyme Ube2d2.
著者: McAlpine, J.M.R.B. / Zhu, J. / Pudjihartono, N. / Teyra, J. / Currie, M.J. / Tillett, Z.D. / Dobson, R.C.J. / Sidhu, S.S. / Day, C.L. / Middleton, A.J.
履歴
登録2024年1月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年9月25日Provider: repository / タイプ: Initial release
改定 1.12024年11月13日Group: Database references / Structure summary
カテゴリ: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22024年12月18日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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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: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin variant D2.1
C: Ubiquitin variant D2.1
D: Ubiquitin-conjugating enzyme E2 D2
E: Ubiquitin variant D2.1
F: Ubiquitin variant D2.1
G: Ubiquitin-conjugating enzyme E2 D2
H: Ubiquitin variant D2.1


分子量 (理論値)分子数
合計 (水以外)103,2288
ポリマ－103,2288
非ポリマー00
水00
1
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin variant D2.1
C: Ubiquitin variant D2.1


分子量 (理論値)分子数
合計 (水以外)37,8683
ポリマ－37,8683
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Ubiquitin-conjugating enzyme E2 D2
E: Ubiquitin variant D2.1
F: Ubiquitin variant D2.1


分子量 (理論値)分子数
合計 (水以外)37,8683
ポリマ－37,8683
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: Ubiquitin-conjugating enzyme E2 D2
H: Ubiquitin variant D2.1


分子量 (理論値)分子数
合計 (水以外)27,4932
ポリマ－27,4932
非ポリマー00
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)129.774, 129.774, 123.106
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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要素

#1: タンパク質 Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


分子量: 17118.488 Da / 分子数: 3 / 変異: C21S, C107S, and C111S / 由来タイプ: 組換発現 / 詳細: Includes N-terminal tag / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: タンパク質
Ubiquitin variant D2.1


分子量: 10374.607 Da / 分子数: 5 / 由来タイプ: 組換発現
詳細: Synthetic construct obtained using phage display. Includes N-terminal linker including FLAG tag.
由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)
Has protein modificationN

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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: 2.9 Å3/Da / 溶媒含有率: 57.57 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.6
詳細: 0.1 M Sodium citrate pH 5.6, 20% w/v PEG 4000, 20% v/v 2-Propanol

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年10月2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: 0.9537 Å / 相対比: 1
反射解像度: 2.99→44.66 Å / Num. obs: 24533 / % possible obs: 99.8 % / 冗長度: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.051 / Rrim(I) all: 0.188 / Χ2: 0.98 / Net I/σ(I): 14.4 / Num. measured all: 331807
反射 シェル解像度: 2.99→3.18 Å / % possible obs: 99 % / 冗長度: 13.7 % / Rmerge(I) obs: 1.699 / Num. measured all: 52886 / Num. unique obs: 3857 / CC1/2: 0.703 / Rpim(I) all: 0.475 / Rrim(I) all: 1.765 / Χ2: 0.99 / Net I/σ(I) obs: 1.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
