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- PDB-9ec2: Crystal structure of SAMHD1 dimer bound to an inhibitor obtained ... -

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基本情報

登録情報
データベース: PDB / ID: 9ec2
タイトルCrystal structure of SAMHD1 dimer bound to an inhibitor obtained from high-throughput chemical tethering to the guanine antiviral acyclovir
要素Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
キーワードHYDROLASE / Inhibitors of SAMHD1 obtained from high-throughput chemical tethering to the guanine antiviral acyclovir
機能・相同性
機能・相同性情報


Nucleotide catabolism / 加水分解酵素; エステル加水分解酵素; 三リン酸モノエステル加水分解酵素 / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / 加水分解酵素; エステル加水分解酵素; 三リン酸モノエステル加水分解酵素 / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
類似検索 - 分子機能
: / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
類似検索 - ドメイン・相同性
: / : / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.72 Å
データ登録者Egleston, M. / Dong, L. / Howlader, A.H. / Bhat, S. / Orris, B. / Lopez-Rovira, L.M. / Bianchet, M.A. / Greenberg, M.M. / Stivers, J.T.
資金援助 米国, 4件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM056834 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)CA233567 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131736 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114259 米国
引用
ジャーナル: Biochemistry / 年: 2025
タイトル: Inhibitors of SAMHD1 Obtained from Chemical Tethering to the Guanine Antiviral Acyclovir.
著者: Egleston, M. / Bhat, S. / Howlader, A.H. / Bianchet, M.A. / Liu, Y. / Lopez Rovira, L.M. / Smith, B. / Greenberg, M.M. / Stivers, J.T.
#1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2024年11月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年3月12日Provider: repository / タイプ: Initial release
改定 1.12025年3月19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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)242,04612
ポリマ－239,2184
非ポリマー2,8298
水1,33374
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: homology
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)81.347, 94.274, 96.579
Angle α, β, γ (deg.)73.047, 71.481, 65.203
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and ((resid 114 and (name N or name...
d_2ens_1(chain "C" and ((resid 114 and (name N or name...
d_1ens_2(chain "B" and ((resid 114 and (name N or name...
d_2ens_2(chain "D" and ((resid 114 and (name N or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1THRTHRTHRTHRAA1144
d_12ens_1LYSLYSPROPROAA116 - 2616 - 151
d_13ens_1GLUGLULEULEUAA263 - 276153 - 166
d_14ens_1GLUGLULYSLYSAA281 - 304171 - 194
d_15ens_1ASNASNALAALAAA306 - 338196 - 228
d_16ens_1VALVALASPASPAA340 - 353230 - 243
d_17ens_1GLUGLUPROPROAA355 - 462245 - 352
d_18ens_1LYSLYSPROPROAA467 - 485357 - 375
d_19ens_1VALVALALAALAAA487 - 495377 - 385
d_110ens_1ASPASPMETMETAA497 - 505387 - 395
d_111ens_1GLNGLNASPASPAA548 - 558438 - 448
d_112ens_1LYSLYSARGARGAA560 - 566450 - 456
d_113ens_1TYRTYRPROPROAA568 - 581458 - 471
d_21ens_1THRTHRTHRTHRCC1144
d_22ens_1LYSLYSPROPROCC116 - 2616 - 151
d_23ens_1GLUGLULEULEUCC263 - 276153 - 166
d_24ens_1GLUGLULYSLYSCC281 - 304171 - 194
d_25ens_1ASNASNALAALACC306 - 338196 - 228
d_26ens_1VALVALASPASPCC340 - 353230 - 243
d_27ens_1GLUGLUPROPROCC355 - 462245 - 352
d_28ens_1LYSLYSPROPROCC467 - 485357 - 375
d_29ens_1VALVALALAALACC487 - 495377 - 385
d_210ens_1ASPASPMETMETCC497 - 505387 - 395
d_211ens_1GLNGLNASPASPCC548 - 558438 - 448
d_212ens_1LYSLYSARGARGCC560 - 566450 - 456
d_213ens_1TYRTYRPROPROCC568 - 581458 - 471
d_11ens_2THRTHRMETMETBB114 - 1154 - 5
d_12ens_2VALVALLEULEUBB117 - 1897 - 79
d_13ens_2ILEILESERSERBB191 - 19281 - 82
d_14ens_2ARGARGPROPROBB194 - 26184 - 151
d_15ens_2GLUGLUGLUGLUBB263 - 277153 - 167
d_16ens_2LEULEUASNASNBB284 - 303174 - 193
d_17ens_2ASNASNLYSLYSBB306 - 332196 - 222
d_18ens_2PHEPHEALAALABB334 - 351224 - 241
d_19ens_2GLUGLULEULEUBB355 - 359245 - 249
d_110ens_2ASPASPARGARGBB361 - 371251 - 261
d_111ens_2ALAALAPROPROBB373 - 462263 - 352
d_112ens_2ILEILEILEILEBB466356
d_113ens_2ILEILEPROPROBB468 - 485358 - 375
d_114ens_2VALVALVALVALBB487377
d_115ens_2ASPASPVALVALBB490 - 491380 - 381
d_116ens_2LEULEUMETMETBB493 - 505383 - 395
d_117ens_2GLNGLNTHRTHRBB548 - 579438 - 469
d_118ens_2PROPROPROPROBB581471
d_21ens_2THRTHRMETMETDD114 - 1154 - 5
d_22ens_2VALVALLEULEUDD117 - 1897 - 79
d_23ens_2ILEILESERSERDD191 - 19281 - 82
d_24ens_2ARGARGPROPRODD194 - 26184 - 151
d_25ens_2GLUGLUGLUGLUDD263 - 277153 - 167
d_26ens_2LEULEUASNASNDD284 - 303174 - 193
d_27ens_2ASNASNLYSLYSDD306 - 332196 - 222
d_28ens_2PHEPHEALAALADD334 - 351224 - 241
d_29ens_2GLUGLULEULEUDD355 - 359245 - 249
d_210ens_2ASPASPARGARGDD361 - 371251 - 261
d_211ens_2ALAALAPROPRODD373 - 462263 - 352
d_212ens_2ILEILEILEILEDD466356
d_213ens_2ILEILEPROPRODD468 - 485358 - 375
d_214ens_2VALVALVALVALDD487377
d_215ens_2ASPASPVALVALDD490 - 491380 - 381
d_216ens_2LEULEUMETMETDD493 - 505383 - 395
d_217ens_2GLNGLNTHRTHRDD548 - 579438 - 469
d_218ens_2PROPROPROPRODD581471

