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- PDB-8a4v: Crystal structure of human cathepsin L with covalently bound E-64 -

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基本情報

登録情報
データベース: PDB / ID: 8a4v
タイトルCrystal structure of human cathepsin L with covalently bound E-64
要素Cathepsin L
キーワードHYDROLASE / cystein protease / drug target / lysosome / virus cell entry / proteinase inhibitor
機能・相同性
機能・相同性情報


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / protein autoprocessing / Collagen degradation / fibronectin binding / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / endocytic vesicle lumen / Attachment and Entry / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / lysosome / Attachment and Entry / immune response / symbiont entry into host cell / apical plasma membrane / cysteine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
類似検索 - 分子機能
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
類似検索 - ドメイン・相同性
Chem-E64 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Procathepsin L
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: 1.65 Å
データ登録者Falke, S. / Lieske, J. / Guenther, S. / Reinke, P.Y.A. / Ewert, W. / Loboda, J. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. ...Falke, S. / Lieske, J. / Guenther, S. / Reinke, P.Y.A. / Ewert, W. / Loboda, J. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. / Chapman, H.N. / Hinrichs, W. / Turk, D. / Meents, A.
資金援助 ドイツ, スロベニア, 6件
組織認可番号国
Helmholtz AssociationFISCOV ドイツ
Helmholtz AssociationSFragX ドイツ
German Federal Ministry for Education and Research031B0405 ドイツ
German Federal Ministry for Education and Research16GW0277 ドイツ
Slovenian Research AgencyP1-0048 スロベニア
Slovenian Research AgencyIO-0048 スロベニア
引用ジャーナル: J.Med.Chem. / 年: 2024
タイトル: Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors.
著者: Falke, S. / Lieske, J. / Herrmann, A. / Loboda, J. / Karnicar, K. / Gunther, S. / Reinke, P.Y.A. / Ewert, W. / Usenik, A. / Lindic, N. / Sekirnik, A. / Dretnik, K. / Tsuge, H. / Turk, V. / ...著者: Falke, S. / Lieske, J. / Herrmann, A. / Loboda, J. / Karnicar, K. / Gunther, S. / Reinke, P.Y.A. / Ewert, W. / Usenik, A. / Lindic, N. / Sekirnik, A. / Dretnik, K. / Tsuge, H. / Turk, V. / Chapman, H.N. / Hinrichs, W. / Ebert, G. / Turk, D. / Meents, A.
履歴
登録2022年6月13日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年7月5日Provider: repository / タイプ: Initial release
改定 1.12024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年5月15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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32024年5月22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
改定 1.42024年10月16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: Cathepsin L
B: Cathepsin L
C: Cathepsin L
D: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)99,00417
ポリマ－96,6474
非ポリマー2,35713
水14,376798
1
A: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,7344
ポリマ－24,1621
非ポリマー5733
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,7845
ポリマ－24,1621
非ポリマー6234
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,7784
ポリマ－24,1621
非ポリマー6173
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,7064
ポリマ－24,1621
非ポリマー5453
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)57.350, 62.750, 68.350
Angle α, β, γ (deg.)105.625, 93.316, 115.454
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Cathepsin L


分子量: 24161.676 Da / 分子数: 4 / 変異: T110A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CTSL, CTSL1 / 発現宿主: Komagataella phaffii GS115 (菌類) / 参照: UniProt: P07711

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非ポリマー , 5種, 811分子

#2: 化合物
ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


分子量: 360.429 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C15H30N5O5 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C4H10O3
#4: 化合物 ChemComp-DMS / DIMETHYL SULFOXIDE / 2-チアプロパン2-オキシド


分子量: 78.133 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H6OS / コメント: DMSO, 沈殿剤*YM
#5: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O4
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 798 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 2.17 Å3/Da / 溶媒含有率: 43.28 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4
詳細: Mature cathepsin L at a concentration of 7 mg/ml was equilibrated against 27% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0. Crystals, which grew at 293 K to final size after ...詳細: Mature cathepsin L at a concentration of 7 mg/ml was equilibrated against 27% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0. Crystals, which grew at 293 K to final size after approximately 3 days, were transferred to a compound soaking solution containing 22% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0 as well as 5% v/v DMSO and 10% v/v PEG 400.