Aimlessデータスケーリング
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.99→41.5 Å / SU ML: 0.47 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 35.18 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2954 1145 4.67 %
Rwork0.2469 --
obs0.2492 24497 99.83 %
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
精密化ステップサイクル: LAST / 解像度: 2.99→41.5 Å
タンパク質核酸リガンド溶媒全体
原子数6499 0 0 0 6499
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.553
X-RAY DIFFRACTIONf_dihedral_angle_d16.192515
X-RAY DIFFRACTIONf_chiral_restr0.0431017
X-RAY DIFFRACTIONf_plane_restr0.0041169
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.130.43041100.3932867X-RAY DIFFRACTION99
3.13-3.290.35751470.31762870X-RAY DIFFRACTION100
3.3-3.50.35951550.31342890X-RAY DIFFRACTION100
3.5-3.770.37511330.30742906X-RAY DIFFRACTION100
3.77-4.150.29461410.24182903X-RAY DIFFRACTION100
4.15-4.750.25551550.21552922X-RAY DIFFRACTION100
4.75-5.980.29271440.22972945X-RAY DIFFRACTION100
5.99-41.50.26341600.21433049X-RAY DIFFRACTION100
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)
15.61412.23420.33168.99776.00314.8385-0.74690.9469-1.3309-3.3504-0.33054.3388-0.4523-1.52271.05941.0462-0.1897-0.06070.9843-0.21940.930354.406-26.333-8.075
28.0006-0.11-1.2975.3986.69818.3570.42751.04581.5026-1.16971.0744-0.8718-2.542-1.5398-0.4140.4292-0.1187-0.14360.92720.3590.726949.897-16.459-0.493
35.35016.45311.92728.07232.26180.7016-0.3529-1.58431.4414-0.98853.48-0.7497-1.94922.447-2.96641.22080.16730.06291.8379-0.64342.379946.625-9.0126.498
46.1551-1.2725-4.21440.1740.55228.24310.1936-0.1035-0.11040.09550.13770.3186-0.774-0.5058-0.41420.7181-0.00940.08270.50180.15770.770149.058-18.82915.032
57.45112.15556.04752.01034.28662.055-0.02291.1019-0.43780.31750.7109-0.16660.77541.669-0.39870.4829-0.22680.14460.70120.04880.781451.456-27.1486.605
62.68520.60341.76.52335.57487.45570.66810.4707-0.07650.61520.9102-0.72652.0899-0.8202-1.04870.4369-0.1931-0.00070.66880.14320.564647.211-28.4046.695
79.66683.01111.2332.5825-1.5482.6222-0.244-0.697-1.90670.18651.24620.31661.2661-1.115-0.99360.6195-0.0035-0.02310.65360.09560.646943.072-30.5320.79
89.55630.58490.45436.96166.17086.99610.2318-1.5664-1.29110.51491.18420.65553.5689-2.2787-1.05240.8836-0.2215-0.20511.48370.31310.818438.486-29.3333.485
92.03911.4875-0.75883.3552-3.23747.5891-0.63531.73851.10640.34890.23330.2749-1.3119-3.6651-0.09090.63950.0030.04860.82660.39960.853338.933-21.15113.029
105.441-4.97822.96694.5419-2.77031.9538-0.88291.46781.2098-1.0485-1.38642.5392-0.3495-0.79121.84670.6898-0.1201-0.25091.1025-0.04321.313133.811-33.97120.193
116.10044.2361-0.29966.542-0.00061.2456-0.0325-1.53410.41.59470.60750.5596-0.8493-0.9905-0.44310.5104-0.02430.35671.09260.36110.793439.12-26.68331.154
123.2724-1.39270.08247.5054-1.37576.8180.75530.98150.3961-0.9080.02370.30130.9153-0.8513-0.5850.64-0.162-0.03280.63390.01770.508263.089-23.017-6.912
