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- PDB-7apo: Crystal structure of RARalpha ligand binding domain in complex wi... -

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基本情報

登録情報
データベース: PDB / ID: 7apo
タイトルCrystal structure of RARalpha ligand binding domain in complex with a fragment of the TIF2 coactivator
要素
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor alpha
キーワードDNA BINDING PROTEIN / Nuclear hormone receptor / coactivator / transcription factor / retinoic acid
機能・相同性
機能・相同性情報


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / embryonic camera-type eye development / chondroblast differentiation / glandular epithelial cell development / negative regulation of granulocyte differentiation / protein kinase B binding / cellular response to corticotropin-releasing hormone stimulus ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / embryonic camera-type eye development / chondroblast differentiation / glandular epithelial cell development / negative regulation of granulocyte differentiation / protein kinase B binding / cellular response to corticotropin-releasing hormone stimulus / growth plate cartilage development / positive regulation of T-helper 2 cell differentiation / prostate gland development / negative regulation of cartilage development / retinoic acid-responsive element binding / regulation of hematopoietic progenitor cell differentiation / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / nuclear glucocorticoid receptor binding / retinoic acid binding / response to vitamin A / apoptotic cell clearance / limb development / regulation of myelination / protein kinase A binding / ureteric bud development / Signaling by Retinoic Acid / DNA-binding transcription repressor activity / heterocyclic compound binding / positive regulation of interleukin-4 production / face development / alpha-actinin binding / germ cell development / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / retinoic acid receptor signaling pathway / cellular response to estrogen stimulus / positive regulation of cell cycle / cellular response to retinoic acid / response to retinoic acid / cellular response to hormone stimulus / positive regulation of neuron differentiation / hormone-mediated signaling pathway / mRNA regulatory element binding translation repressor activity / negative regulation of miRNA transcription / nuclear receptor coactivator activity / liver development / response to cytokine / neural tube closure / female pregnancy / hippocampus development / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of synaptic plasticity / multicellular organism growth / chromatin DNA binding / mRNA 5'-UTR binding / transcription coactivator binding / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / actin cytoskeleton / response to estradiol / cellular response to lipopolysaccharide / regulation of apoptotic process / response to ethanol / transcription regulator complex / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / dendrite / positive regulation of cell population proliferation / chromatin / nucleolus / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
: / : / Retinoic acid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein ...: / : / Retinoic acid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
類似検索 - ドメイン・相同性
Chem-EQN / Nuclear receptor coactivator 2 / Retinoic acid receptor alpha
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: 2.4 Å
データ登録者le Maire, A. / Guee, L. / Bourguet, W.
引用ジャーナル: J.Mol.Biol. / 年: 2021
タイトル: Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR).
著者: Senicourt, L. / le Maire, A. / Allemand, F. / Carvalho, J.E. / Guee, L. / Germain, P. / Schubert, M. / Bernado, P. / Bourguet, W. / Sibille, N.
履歴
登録2020年10月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年8月4日Provider: repository / タイプ: Initial release
改定 1.12024年1月31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

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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: Retinoic acid receptor alpha
B: Retinoic acid receptor alpha
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,1738
ポリマ－62,2864
非ポリマー8874
水2,324129
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-41 kcal/mol
Surface area21470 Å2
手法PISA
単位格子
Length a, b, c (Å)53.694, 47.573, 120.999
Angle α, β, γ (deg.)90.000, 96.169, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

#1: タンパク質 Retinoic acid receptor alpha / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


分子量: 28078.508 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RARA, NR1B1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P10276
#2: タンパク質・ペプチド Nuclear receptor coactivator 2


分子量: 3064.559 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NCOA2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: E7EWM1
#3: 化合物 ChemComp-EQN / 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid / Am-580


分子量: 351.439 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C22H25NO3
#4: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 129 / 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N

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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: 2.47 Å3/Da / 溶媒含有率: 50.14 %
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 / 詳細: 0.2M Lithium Chloride, 0.1M MES pH6.0, 20% PEG6000

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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 / ビームライン: X6A / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年3月19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 Å / 相対比: 1
反射解像度: 2.4→46.96 Å / Num. obs: 22707 / % possible obs: 93.85 % / 冗長度: 2.4 % / Biso Wilson estimate: 39.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05802 / Net I/σ(I): 9.35
反射 シェル解像度: 2.4→2.486 Å / Rmerge(I) obs: 0.2506 / Num. unique obs: 2250 / CC1/2: 0.923