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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: PETRA III, DESY / ビームライン: P11 / 波長: 1.033 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2021年10月4日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.033 Å / 相対比: 1
反射解像度: 1.65→44.42 Å / Num. obs: 95327 / % possible obs: 97.57 % / 冗長度: 7 % / Biso Wilson estimate: 18.99 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.3106 / Rpim(I) all: 0.1258 / Rrim(I) all: 0.3356 / Net I/σ(I): 5.97
反射 シェル解像度: 1.65→1.709 Å / 冗長度: 7.2 % / Rmerge(I) obs: 2.574 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 9473 / CC1/2: 0.368 / CC star: 0.733 / Rpim(I) all: 1.026 / Rrim(I) all: 2.774 / % possible all: 96.99

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解析

ソフトウェア
名称バージョン分類
Cootモデル構築
PHENIX1.18-3855_9999精密化
XDSデータ削減
XSCALEデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3OF9

3of9


解像度: 1.65→44.42 Å / SU ML: 0.1929 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 22.061
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2029 2011 2.11 %
Rwork0.1612 93307 -
obs0.1621 95318 97.56 %
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: 25.8 Å2
精密化ステップサイクル: LAST / 解像度: 1.65→44.42 Å
タンパク質核酸リガンド溶媒全体
原子数6780 0 157 798 7735
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00977271
X-RAY DIFFRACTIONf_angle_d0.89029833
X-RAY DIFFRACTIONf_chiral_restr0.0546968
X-RAY DIFFRACTIONf_plane_restr0.00621323
X-RAY DIFFRACTIONf_dihedral_angle_d7.58621083
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.28921410.27086643X-RAY DIFFRACTION96.73
1.69-1.740.32031570.27046599X-RAY DIFFRACTION97.11
1.74-1.790.27971380.26166611X-RAY DIFFRACTION97.15
1.79-1.850.31651390.25096671X-RAY DIFFRACTION96.98
1.85-1.910.27541370.23936376X-RAY DIFFRACTION93.91
1.91-1.990.26041530.19736688X-RAY DIFFRACTION97.8
1.99-2.080.23561350.17186709X-RAY DIFFRACTION98.21
2.08-2.190.20591470.16126704X-RAY DIFFRACTION98.28
2.19-2.330.21191430.14786753X-RAY DIFFRACTION98.49
2.33-2.50.17551430.14476737X-RAY DIFFRACTION98.57
2.51-2.760.21521410.14496560X-RAY DIFFRACTION96.14
2.76-3.160.18581490.14076796X-RAY DIFFRACTION99.48
3.16-3.980.15651470.12576796X-RAY DIFFRACTION99.43
3.98-44.420.16231410.14436664X-RAY DIFFRACTION97.51
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)
13.178071445170.9888843787750.325054296923.103005243760.7816884842122.99243935924-0.01713243565720.009451442848890.0347497800139-0.06395561354610.0439827809199-0.158868464506-0.108401669968-0.0260790055872-0.02778471689940.1336694213410.0137377828660.002672641245490.126850086564-0.01897522117830.10572773759926.7168922202-12.0707786268-8.29079469186
25.385422087693.082813919472.400736270835.771055262692.024376235841.50696129436-0.09487648236660.1278170902120.11349575048-0.2396355546250.1025378088730.142343744004-0.051220291761-0.0749608886626-0.007153151596060.146742154408-0.002059563767250.01720416049480.164806768338-0.03042348303570.080705679853218.756607835-20.0133447507-15.7434982936
32.715754381940.1871938322581.300157226733.6663515574-0.007779444742946.089275363720.01294940879980.0117479347416-0.070242605414-0.08115997771360.02463974673710.01440628737020.0331399508138-0.328770894214-0.04384887141320.120412806217-0.03105331489515.09251411331E-50.144074484322-0.04247705821110.15257021587216.5731079898-22.3681596372-15.9541837688
41.950503321580.7351210557451.53513778572.089355947910.8067667907955.911723612050.247701623199-0.0507391515232-0.4176677122750.1787811569920.198447560043-0.556374494730.4639414516460.238874583605-0.4403129451640.1513523347620.0449667655832-0.04263609907050.182208609947-0.0519889842310.31985063776333.7034193233-21.1062007836-4.07190996769
51.161523171010.4999962181851.321869214441.560087956081.719973008773.488448550410.158925946618-0.378781418157-0.035682971980.224161260209-0.1498587832790.08244627330290.19655429352-0.684661966799-0.02194119590480.160329011935-0.0190596972289-0.00219964274160.2590709828370.00500534626220.16429389945924.6570557508-11.13258127217.68051377217