136.229-0.48261.03319.3778-1.46981.87170.00130.115-0.4136-0.56730.3018-0.1533-0.5010.1224-0.23320.6005-0.02530.12480.4230.12080.434864.894-17.305-4.54
148.12091.9823-0.05172.27671.47726.3480.34161.80211.2027-1.59970.249-0.3441-1.0396-0.518-0.54810.66110.01370.18750.45350.02950.629171.295-13.238-8.139
153.1963-2.0861-0.02719.3142-2.21868.7669-0.07240.1220.367-0.0838-0.0616-1.7567-0.61530.4448-0.04270.4976-0.07390.20810.4605-0.03150.597775.983-16.599-0.005
162.03993.43791.33222.06520.16056.9347-0.72670.4026-0.8569-1.43020.71360.14440.014-0.02140.10570.743-0.05140.11550.36780.02290.553769.177-26.815-1.624
176.6623-5.70262.73849.3911-8.56279.84710.2871-0.93972.47680.5352-0.2904-2.0702-4.41782.207-0.80650.8553-0.36280.40190.6493-0.39180.603172.463-8.8483.098
184.5858-1.5279-5.77642.76310.51277.94740.7682-0.12830.8411-1.3006-0.1876-0.7951-1.35090.4409-0.40081.1388-0.38680.03590.7024-0.03830.95166.412-11.614.381
192.9648-4.6575-5.12777.40318.10988.8913-1.4437-2.7427-0.35761.36262.6033-0.71230.04554.2973-0.34721.04510.6847-0.16232.34080.34991.06972.281-15.7525.638
207.1973-6.9141-2.70868.23910.29424.09320.353-2.30042.66162.2538-0.0344-1.2168-0.31290.9541-0.58481.1738-0.2633-0.07261.4779-0.6140.991864.899-5.47924.526
215.6-6.3424-4.8578.6345.96884.5081-1.5443-0.7509-0.91452.3128-0.04082.07281.75680.00241.09381.0171-0.07390.17761.10540.03420.527859.344-16.05922.833
225.5281-4.29760.22135.5411.32251.00910.0542-2.6091-2.16922.7176-0.53020.49862.36981.1506-0.60841.32180.0014-0.03091.5930.49370.960961.641-20.85926.864
234.85365.21231.92735.7560.93148.9262.2731-4.0335-2.03974.7450.0646-0.63672.33940.9962-1.74371.4875-0.2616-0.17921.99940.10570.926871.271-23.27925.11
248.73650.9116-0.47186.01822.37872.68570.0957-0.36910.52160.83391.0118-0.7826-0.56411.1868-1.13660.7768-0.15020.02620.68090.02760.542563.501-17.10318.414
253.4687-4.03814.29254.8985-5.15145.48111.0332-0.0578-0.6024-0.5859-0.3451-0.19530.91770.5853-0.3720.5936-0.21860.20681.183-0.46190.902141.748-59.7310.827
266.75913.1985-4.63272.0021-6.20469.89680.06333.106-0.5098-1.79893.17992.85222.30750.2086-2.11711.1174-0.3448-0.10151.6317-0.8462.433939.114-63.647-1.729
273.7444-0.0444-4.23597.9518-4.70417.70050.385-1.75350.85470.1293-0.379-0.9348-0.1710.3328-0.02530.6597-0.19230.11191.0496-0.51811.198247.004-52.8922.493
285.9679-1.82725.73762.1187-3.15486.87210.6812-0.209-0.1162-0.69970.2419-0.46980.16360.3262-0.68510.8336-0.27220.45110.8681-0.37571.183838.233-48.687-13.627
291.41410.19141.41290.57130.53411.75840.7579-1.87541.63770.49250.2211-0.4358-1.57631.8723-0.43530.5438-0.33320.21441.3326-0.49910.75739.328-48.1689.323
307.0077-3.0375-5.34598.3511-1.98836.6756-0.3255-0.17682.4346-0.12240.9026-1.8684-1.68322.30870.41771.2456-0.52770.48851.0384-0.26161.386640.869-39.785-8.415