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
SCALAデータスケーリング
MOLREP位相決定
PHENIX1.17.1_3660精密化
精密化構造決定の手法: 分子置換
開始モデル: 3KMR

3kmr


解像度: 2.4→46.96 Å / SU ML: 0.2611 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.6338
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2407 1080 4.76 %
Rwork0.1852 21606 -
obs0.1877 22686 93.88 %
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: 53.17 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→46.96 Å
タンパク質核酸リガンド溶媒全体
原子数4005 0 64 129 4198
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00924167
X-RAY DIFFRACTIONf_angle_d0.85415654
X-RAY DIFFRACTIONf_chiral_restr0.0547673
X-RAY DIFFRACTIONf_plane_restr0.0049716
X-RAY DIFFRACTIONf_dihedral_angle_d20.91361585
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.29071410.25332670X-RAY DIFFRACTION93.95
2.51-2.640.27611390.23582617X-RAY DIFFRACTION91.81
2.64-2.810.26641320.21242796X-RAY DIFFRACTION97.34
2.81-3.020.29761670.21392728X-RAY DIFFRACTION97.34
3.02-3.330.23561250.20862750X-RAY DIFFRACTION95.93
3.33-3.810.2141230.1692649X-RAY DIFFRACTION91.45
3.81-4.80.20651200.15122773X-RAY DIFFRACTION95.1
4.8-46.960.23511330.1732623X-RAY DIFFRACTION88.39
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)
13.39053074764-2.05913006124-5.434514702372.378015121773.561724651598.819718115490.2955866241580.5520243304710.238140576213-1.0563037130.2561281615120.71208991523-0.0833174030574-1.2346926982-0.5376187503670.6549497184190.127825469694-0.08836712410270.785254800510.05128716149450.553913530252-39.64956950458.64555199254-42.0437565288
29.864715949960.4100684493184.055202456197.018011854792.538153532945.210280686930.2686473488440.585897548341-0.842269265181-0.8369886813-0.215403232910.1656451325570.5856720256690.253624242651-0.1391867772160.7903455976940.04047833597660.04788212848420.3743813419460.08054038527810.341109846938-18.3598848066-9.3007148103-49.986263642
38.12248800488-5.68312203941-3.568015253817.194825644532.057252031013.953635577850.1001550168540.373309995838-0.0312852747396-0.49818432467-0.203263531095-0.117031903309-0.132442446013-0.2478462307860.07798274890380.542651845022-0.0234293124597-0.02193918323490.3982875473560.02155739277070.193999022465-20.45789374545.73583584809-49.6321244312
41.262673944730.6710343139630.2336880659734.219930945282.174335357321.03986569250.08490978028990.1151824512640.0880070192288-0.430851987026-0.00639250675861-0.180726619511-0.321707626786-0.103523786038-0.08868031668060.5759178537870.0367519289373-0.004088432672940.3271840883170.03086609497710.173283508391-24.684456439813.0165400288-39.6760777225
54.39227808512-6.305431023981.577581491459.12095802184-2.595335335932.20544929078-0.0190405564969-0.0565780346641-0.379837112801-0.2446408057930.1528695649490.2750026107960.4763018721720.390738788821-0.1116732069050.704817721567-0.06651340912830.02973315796650.366740707312-0.04050869721710.312842611432-24.9141277216-11.9606792764-43.3637567968
62.700094593850.535954992629-1.485867133421.811018642441.428055202225.96895158158-0.0332636219321-0.287595948625-0.289421423599-0.125217920491-0.004353149696-0.1061633045180.3330463288030.111705163338-0.007111856458270.4100906008140.0497625387734-0.06956123043070.2290317475330.03828381209150.260598806775-18.7168142505-7.24698908937-40.6667274195
73.993554714524.184047959992.1157036617.367576139292.936168612528.60071880870.2657514560820.106650377962-0.3587951033990.246972995763-0.204058970451-0.62697854398-0.219160435105-0.0273369650896-0.2039972179660.4510281925090.0761343187735-0.05343601700290.3343785150470.0115280925220.313943321409-28.487776472910.5614110536-34.1019180398
87.540764286654.857085418340.8108366144354.260618848931.06899326373.352307566750.831277661933-0.768240844435-0.4442468363481.11187032447-0.860340353615-0.282530970425-0.182712793018-0.363381605636-0.02580751505030.4403424104230.02619833832730.03133549339830.4653417952810.00495915636750.314446656849-37.43853421318.39508708109-28.5942370243
