[日本語] English
万見
- PDB-6vpf: Estrogen Receptor Alpha Ligand Binding Domain in Complex with the... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6vpf
タイトルEstrogen Receptor Alpha Ligand Binding Domain in Complex with the Selective Estrogen Receptor Modulator Clomiphene
要素Estrogen receptor
キーワードTRANSFERASE / Breast Cancer / Hormone / Selective Estrogen Receptor Modulator / Antiestrogen / Alpha Helical Bundle
機能・相同性
機能・相同性情報


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / transcription corepressor binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / calmodulin binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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 / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Clomifene / Estrogen receptor
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: 1.6 Å
データ登録者Fanning, S.W. / Greene, G.L.
引用ジャーナル: Elife / 年: 2022
タイトル: Stereospecific lasofoxifene derivatives reveal the interplay between estrogen receptor alpha stability and antagonistic activity in ESR1 mutant breast cancer cells.
著者: Hosfield, D.J. / Weber, S. / Li, N.S. / Suavage, M. / Joiner, C.F. / Hancock, G.R. / Sullivan, E.A. / Ndukwe, E. / Han, R. / Cush, S. / Laine, M. / Mader, S.C. / Greene, G.L. / Fanning, S.W.
履歴
登録2020年2月3日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年9月16日Provider: repository / タイプ: Initial release
改定 1.12022年6月15日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023年10月11日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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

-
集合体

登録構造単位
B: Estrogen receptor
A: Estrogen receptor
C: Estrogen receptor
D: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)122,4138
ポリマ－120,7894
非ポリマー1,6244
水8,017445
1
B: Estrogen receptor
D: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,2064
ポリマ－60,3942
非ポリマー8122
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-14 kcal/mol
Surface area20230 Å2
手法PISA
2
A: Estrogen receptor
ヘテロ分子

C: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,2064
ポリマ－60,3942
非ポリマー8122
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2950 Å2
ΔGint-15 kcal/mol
Surface area19800 Å2
手法PISA
単位格子
Length a, b, c (Å)58.33, 58.33, 275.88
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

-
要素

#1: タンパク質
Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


分子量: 30197.201 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: ESR1, ESR, NR3A1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P03372
#2: 化合物
ChemComp-53Q / Clomifene / 1-[(E)-2-chloro-1,2-diphenylethenyl]-4-methoxybenzene / clomiphene


分子量: 405.960 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C26H28ClNO / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 445 / 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

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.24 Å3/Da / 溶媒含有率: 45.17 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG 3,350, Tris pH 7.5, MgCl2

-
データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-BM / 波長: 0.987 Å
検出器タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2019年6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: 0.987 Å / 相対比: 1
反射解像度: 1.6→50 Å / Num. obs: 98256 / % possible obs: 94.9 % / 冗長度: 3.1 % / Biso Wilson estimate: 14.5417884521 Å2 / Rpim(I) all: 0.04 / Net I/σ(I): 20
反射 シェル解像度: 1.6→1.63 Å / Num. unique obs: 4958 / CC1/2: 0.75

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692+SVN精密化
HKL-2000データ削減
HKL-3000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: 6VIG