315.28953.0146-1.7517.4089-2.30625.5361-0.6037-0.8081-0.21190.8489-0.22430.3885-0.22730.50190.2159-0.1367-1.76180.8178-0.6344-0.18551.414235.139-37.786-3.899
323.3666-2.2321-2.85561.5821.11248.43670.38430.00981.42440.87920.1904-0.1884-2.8489-0.31530.81141.0454-0.36810.35741.0389-0.73631.075828.7-43.9755.332
332.0484-0.98462.47626.2782-4.5019.0617-0.0895-0.05020.5709-0.27590.12490.1764-0.7811-0.76740.03910.7997-0.19060.34730.7401-0.28121.106329.45-41.706-7.986
344.93380.83693.56524.2675-2.59644.9203-0.77991.2804-1.607-2.12920.0285-0.77661.11220.68840.92511.4535-0.2170.62521.2055-0.41861.418441.673-39.435-17.87
359.1398-2.95665.05585.4815-1.86754.63410.0258-0.93-0.50170.20860.0187-0.0289-0.31320.307-0.15430.7379-0.28540.20731.485-0.70071.295153.058-61.26510.784
360.84210.00341.79252.4803-0.07634.0349-0.1689-1.57450.28071.08560.0855-0.38920.5493-0.82830.2410.7349-0.1249-0.05821.8174-0.7361.181959.767-63.60718.277
375.81692.4302-2.3252.4321-1.77971.3787-0.5647-3.20260.54850.93870.39740.15781.75622.6325-0.16420.4920.1049-0.30391.4164-0.46611.206961.668-71.74111.088
382.28750.11510.4741.6336-0.42360.3074-0.40630.5567-0.2005-0.0259-0.1048-0.99250.19461.2074-0.58220.1415-0.3540.15242.4357-1.19651.747964.675-61.4397.192
393.8580.5702-4.41496.14411.82756.09251.7-1.5511-0.65670.7529-0.6136-0.4451-1.33821.7089-0.53530.9766-0.1947-0.08591.4699-0.551.844868.598-56.23312.049
404.1174-0.73033.89999.8778-1.81113.8579-0.57560.6791-0.11021.10050.949-1.0961-1.52780.64021.48691.3724-0.6458-0.1082.198-1.97441.386964.017-52.8218.129
415.7782-3.1136-1.4326.8252-3.07893.25480.61651.5605-0.54090.7645-2.2558-1.2881-0.475-1.20280.67270.7881-0.2573-0.21361.4629-0.63271.59256.198-55.68211.688
426.32572.4096-3.59632.1306-4.08848.07211.4502-1.11061.6662-1.7141-1.36061.7083-0.6231.4899-0.34470.9550.0509-0.09121.2912-0.65511.081668.021-69.092.452
431.9899-6.75828.49486.9087-7.79598.93621.0601-3.0105-0.93931.01352.1784-0.0384-0.8150.6336-1.89561.0631-0.03090.38151.6512-0.54741.356754.21-57.877-6.371
446.50021.29451.23983.2832-1.88988.61480.668-0.46451.46641.99071.5123-2.54310.403-0.6069-1.51121.41130.6163-0.61761.9876-0.85172.016861.801-59.045-5.69
454.20885.28924.01686.6374.86547.8784-1.92681.25231.9807-1.45792.03650.9649-1.99880.57850.18271.4037-0.28160.55321.8012-0.11552.661769.627-47.257-7.002
468.89476.5845-4.59586.293-5.29276.2994-1.0848-0.33890.2809-0.0148-0.7974-2.19442.17250.80432.17211.8172-0.54790.13561.0534-0.01771.485964.081-48.443-15.134
473.39443.72272.93557.5751-0.96448.63710.68041.03060.31912.96670.59620.01220.6286-3.4274-1.46671.68330.10890.30191.6897-0.42960.873362.108-58.342-16.51
486.5723-2.82132.8137.6595-4.90813.67910.88921.39961.99880.6981-0.511-0.5721-3.0839-0.4609-0.44633.6099-0.39291.09971.71830.47441.593457.1-51.34-20.401
493.13812.00773.84348.65514.57245.328-0.691-0.98660.56540.09921.16941.1601-0.66422.2969-0.81121.0181-0.43240.09462.12180.03040.984853.1-45.683-8.558