94.224881086751.81430801966-5.966750191392.80431634755-2.563802564678.27133458637-0.332375523745-1.23404953631-0.780563897176-0.0562515714172-0.162641126007-0.5304958809020.1684998467450.8289684080780.4355748262250.5795766476720.0368354729143-0.1440791581140.410165479767-0.03244209424020.407348150986-17.81409858992.50523456026-32.8307315852
104.99130051666-5.73003053582-2.586793961766.544985991113.323423696176.78653982094-0.2694579080620.3686289482790.7985534922530.1362154665470.618540621348-1.423730050310.4327692483590.236804175029-0.5018170368970.639114335937-0.100226018589-0.009901356078630.41590793531-0.03189505779750.375771057018-9.7217496068510.1731037234-46.9688065034
115.596853131965.471631893192.66407560799.379842041281.155961699496.880222993170.60434902491-3.07736659719-0.424575526481.61387789515-0.6930365055680.3175936582590.0524394313297-1.287792752680.06557202758630.574279861958-0.08787267928110.09717305319420.7137366712310.01769459208270.471790526748-27.70972962661.13873756932-3.27414250317
125.409047666732.026346619-4.095651204389.58823124985-0.7734097892357.659167161410.6811528940780.08107029916790.678660854410.899885652365-0.388290231917-0.027491846758-1.53054624883-0.023512373708-0.3827409392710.5842812161030.0556003158614-0.1921328427230.3167258801240.06242846009740.49170678991-4.4144607698719.743080457-9.80537410533
131.229242742391.659452934920.6686097193036.5865007151-0.3970165659251.365115693190.103161719866-0.0996096237961-0.1847767416370.3480087101790.0363541195718-0.170026603980.213585185252-0.0135105597792-0.1576729662080.2902293867760.0269617484982-0.0705334008380.2993415052030.02081663551070.198611440717-11.36695883891.18239980236-11.3560282602
144.98860450109-6.414707831215.412901808078.4273743585-7.087595291375.97896275309-0.562769627493-0.1112852658460.8920609888750.802993862503-0.0717082204416-0.538180140775-0.8717573605180.1434285165070.6637750723480.524876626995-0.0179886210044-0.1243059729680.403096110831-0.01508764818260.415168863587-11.488629864120.2835598781-9.36933365188
158.45222922578-2.5681580422.986891102882.511469898780.4241476198143.24107615855-0.1752561784230.5502067298050.377140090759-0.244051910755-0.142142363537-0.122387333531-0.3686353745230.156161246370.2539032305290.350517915549-0.0390973283099-0.05679895941830.2878210569830.07637195746810.277532250708-11.165339070718.1752052431-18.502249899
169.52663917462-5.93459272472-3.616827611379.568636459875.485419513377.216915282570.5839133165040.2913822466520.0616855034141-0.402605535147-0.273719639176-0.5893575390610.213930424565-0.603873378597-0.3619818877460.467175081579-0.0651839184336-0.1212247344240.3716095117110.09965475180830.241991846997-22.2477381449-0.156121845571-16.141306446
178.56487622711-3.28471960927-0.2514745133614.054373479971.443247328316.969039283810.368258066087-0.106440101695-0.727863683351-0.65906540591-0.3130815139891.583316431530.0372451199286-0.92479539952-0.07437910847610.25996290833-0.0628819105303-0.1029962246450.4781697802070.06483232434240.421036599077-32.5899353551.15205995603-14.9760994441
188.092023492020.6593742909511.758955160191.30938359844-0.3281471033842.543117524660.129829848560.1185350931010.042442680689-0.254059534729-0.0886572749386-0.101273203982-0.2255151036540.0448607760515-0.1414663242730.5575340332730.0187093332489-0.03377971076180.295309154831-0.0211304044640.242170488512-14.70496371997.84597257125-23.4786351284
193.139730138740.857492992621-4.00445270773.66362836016-4.915082702219.39866356753-0.3683861496530.0956678491262-0.855356202517-0.982815792881-0.130931575496-0.6332555727770.3072942565110.1365323561620.5915980489960.4852029092830.01031014773050.05076737814560.372683058887-0.00736892620670.4604966091910.3615137692140.0575793060918-17.1791546286