63.93826459052-0.1505592761231.179216536462.865545469671.394518715513.214036216010.0955095824179-0.335605056799-0.0009220081146480.175232248415-0.0557989160269-0.2008268934630.164938320891-0.227611864483-0.03209086777280.121445255165-0.04765820912210.005485113088050.1650167624260.0002593020640920.14219242228725.2591067566-13.0780922212.32334718267
73.31696473311-0.0250246724089-0.1808777233554.43061590710.3356056277442.362670772430.01224917134270.09527871801830.183563579398-0.1418535299150.0186092879933-0.135224645229-0.117502719751-0.02117314316920.01285803055920.08337084676420.004234824380160.01970479037960.134187518335-0.000475001336390.07467155795956.54389344056.4322396712917.4668682172
82.31157877432-0.579352909794-0.3380778353385.407784543454.002226687875.888707561850.0888876094085-0.05823110524890.03372863647610.0257172676578-0.1157774235960.0274350854854-0.0871260445586-0.1466342547890.05380987181410.1008261259090.004879170802420.01739315332240.1009460348250.02096087146260.10951175334149.72938031782.4005325167623.3696679644
92.184614911081.629186855860.5908759472692.926682999990.302836522771.808670242750.02129917523630.00674328725491-0.164384960630.02939713346620.0676839418771-0.1562483083940.1101177501520.0401627995024-0.09308071792150.1186872153190.0256105891722-0.00267513445060.1068996439730.02331537914230.13399874522847.8036704842-7.736834494224.0474295982
107.60272372612-1.00647118382-4.099957561454.15402232017-0.4295637983476.51228793062-0.0779091893332-0.192101903618-0.2303699131430.15748044812-0.0486936053119-0.1904157311370.1691931561910.1621586904090.1119510718350.1629476043450.0162231789892-0.06587168887990.1524175900110.03763566274390.15823681540653.9938476368-9.6646698011932.0538272866
112.341957510270.5366022242810.01007268898262.52050772071-2.027282954925.18483220968-0.0009742387790210.3266560901350.140800302144-0.117452598050.1948536979010.1730224604010.0241698959488-0.299821706683-0.2128565638410.08429039454180.04111327170320.005577904387550.1360730680610.001562183006860.14840290393542.43160720165.2661260421515.6443373501
123.91451934183-0.785282627257-0.8064218701332.790729722080.7434034766933.29141510050.05680363103960.48797147262-0.220410976003-0.245464630519-0.064967000067-0.1953259396830.134649540057-0.07455883175380.001159456761830.1361386742470.006840516056690.01532208461310.1567837765930.004320151457550.14222517903155.7237128857-1.627817764357.28212403611
132.83949250628-0.430016152616-0.286286133713.508949650221.121466878572.873064608940.01297992648890.509825142730.0917632463814-0.3593317280160.0789137978048-0.0400727655565-0.1465741218860.0413908867308-0.04499822265140.14241990565-0.01028953911670.002312976275440.206416656730.01249355912760.1198190333456.14881269035.978284735043.55905650962
142.30619544423.08950927183-2.986214586686.95267199556-2.934561383594.36758309401-0.0227737688327-0.127466434974-0.07261688790410.350520215909-0.0707964266661-0.121224849981-0.2596893523030.3577789062750.109207113070.192644469149-0.00497994345555-0.0002792547167480.1946307411410.001380701890280.18046303092365.49204466830.67994366289112.9297676526
155.55167922916-1.670365056573.901149432272.22367575519-2.921326292485.121036068640.03337268174540.6240372924890.0189460667653-0.12940020885-0.006682384381440.027442500831-0.1490571917060.331612656789-0.01816289665710.1756877313260.01298351956120.0430810714290.193808229574-0.008207231186690.13680609067654.28079754446.319325699342.763685245
166.24629547015-0.234343527244-5.329740793381.95796993276-0.01105323875766.657413622690.0835114023150.1817419500730.0440982015262-0.0956296412440.04300170049470.0172024997729-0.228756947377-0.0309712929367-0.1318135781120.1419783617570.0100209272627-0.01367558525460.1417089002050.01517285866930.15219118822445.40509836812.0565847861711.5921238414