500.02810.3177-0.50343.0913-4.81737.50830.18462.19282.2037-1.1332-1.9472-1.9653-0.01080.47730.15231.6639-0.94430.3523.74280.36441.67259.75-40.288-13.511
513.76972.78932.03097.55440.16641.4251-0.2441-1.00960.41150.0924-0.7665-1.82120.2628-0.24020.67660.8441-0.71910.47962.8547-0.01391.463863.152-41.221-6.126
523.93763.0925.6726.67934.78118.19281.86982.73731.96740.3844-0.1396-2.14230.27782.8686-1.2210.5685-0.02590.27051.9041-0.38872.039361.719-48.785-0.103
531.2378-0.73380.96989.6749-3.13931.55230.1526-0.3177-0.869-0.48180.21971.28840.95122.22410.76970.5330.22090.35841.4953-0.59931.975652.407-53.047-12.498
545.68911.96120.71492.55810.38891.6892-0.06150.32490.049-1.11250.16462.19810.0905-0.2922-0.02051.69491.6517-0.51611.21590.23171.011524.23-3.499-13.354
558.4399-2.3404-2.06475.0739-3.44288.7177-0.4831-1.3788-1.2289-0.6198-0.172-0.70191.9362.00821.20780.77440.08820.04821.11080.45430.987132.854-0.384-4.364
566.58475.04645.23078.77760.41546.7807-0.1722-1.1348-1.18670.7907-0.4583-1.62790.69940.91920.23331.0912-0.3313-0.05342.04740.0552.276639.163.8244.778
574.75073.88222.70594.96343.93823.2826-0.58121.73162.7938-1.7997-0.34421.4307-1.01730.06650.79540.83560.1495-0.14921.4220.33431.099724.3871.5383.284
582.95620.16173.43210.00950.19754.02451.7185-0.5162-1.2851-1.10450.0547-0.5129-1.5984-0.9199-0.93011.33820.44420.13661.3716-0.03261.216131.31916.65713.229
590.989-0.8509-0.75326.35140.910.71720.0747-1.1349-0.07670.22560.06-0.78420.0158-0.03730.04971.17150.0673-0.15391.53570.2150.669624.11412.1629.046
605.35746.7938-4.57741.9775-4.60344.9152-1.98850.98730.1925-1.65473.2722.2698-0.1166-2.0345-1.65691.58170.12960.13561.22030.18620.595223.9665.988-12.16
613.66992.28120.18658.04341.41353.55290.2753-2.0448-0.37270.6144-0.90760.2377-0.5066-0.87210.70020.57930.05660.02371.5974-0.12410.888219.89516.9225.939
626.2420.39832.08313.7681-1.09951.10460.6489-0.18660.2298-0.5739-0.5458-0.0059-0.4496-0.9139-0.10041.05320.28760.13321.0660.14890.644926.48116.304-2.13
639.90743.32915.18017.80754.52333.8136-0.8524-0.98282.5403-1.4751-0.13730.6939-1.83470.81110.36060.79870.03740.22641.9440.03730.515122.05629.9736.2
643.32561.8986-4.25175.0739-2.16965.57531.197-1.78610.4810.6786-1.9123-0.4296-3.6771-0.0130.80021.52960.0161-0.31942.10870.1030.896322.69729.65517.942
659.09360.273-4.49067.51673.08945.7836-0.9533-1.17410.31341.25021.62430.4234-1.3865-0.939-1.00811.3323-0.391-0.19642.41340.48910.867818.75917.9419.281
665.39072.0375-3.75284.36163.21988.55880.321-2.9880.8099-0.3764-0.8582-2.3371-2.2995-0.11210.45440.68280.1866-0.00141.29620.29231.637722.457-10.911-9.524
674.9094.01180.84398.5959-0.06414.34830.76360.67671.37970.1504-0.21390.44690.298-0.0979-0.28840.7278-0.136-0.15290.96510.15851.082529.962-10.4492.897
688.09343.16371.66344.64254.1054.96370.31242.2397-0.4640.20870.85321.01380.8970.9801-1.28381.13060.5868-0.0461.59650.42581.557721.868-16.046-10.495