205.3834359875-2.86707956263-4.209303427943.44272800625-1.055402550178.99739461391.51202813059-0.3108060997971.78934609224-0.384377870881-0.405098651576-0.766138825091-1.710165451421.22285789899-0.8314994496821.22357543962-0.1352562568430.2008945007250.466630309295-0.1280129846480.583986536337-19.048474881420.6056728158-49.0065403212
218.335931624995.920828956884.200967821274.487936623884.334885239078.20772161332-2.07573612398-1.275431853831.013060833851.4593582753-0.1615301115320.793933921961-3.14196866248-0.7336306857292.293347526311.08766079680.0971452990668-0.2311485171060.486656520502-0.06767611658080.723997338627-28.228320645720.0724637867-55.5182031757
224.27112683976-3.716601152765.469845290218.9902357394-5.491282150657.1297651011-0.1057340588220.7557041021240.614601934966-0.0707219936925-0.251623321597-0.441176641873-0.04698943717071.153370773230.3266216378440.568770561441-0.05669358386440.05090015565480.571646660037-0.01600564074560.222756896799-19.661280120514.648385356-57.9385106369
236.822000208585.355283926451.035102089524.664550150272.780445181088.552716428031.12027899676-1.19544500646-2.098023752560.7001139430510.251107577175-1.09789478069-0.2126875702310.43289997292-0.7363551618590.557877511545-0.0182184142064-0.2658844274140.3982572249060.01665269567420.816585482256-5.80507116713-10.3781983849-9.30955150935
245.308951008260.5784293100065.125950930529.11951203584.643850985378.390069357980.661674698974-0.212463533144-0.6713972197970.8310565225350.07354175529451.039546632682.23569822468-3.43320227915-0.8495012589970.957030575622-0.277996987547-0.05986742541671.268488553180.5032876583410.500495974713-8.7866850435-9.318271784981.8418907471
256.71325415267-1.74455379283-2.862356575937.76241001599-3.366218810017.29916063854-0.2527608789940.266570577669-0.0644814365319-0.3623171740190.2588110179870.01018524122560.7470898941641.222174845870.0310408299870.4645543723280.0341267382561-0.1996310999280.475811409959-0.02445049716140.391844420247-0.987983087299-4.61383132206-1.95009315467
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 183 through 198 )
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 221 )
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 245 )
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 275 )
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 285 )
6X-RAY DIFFRACTION6chain 'A' and (resid 286 through 319 )
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 344 )
8X-RAY DIFFRACTION8chain 'A' and (resid 345 through 372 )
9X-RAY DIFFRACTION9chain 'A' and (resid 373 through 401 )
10X-RAY DIFFRACTION10chain 'A' and (resid 402 through 415 )
11X-RAY DIFFRACTION11chain 'B' and (resid 182 through 198 )
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 221 )
13X-RAY DIFFRACTION13chain 'B' and (resid 222 through 276 )
14X-RAY DIFFRACTION14chain 'B' and (resid 277 through 290 )
15X-RAY DIFFRACTION15chain 'B' and (resid 291 through 319 )
16X-RAY DIFFRACTION16chain 'B' and (resid 320 through 344 )
17X-RAY DIFFRACTION17chain 'B' and (resid 345 through 372 )
18X-RAY DIFFRACTION18chain 'B' and (resid 373 through 401 )
19X-RAY DIFFRACTION19chain 'B' and (resid 402 through 416 )
20X-RAY DIFFRACTION20chain 'C' and (resid 687 through 694 )
21X-RAY DIFFRACTION21chain 'C' and (resid 695 through 700 )
22X-RAY DIFFRACTION22chain 'C' and (resid 701 through 712 )
23X-RAY DIFFRACTION23chain 'D' and (resid 687 through 694 )
24X-RAY DIFFRACTION24chain 'D' and (resid 695 through 700 )
25X-RAY DIFFRACTION25chain 'D' and (resid 701 through 654 )

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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://pdbjlvh1.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