174.165952387481.923785693971.182335829394.32777952890.4012355433753.239968787940.103138185096-0.0803185924469-0.1291940124170.0501001455953-0.101104449410.1158188571860.312820708005-0.367760193178-0.02524869997910.159892904208-0.01701253766990.05867609339230.1923226604840.007216506179590.12442690206523.38006613865.86059628035-12.2305215931
182.989947267782.096492279482.536282100843.873607835555.577544394338.2856360215-0.1115450675540.135748845979-0.186898013941-0.1241057890110.113175741816-0.008659991586380.03568232791420.0898405112636-0.01859673673720.186867033498-0.009445732538630.01762557659250.1542711185730.01267551596950.14959288118630.51707168259.51690196232-17.9515506205
193.443231293921.558988651310.3317033745845.12706713757-0.09329553900341.67478853267-0.0722770097287-0.005996792667490.1049674282280.118015801748-0.00662966385355-0.149848037989-0.1048733634680.1447619771780.07568827669370.143622412421-0.002223151746850.0007577391120530.1716913271430.009145116879040.10571804809736.563599028117.6004622667-15.5169803216
205.763037963450.303116494626-1.653750109953.79427153729-0.373433449567.3814445796-0.0994229002584-0.373932481142-0.3185516338730.137847446654-0.0648136351598-0.2890121562860.266316264360.5474787426220.08179349798970.1149261872610.0310832746334-0.02390349760620.2046799043660.02463623847990.17961560368244.465262138412.0488364031-11.8417081379
219.11563506781-3.412043821150.5059434923773.91789713429-1.851781187864.031292716850.2238683280490.9798774972620.448018414427-0.183412482744-0.231415830997-0.0592193151707-0.156656159564-0.213510009827-0.0008096708442920.215248006405-0.0402989665982-0.02028358823430.204715051754-0.006700141943470.14312284390227.52166982216.8522764178-23.4593660056
224.53891260219-4.63405973901-6.159451340594.746685213616.28651199718.359839650530.1225479877810.2974817928440.00805093113509-0.405542764768-0.001631901693740.271104235372-0.248237921131-0.603895956081-0.04142181739810.228500330888-0.0163208208585-0.005309747396970.342565074710.05443743479460.2304684395714.373121017512.5381082695-22.4508469841
232.890529506970.297452991873-0.4652576224392.079358620560.1884886289863.5068369989-0.0190244449486-0.03001591071060.04413831995230.181566001519-0.006779286700770.2456787122910.0251057002387-0.4672705837350.009567790199320.149195584878-0.010047783610.04204768146530.2145598041130.01172021516140.15575117608315.243602783112.5122068212-6.3024582047
246.66941034122-1.747943065472.243402735993.84122545772-2.612742439053.988185638390.1001724301230.0871941555503-0.134714576551-0.155129511070.1000848736780.4330195848850.0453557885797-0.535956227948-0.1716687941470.171927356247-0.02286888261940.03952644482520.254707945852-0.02052926673240.1618470022111.183486917113.7682188837-9.59892493013
258.0824805649-0.474094143593-4.779207056212.634986773550.1806820317238.186066161940.1270016901050.3729634713120.2418991622850.02543728637250.06848283570410.03238416010690.112406719334-0.417256230345-0.1794692959790.172462477858-0.00812939198481-0.01859554120520.1785954121460.05189997161010.1536391114320.930777718717.433800773-17.9352441267
262.553781650640.09929576673480.3375614961663.35869490168-1.657097421723.358033132470.104838456922-0.0308809014917-0.0425617618463-0.0367257727542-0.05766282968650.1883855272980.0700268928731-0.04606746544-0.07917965067690.1339500978510.03566745061920.01093151551010.108363587738-0.0310193196060.09578583179512.625421594311.907201971424.6717529825
275.783547633433.72328312913-4.723074400834.08118573689-4.276802944037.24191767611-0.03264635306850.00335592059692-0.1255958829130.0652227631812-0.10288540383-0.0916157838094-0.0272182626481-0.1057626987180.1434681623330.1652154771670.02201295970520.000531638040130.0963423595427-0.006961857290910.1325382691511.752338020620.081150633630.1587924667
282.918539985582.74347317385-0.2205161988642.97640700701-0.631832996860.72072722842-0.07384089683890.07241991245550.0156907845033-0.0814691385390.01960973625670.0755738024643-0.00725810344566-0.0456698196121-0.07086402239310.1679701402750.0276079511241-0.004825453923040.136549491729-0.01442207413860.17324654632910.481313806828.272287913826.427918665