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.981229782409, 0.0956921989893, -0.167424959807), (0.0762985362863, -0.604706327284, -0.792785463479), (-0.177106316868, -0.790678987197, 0.586054683225)6.82009720683, -24.622828228, -11.5156802765
2given(-0.982485005545, -0.0703596750914, 0.172547761506), (-0.0896716511733, -0.633189661244, -0.76878465637), (0.163346897294, -0.770792040057, 0.615790079596)22.4847185609, -44.7022492306, -23.5381190569

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要素

#1: タンパク質
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM domain and HD domain-containing protein 1 / hSAMHD1


分子量: 59804.383 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SAMHD1, MOP5 / 発現宿主: Escherichia coli BL21 (大腸菌)
参照: UniProt: Q9Y3Z3, 加水分解酵素; エステル加水分解酵素; 三リン酸モノエステル加水分解酵素
#2: 化合物
ChemComp-A1BHL / N-[5-({2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methoxy]ethyl}amino)-5-oxopentyl]-4,7-dibromo-3-hydroxynaphthalene-2-carboxamide


分子量: 651.307 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C24H25Br2N7O5
#3: 化合物
ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Fe
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 74 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるか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: 2.62 Å3/Da / 溶媒含有率: 53.05 % / 解説: Large crystal rods and plates
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: Apo DELTA 112- SAMHD1 crystals were obtained by the hanging drop method using 1 micro L of 5 mg/mL Delta 112-SAMHD1 (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP) and 2 L 17% ...詳細: Apo DELTA 112- SAMHD1 crystals were obtained by the hanging drop method using 1 micro L of 5 mg/mL Delta 112-SAMHD1 (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP) and 2 L 17% PEG3350, 0.15 M Ammonium citrate pH 7.3. Drops were placed in 20 degrees C for over a week, and large crystal rods and plates were observed