692.0636-2.98461.90458.6217-5.13633.09452.64640.83530.16020.16811.53191.83821.1091-0.8906-3.52451.0865-0.0529-0.09441.34280.50391.982619.392-23.298-5.757
703.30461.9549-0.09374.2831-3.28525.30460.7447-0.5024-0.93410.8622-1.1225-1.0792-0.951-1.71020.28020.5779-0.0009-0.19981.15730.21510.86928.293-22.479-3.394
716.0352-2.80061.03111.36490.18567.22120.6883-0.457-1.97661.5409-1.8572-1.71-0.84540.5170.95580.8244-0.0556-0.2531.39480.18930.854531.647-22.9851.181
728.9594-6.6097-3.23114.85542.57713.3344-1.98170.7309-1.8212-0.43660.71642.22461.5253-1.2920.77320.9649-0.2496-0.15661.38280.17531.019224.498-20.8786.506
730.35781.22691.47424.11794.88377.29520.89730.87721.38270.38330.131-0.48181.1133-0.2736-0.51670.64020.0324-0.00141.41210.51971.6715.685-18.4734.498
748.50974.85952.61634.52892.96387.3526-0.7045-00.67140.1328-0.03242.7137-1.5335-0.59360.9780.71190.0743-0.35671.48460.20491.625312.585-17.379-2.938
750.0144-0.3151-0.07225.00261.19080.28320.3683-0.26350.48620.51650.352.05230.5374-0.7776-0.37710.52620.4229-0.02351.93720.27870.974520.189-9.251-1.914
76-0.0099-0.1811-0.18459.54579.80922.0061-0.5199-1.04240.19751.46751.0102-0.40051.3644-1.928-0.73290.60450.0013-0.08621.35950.63481.3829.199-20.6739.301
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -3:4 )A-3 - 4
2X-RAY DIFFRACTION2( CHAIN A AND RESID 5:13 )A5 - 13
3X-RAY DIFFRACTION3( CHAIN A AND RESID 14:19 )A14 - 19
4X-RAY DIFFRACTION4( CHAIN A AND RESID 20:50 )A20 - 50
5X-RAY DIFFRACTION5( CHAIN A AND RESID 51:59 )A51 - 59
6X-RAY DIFFRACTION6( CHAIN A AND RESID 60:71 )A60 - 71
7X-RAY DIFFRACTION7( CHAIN A AND RESID 72:86 )A72 - 86
8X-RAY DIFFRACTION8( CHAIN A AND RESID 87:97 )A87 - 97
9X-RAY DIFFRACTION9( CHAIN A AND RESID 98:113 )A98 - 113
10X-RAY DIFFRACTION10( CHAIN A AND RESID 114:120 )A114 - 120
11X-RAY DIFFRACTION11( CHAIN A AND RESID 121:147 )A121 - 147
12X-RAY DIFFRACTION12( CHAIN B AND RESID -2:6 )B-2 - 6
13X-RAY DIFFRACTION13( CHAIN B AND RESID 7:21 )B7 - 21
14X-RAY DIFFRACTION14( CHAIN B AND RESID 22:35 )B22 - 35
15X-RAY DIFFRACTION15( CHAIN B AND RESID 36:55 )B36 - 55
16X-RAY DIFFRACTION16( CHAIN B AND RESID 56:66 )B56 - 66
17X-RAY DIFFRACTION17( CHAIN B AND RESID 67:74 )B67 - 74
18X-RAY DIFFRACTION18( CHAIN C AND RESID 1:18 )C1 - 18
19X-RAY DIFFRACTION19( CHAIN C AND RESID 19:26 )C19 - 26
20X-RAY DIFFRACTION20( CHAIN C AND RESID 27:39 )C27 - 39
21X-RAY DIFFRACTION21( CHAIN C AND RESID 40:47 )C40 - 47
22X-RAY DIFFRACTION22( CHAIN C AND RESID 48:52 )C48 - 52
23X-RAY DIFFRACTION23( CHAIN C AND RESID 54:58 )C54 - 58
24X-RAY DIFFRACTION24( CHAIN C AND RESID 59:72 )C59 - 72
25X-RAY DIFFRACTION25( CHAIN D AND RESID 1:11 )D1 - 11
26X-RAY DIFFRACTION26( CHAIN D AND RESID 12:19 )D12 - 19
27X-RAY DIFFRACTION27( CHAIN D AND RESID 20:35 )D20 - 35
28X-RAY DIFFRACTION28( CHAIN D AND RESID 36:51 )D36 - 51
29X-RAY DIFFRACTION29( CHAIN D AND RESID 52:68 )D52 - 68