294.24978115551-1.12509505061-1.578933453513.346383996641.955776513695.58884005439-0.05279873743030.08824645489690.06293398607760.0255421652567-0.0411254698439-0.0863919645154-0.09297237852660.1568670024890.09651865811090.1615871101980.00296942067552-0.02431946160820.08854152335520.01594426215380.16480533678919.473308227630.40896315428.2902669717
301.02757980024-0.579216068649-0.7827787711475.932558287992.42701570872.316768366710.09272284484330.1269056777090.154242494175-0.289253076669-0.05489518402370.297114932594-0.313527525665-0.0880810423114-0.06205602027970.1797051482770.0327239405867-0.01877736246570.1860397015230.00661589149760.2293907858986.4210026527832.740811488223.3275802387
315.864625391-2.755775927830.02504803161463.936616268460.3886571477080.796798538504-0.164400373708-0.2890687351560.1949074668670.473881321540.154987443915-0.298892006854-0.01247016979470.136753410909-0.006896755810660.2088972777960.00222744827891-0.02162784753910.164786312173-0.0007058200624610.085591634919621.070738920615.962743446535.4571041597
321.47181401432-0.092449583888-0.6743645799231.906812914170.2521866780382.79570037275-0.03155743769920.0780402385758-0.0695507314015-0.0295349167389-0.00417662992259-0.1059909097730.1386217219330.1651840441410.01081405272880.101615577690.0213774542081-0.005227206952660.1008723157620.0122899705250.12275234581522.91289889388.7088428020519.2890482916
332.63493154608-0.8781607453560.07830655554052.609039241570.9460778510671.1821893625-0.0801898841227-0.07815448641650.06812453890720.1938106570630.117996069903-0.142630471070.08421960166910.134531909531-0.02352558764980.1575414803620.007241586646980.0005883612570930.1111545379480.03028948047780.11469551912324.667339006111.435591850327.1608054969
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 42 )AA1 - 421 - 42
22chain 'A' and (resid 43 through 60 )AA43 - 6043 - 61
33chain 'A' and (resid 61 through 104 )AA61 - 10462 - 107
44chain 'A' and (resid 105 through 128 )AA105 - 128108 - 131
55chain 'A' and (resid 129 through 186 )AA129 - 186132 - 189
66chain 'A' and (resid 187 through 220 )AA187 - 220190 - 225
77chain 'B' and (resid 1 through 24 )BC1 - 241 - 24
88chain 'B' and (resid 25 through 42 )BC25 - 4225 - 42
99chain 'B' and (resid 43 through 80 )BC43 - 8043 - 80
1010chain 'B' and (resid 81 through 104 )BC81 - 10481 - 105
1111chain 'B' and (resid 105 through 128 )BC105 - 128106 - 130
1212chain 'B' and (resid 129 through 144 )BC129 - 144131 - 147
1313chain 'B' and (resid 145 through 186 )BC145 - 186148 - 189
1414chain 'B' and (resid 187 through 197 )BC187 - 197190 - 202
1515chain 'B' and (resid 198 through 207 )BC198 - 207203 - 213
1616chain 'B' and (resid 208 through 220 )BC208 - 220214 - 226
1717chain 'C' and (resid 1 through 24 )CE1 - 241 - 24
1818chain 'C' and (resid 25 through 42 )CE25 - 4225 - 42
1919chain 'C' and (resid 43 through 80 )CE43 - 8043 - 80
2020chain 'C' and (resid 81 through 104 )CE81 - 10481 - 105
2121chain 'C' and (resid 105 through 118 )CE105 - 118106 - 119
2222chain 'C' and (resid 119 through 129 )CE119 - 129120 - 130
2323chain 'C' and (resid 130 through 197 )CE130 - 197131 - 200
2424chain 'C' and (resid 198 through 207 )CE198 - 207201 - 211
2525chain 'C' and (resid 208 through 220 )CE208 - 220212 - 224
2626chain 'D' and (resid 1 through 24 )DH1 - 241 - 24
2727chain 'D' and (resid 25 through 42 )DH25 - 4225 - 42
2828chain 'D' and (resid 43 through 60 )DH43 - 6043 - 60
2929chain 'D' and (resid 61 through 80 )DH61 - 8061 - 80
3030chain 'D' and (resid 81 through 104 )DH81 - 10481 - 105
3131chain 'D' and (resid 105 through 128 )DH105 - 128106 - 129
3232chain 'D' and (resid 129 through 197 )DH129 - 197130 - 201
3333chain 'D' and (resid 198 through 220 )DH198 - 220202 - 226

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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