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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: NSLS-II / ビームライン: 17-ID-1 / 波長: 0.9201 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2024年8月22日
詳細: The beamline has an adaptable optical system consisting of white beam slits, a double crystal Si(111) monochromator with horizontal axis, tandem flat beam deflecting mirrors (Pd coating), and ...詳細: The beamline has an adaptable optical system consisting of white beam slits, a double crystal Si(111) monochromator with horizontal axis, tandem flat beam deflecting mirrors (Pd coating), and Kirkpatrick-Baez focusing mirrors, which are Pd coated and able to bend adaptively using 16 piezo actuators. Each optical element is preceded by slits and its transmitted beam is monitored by beam position monitors or retractable screens.
放射モノクロメーター: SYNCHROTRON / 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: 0.9201 Å / 相対比: 1
反射解像度: 2.72→34.01 Å / Num. obs: 64250 / % possible obs: 99 % / 冗長度: 6.4 % / Biso Wilson estimate: 65.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.064 / Χ2: 0.99 / Net I/σ(I): 8.5
反射 シェル解像度: 2.72→2.87 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 9315 / CC1/2: 0.497 / Χ2: 0.93 / % possible all: 98.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21rc1_5156精密化
autoPROCデータ削減
Aimlessデータスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.72→33.65 Å / SU ML: 0.3997 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 27.1253
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2342 3133 4.89 %
Rwork0.1878 60924 -
obs0.19 64057 98.74 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 80.61 Å2
精密化ステップサイクル: LAST / 解像度: 2.72→33.65 Å
タンパク質核酸リガンド溶媒全体
原子数14465 0 156 74 14695
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.010814965
X-RAY DIFFRACTIONf_angle_d1.068220194
X-RAY DIFFRACTIONf_chiral_restr0.06292123
X-RAY DIFFRACTIONf_plane_restr0.00942610
X-RAY DIFFRACTIONf_dihedral_angle_d18.23475655
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.803475468399
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.802361989958
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.770.3331600.29882645X-RAY DIFFRACTION94.73
2.77-2.810.37071330.28662711X-RAY DIFFRACTION97.26
2.81-2.860.29891360.28782772X-RAY DIFFRACTION98.34
2.86-2.910.34221380.28582801X-RAY DIFFRACTION98.72
2.91-2.970.3421270.30222752X-RAY DIFFRACTION98.43
2.97-3.030.40921510.30262763X-RAY DIFFRACTION98.58
3.03-3.10.35671180.2792775X-RAY DIFFRACTION98.64
3.1-3.170.34461510.24912776X-RAY DIFFRACTION98.95
3.17-3.250.27431300.22792808X-RAY DIFFRACTION98.82
3.25-3.330.27621520.22732733X-RAY DIFFRACTION98.97
3.33-3.430.28851300.22472788X-RAY DIFFRACTION98.92
3.43-3.540.28731540.22012787X-RAY DIFFRACTION99.06
3.54-3.670.25441580.18952741X-RAY DIFFRACTION99.01
3.67-3.820.2291300.18262801X-RAY DIFFRACTION99.25
3.82-3.990.25151460.16692781X-RAY DIFFRACTION99.19
3.99-4.20.20051380.16162785X-RAY DIFFRACTION99.19
4.2-4.460.17741400.14582776X-RAY DIFFRACTION99.25
4.46-4.810.17291570.14062797X-RAY DIFFRACTION99.39
4.81-5.290.18161610.14152762X-RAY DIFFRACTION99.46
5.29-6.050.23111380.17342798X-RAY DIFFRACTION99.53
6.05-7.610.22891410.18362796X-RAY DIFFRACTION99.53
7.61-33.650.17811440.15242776X-RAY DIFFRACTION99.15
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)
12.652858731340.788361519354-0.07417643423765.804867285010.2600680519982.65802396470.237915892017-0.4887052598190.3407335468390.535055865823-0.2570212589660.119822986299-0.595809908543-0.2987831632140.04208408409230.594196470889-0.0006489269957890.01208815401730.619225143219-0.04002432449610.399491795611-1.75765329794-3.58758112608-8.73279977571
24.50466305329-4.45765069525-2.259594823959.478444432864.925584881636.31426560719-0.223489739952-0.3733909204910.1082827616690.4381282097030.0471037906170.760014286492-0.399931496074-0.8210826846690.1263246788270.6936588108550.06942712322210.08632090568080.7463106005740.05352583745380.725661216847-8.386085770933.08433182638-20.3943652742