30X-RAY DIFFRACTION30( CHAIN D AND RESID 69:74 )D69 - 74
31X-RAY DIFFRACTION31( CHAIN D AND RESID 75:85 )D75 - 85
32X-RAY DIFFRACTION32( CHAIN D AND RESID 86:92 )D86 - 92
33X-RAY DIFFRACTION33( CHAIN D AND RESID 93:136 )D93 - 136
34X-RAY DIFFRACTION34( CHAIN D AND RESID 137:147 )D137 - 147
35X-RAY DIFFRACTION35( CHAIN E AND RESID -1:12 )E-1 - 12
36X-RAY DIFFRACTION36( CHAIN E AND RESID 13:30 )E13 - 30
37X-RAY DIFFRACTION37( CHAIN E AND RESID 31:39 )E31 - 39
38X-RAY DIFFRACTION38( CHAIN E AND RESID 40:45 )E40 - 45
39X-RAY DIFFRACTION39( CHAIN E AND RESID 46:54 )E46 - 54
40X-RAY DIFFRACTION40( CHAIN E AND RESID 55:60 )E55 - 60
41X-RAY DIFFRACTION41( CHAIN E AND RESID 61:69 )E61 - 69
42X-RAY DIFFRACTION42( CHAIN E AND RESID 70:74 )E70 - 74
43X-RAY DIFFRACTION43( CHAIN F AND RESID 3:11 )F3 - 11
44X-RAY DIFFRACTION44( CHAIN F AND RESID 12:16 )F12 - 16
45X-RAY DIFFRACTION45( CHAIN F AND RESID 17:22 )F17 - 22
46X-RAY DIFFRACTION46( CHAIN F AND RESID 23:28 )F23 - 28
47X-RAY DIFFRACTION47( CHAIN F AND RESID 29:36 )F29 - 36
48X-RAY DIFFRACTION48( CHAIN F AND RESID 37:41 )F37 - 41
49X-RAY DIFFRACTION49( CHAIN F AND RESID 42:49 )F42 - 49
50X-RAY DIFFRACTION50( CHAIN F AND RESID 50:54 )F50 - 54
51X-RAY DIFFRACTION51( CHAIN F AND RESID 55:59 )F55 - 59
52X-RAY DIFFRACTION52( CHAIN F AND RESID 60:66 )F60 - 66
53X-RAY DIFFRACTION53( CHAIN F AND RESID 67:71 )F67 - 71
54X-RAY DIFFRACTION54( CHAIN G AND RESID -3:3 )G-3 - 3
55X-RAY DIFFRACTION55( CHAIN G AND RESID 4:13 )G4 - 13
56X-RAY DIFFRACTION56( CHAIN G AND RESID 14:19 )G14 - 19
57X-RAY DIFFRACTION57( CHAIN G AND RESID 20:35 )G20 - 35
58X-RAY DIFFRACTION58( CHAIN G AND RESID 36:43 )G36 - 43
59X-RAY DIFFRACTION59( CHAIN G AND RESID 44:56 )G44 - 56
60X-RAY DIFFRACTION60( CHAIN G AND RESID 57:63 )G57 - 63
61X-RAY DIFFRACTION61( CHAIN G AND RESID 64:77 )G64 - 77
62X-RAY DIFFRACTION62( CHAIN G AND RESID 78:108 )G78 - 108
63X-RAY DIFFRACTION63( CHAIN G AND RESID 109:129 )G109 - 129
64X-RAY DIFFRACTION64( CHAIN G AND RESID 130:140 )G130 - 140
65X-RAY DIFFRACTION65( CHAIN G AND RESID 141:146 )G141 - 146
66X-RAY DIFFRACTION66( CHAIN H AND RESID 0:4 )H0 - 4
67X-RAY DIFFRACTION67( CHAIN H AND RESID 5:14 )H5 - 14
68X-RAY DIFFRACTION68( CHAIN H AND RESID 15:19 )H15 - 19
69X-RAY DIFFRACTION69( CHAIN H AND RESID 20:25 )H20 - 25
70X-RAY DIFFRACTION70( CHAIN H AND RESID 26:32 )H26 - 32
71X-RAY DIFFRACTION71( CHAIN H AND RESID 33:39 )H33 - 39
72X-RAY DIFFRACTION72( CHAIN H AND RESID 40:44 )H40 - 44
73X-RAY DIFFRACTION73( CHAIN H AND RESID 45:53 )H45 - 53
74X-RAY DIFFRACTION74( CHAIN H AND RESID 54:61 )H54 - 61
75X-RAY DIFFRACTION75( CHAIN H AND RESID 62:68 )H62 - 68
76X-RAY DIFFRACTION76( CHAIN H AND RESID 69:73 )H69 - 73

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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

+
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