32.19232384228-0.0967203097350.8096742469726.543201675740.6571906796333.46523171359-0.1847142822240.06799907047880.389057698116-0.8362143838160.08426221170130.404044552383-0.755171634079-0.3788806995450.2290558677020.7305368201230.0829641367309-0.002511497892570.7388496071630.1946235020930.606254497907-8.268081177361.94246291095-34.5325884132
41.674791369720.22195135252-0.3479919130642.475617108630.6327973403112.106677583240.101365936161-0.219370504102-0.2015296401030.343608595651-0.0495359374551-0.1574397930860.07713589996530.151881193338-0.04056178368210.496197299671-0.0785017815595-0.01757859831980.6967617134660.1942544574540.483193695367-2.81356943646-25.1235758326-12.2029226858
51.367563027120.871636619459-0.29062190334.70973291661-0.4247752134672.564029737960.1064494200330.005365595170460.411676919503-0.2167816608140.06965469452540.725250689492-0.175984532499-0.62969211801-0.2367047589430.4645260190720.0140420697415-0.04891721410330.9002913520760.04111408192940.72168667676-18.4186963684-18.2410478852-23.2136693695
65.44964437927-1.39888526262-0.3618072019552.123066085521.000573057364.276127812540.1760650981250.4450567057620.0196787303494-0.3687509762750.03720974056130.8200764136980.659782581593-1.07686362809-0.2798894050210.511805859724-0.192381787229-0.0736655466641.045547261090.01146543022370.614969254799-23.8634627887-33.7506689132-23.4206600578
72.001998470381.642799713850.1088478490376.22576780629-0.5129605522033.474369672540.02716289271720.228656862423-0.538697258103-0.0388921376495-0.0906808585997-0.3963207661330.6804251379250.434745197220.06679712565820.4513667634540.05178582182-0.009711771008010.530228401002-0.01418629885160.5233505945126.17867416063-0.42716360946-66.9688149585
82.7658387056-2.087725920570.5049483030736.74747356381-0.08400209277792.585446918070.1845722077060.722469187905-0.377926264364-0.336216463609-0.2390988421340.1462994301270.617438446159-0.205434187199-0.0009777515903940.500672560768-0.06687493830070.01987561835710.635401284216-0.0821417373980.461831690026-1.935816790753.69911227015-78.9620798953
94.106654014042.135854274391.852268084816.213065066762.19911172115.548696345750.01886085015960.118113646981-0.276352936205-0.743893938911-0.04860848770150.7899270483220.473573744134-0.9886639277620.09093404974020.60938310019-0.0861497591465-0.08561053671310.546551449360.05940296848550.627445836261-8.75486889983-3.32315068745-67.3661735732
101.064666391630.0530638159213-0.313539242543.51896041664-1.39479162143.374688357810.01278857943220.17869509888-0.164261164419-0.08546101081640.1154566493480.07145907882480.187711579427-0.187768668983-0.1383335087270.309822058403-0.0719919116543-0.0590835421830.6046452722460.07549785080810.471893864952-3.7385002637311.1418627648-66.9907779131
114.036056067340.1104460512680.9327989251473.306244996120.4151705055863.04057456611-0.275577796542-0.1206617276720.212512734337-0.06600646224790.2354000098830.323913042584-0.0119548996034-0.06058082163080.02658407634620.4230176179350.06979322964640.006623869103730.401110532410.08239236546470.416155941283-8.6224011359829.9669353122-69.1311466768
121.86936644579-1.499866994970.9231265054744.67787062081-1.461596497762.18968569382-0.0722210993118-0.156532077096-0.3887565683110.1695165506370.433596119660.7333359434990.10481630837-0.718418869739-0.3448133140540.415303445042-0.07137506582690.03501238346160.9156065639520.02515927899420.647658890698-18.631222705218.1465909237-64.7144105338
137.914687173525.22597436208-0.8170707573043.81610980006-0.6322777569065.56013921780.406525541767-0.8750058111470.6853779102720.872827336023-0.5052925244991.97672196429-0.315825293533-0.902672043561-0.08169810673990.4580785018150.1221397436720.1131009663890.924076678238-0.03101480514670.839548224252-24.231171684833.2195174846-63.141598358
140.9921843298810.0479889952431-0.4138334736951.97363340180.7240392362632.654645403950.0123271956581-0.0536682761988-0.270768906511-0.03786364858110.00463919028631-0.3732815870830.4033609355520.231045150879-0.04050201636770.4021829315360.05961777342610.01951907698030.5162636270810.1163617059370.56268870616416.0482191152-31.2954588141-31.5547661363
153.99669163771-1.72015905753-1.497852845543.569228428871.119484105392.82440168890.170614676252-0.180995919053-0.0312344905552-0.3379152939080.135667960256-1.527060775370.5522510423641.0593825994-0.263917991920.6312373295930.2348101495170.009104635814740.962078625586-0.04453236607730.93317306510426.5278229726-33.4655094265-39.1695533663
161.594763972410.1934297867420.4349073551862.560996830881.011565753293.170518757080.0110454974148-0.0144330680308-0.0970092182721-0.2006642128950.018418347985-0.47893980635-0.1723757257640.877200236527-0.002880333449330.3843965376-0.008014528471340.02077229113980.8691801964530.08616479309640.72954989781822.8850105532-20.7007092617-25.6135655549
176.96220881748-0.159021690011-1.289386466233.92224042380.6644914483122.54610303774-0.00659014952943-0.2317682741060.422173060601-0.00144601744897-0.0145521736044-0.776191677958-0.3198932763740.764459069658-0.04043541441440.51360561139-0.100719887358-0.07084828941011.118397843260.07267565361840.85161444413340.5227664036-8.27919766732-16.2767033099
181.413221677030.2256912691440.3225930230641.887864098080.6979141722512.512321055820.01643975798520.05019278633020.14659184170.0176672652519-0.148161264894-0.291304631853-0.4758908710260.1863902906090.1022541008460.396472911851-0.0712288570121-0.04800437025240.4860998772340.1320590541960.41555208433216.07634710930.7975757329-55.7668476787
192.83807905554-0.3747507251080.9703757655313.817016139463.663181457054.140935663980.127016660302-0.469092718907-0.2431740347110.8851716490790.24811232432-1.110530661830.4324171526650.830854299115-0.2638704305130.654462720761-0.041657639874-0.1339980711550.8032605512190.09489782622350.64130362353225.13795866426.5080827972-44.1042113537
204.15427033967-2.039751266930.21876239694.51172931854-0.202167951381.889203356980.07366208059160.485789502491-0.0524539287345-0.228786221556-0.18486977234-0.8097039057660.2581165987970.556074088180.08219210861740.418436455234-0.006273950371560.08179176133920.9185665274370.05472938259220.63182504658132.19076751414.6778970863-73.7456733282
211.52355280711-1.54352748252-0.147460795497.05596056850.3095085604152.05323391468-0.0370269289282-0.1270231227230.400665166828-0.1916750164540.10112683577-0.466549904007-0.5018546259560.351886727534-0.0181993377650.486479708883-0.09405883562750.04768649068670.5595718316280.03736007613350.4841472815316.210548845990.161873649247-20.8974941526
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 'D' and (resid 206 through 273 )DG206 - 27395 - 162
22chain 'D' and (resid 274 through 323 )DG274 - 323163 - 209
33chain 'D' and (resid 324 through 372 )DG324 - 372210 - 258
44chain 'D' and (resid 373 through 469 )DG373 - 469259 - 355
55chain 'D' and (resid 470 through 558 )DG470 - 558356 - 428
66chain 'D' and (resid 559 through 582 )DG559 - 582429 - 452
77chain 'A' and (resid 111 through 205 )AA111 - 2051 - 95
88chain 'A' and (resid 206 through 273 )AA206 - 27396 - 163
99chain 'A' and (resid 274 through 323 )AA274 - 323164 - 210
1010chain 'A' and (resid 324 through 435 )AA324 - 435211 - 322
1111chain 'A' and (resid 436 through 469 )AA436 - 469323 - 356
1212chain 'A' and (resid 470 through 558 )AA470 - 558357 - 427
1313chain 'A' and (resid 559 through 584 )AA559 - 584428 - 453
1414chain 'B' and (resid 111 through 260 )BC111 - 2601 - 150
1515chain 'B' and (resid 261 through 323 )BC261 - 323151 - 213
1616chain 'B' and (resid 324 through 449 )BC324 - 449214 - 339
1717chain 'B' and (resid 450 through 585 )BC450 - 585340 - 435
1818chain 'C' and (resid 114 through 260 )CE114 - 2601 - 147
1919chain 'C' and (resid 261 through 372 )CE261 - 372148 - 259
2020chain 'C' and (resid 373 through 582 )CE373 - 582260 - 430
2121chain 'D' and (resid 112 through 205 )DG112 - 2051 - 94

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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