6vig
PDB 未公開エントリ


解像度: 1.6→49.69 Å / SU ML: 0.196 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 27.5
Rfactor反射数%反射
Rfree0.2344 4059 5.03 %
Rwork0.2008 --
obs0.2024 80723 58.5 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 24.02 Å2
精密化ステップサイクル: LAST / 解像度: 1.6→49.69 Å
タンパク質核酸リガンド溶媒全体
原子数7468 0 116 445 8029
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005257061511447856
X-RAY DIFFRACTIONf_angle_d0.95568711617510653
X-RAY DIFFRACTIONf_chiral_restr0.03404985325851250
X-RAY DIFFRACTIONf_plane_restr0.003791100470391324
X-RAY DIFFRACTIONf_dihedral_angle_d15.01675801062889
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6023-1.62110.36541342455220.262045137466422X-RAY DIFFRACTION9.05752753978
1.6211-1.64090.235863537408570.243543924012749X-RAY DIFFRACTION17.3370617337
1.6409-1.66170.353478887303740.2527773974961120X-RAY DIFFRACTION25.0682343061
1.6617-1.68350.255974987982600.2391578653711440X-RAY DIFFRACTION31.7729294641
1.6835-1.70660.270318034107720.2399631694171576X-RAY DIFFRACTION34.6947368421
1.7066-1.7310.2956768317341170.2502243885241763X-RAY DIFFRACTION39.5207063275
1.731-1.75680.331474107451040.2412995621331941X-RAY DIFFRACTION43.1981411069
1.7568-1.78430.3268341766361010.2554255246872221X-RAY DIFFRACTION48.9563567362
1.7843-1.81350.2961078546351400.2582644003312588X-RAY DIFFRACTION56.3869367507
1.8135-1.84480.2571071463651480.2606112574092873X-RAY DIFFRACTION64.4961571307
1.8448-1.87840.3029981769651620.2457951045283094X-RAY DIFFRACTION67.3701634595
1.8784-1.91450.2365302529751890.2415016640173098X-RAY DIFFRACTION70.5364806867
1.9145-1.95360.2766184882321890.2460601437293253X-RAY DIFFRACTION70.7502569373
1.9536-1.9960.324530298441540.2347548565143159X-RAY DIFFRACTION70.7452487722
1.996-2.04250.2933290375811330.230735537763223X-RAY DIFFRACTION70.3269069573
2.0425-2.09360.2521453244021510.2273138138773094X-RAY DIFFRACTION68.2726698927
2.0936-2.15020.2396475626241510.2080276375673103X-RAY DIFFRACTION67.6507276507
2.1502-2.21340.2708772869551600.2090400342762970X-RAY DIFFRACTION66.8232280102
2.2134-2.28490.2388367633211930.2060993495082933X-RAY DIFFRACTION65.6171284635
2.2849-2.36650.2736477865881880.2023511171292913X-RAY DIFFRACTION64.996856005
2.3665-2.46130.249016080711440.2039643419942872X-RAY DIFFRACTION63.5348641247
2.4613-2.57330.2436937255921700.2021797273812816X-RAY DIFFRACTION62.731092437
2.5733-2.7090.2257779107051520.2034492287082805X-RAY DIFFRACTION62.1740958789
2.709-2.87870.3083087380471460.2031922734232843X-RAY DIFFRACTION62.7545664497
2.8787-3.10090.2369634324211260.1963101624552895X-RAY DIFFRACTION63.280268119
3.1009-3.41290.1841650930551540.190985929923112X-RAY DIFFRACTION68.6711522288
3.4129-3.90660.1861184117631530.1695884509793624X-RAY DIFFRACTION79.1160452451
3.9066-4.92120.1773586457312240.1596358108963866X-RAY DIFFRACTION86.6341876721
4.9212-490.2106002170942250.1819239340954298X-RAY DIFFRACTION94.8814768198
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)
16.28136363275-2.32450852769-0.9213002702145.5928191073-1.418504646491.67334901602-0.486974964246-0.7966536036030.5290015211261.229892257470.437025931932-0.425920409627-1.091753592340.523129997490.02448404873250.422428016004-0.25227619228-0.1049035484270.245980180684-0.08009566953950.3325233245217.896585965415.602448049331.5952258325
22.44153453782-1.47968191466-0.9485846304441.93238273226-1.18901054392.820090380670.0234046806299-0.247336025177-0.0438574772193-0.313251942965-0.119921193665-0.3678471963140.2473080616260.8053185608930.06922628811360.0222495383389-0.03335261080330.01696333223280.2652966612850.01094452168520.17672809998922.4053904126-6.7796949266523.5505597248
33.57063969941-1.46468435606-0.3158236452711.801889818080.4254898345684.11139007123-0.04936699082720.375853904152-0.236580465537-0.15673021209-0.1480731341780.0480976972180.2417308320470.1260779577880.1180536585480.0397779043497-0.01603559891730.01596986989420.122016396706-0.01481124453640.13785577155614.3490674818-5.3684352512318.9701914536
44.02822049979-1.5320476041-0.2020521195472.07282827010.9329313920394.655291188340.1795100225190.31227164541-0.150666076695-0.544116927462-0.3318761702950.275407802680.0204119775255-0.3371292022730.1089902043320.09724334079250.01241086561750.02077351785060.223383190953-0.03035994607840.1027817835178.17098793513-2.2229508011710.9893229897
52.92440142611-1.24025212478-0.4741091492861.63109696544-0.2394232081675.904695148680.2589781725080.1890003818310.2548538122340.0491320210795-0.132267715245-0.149384938597-0.6648632747390.331759261195-0.05694061857690.0426175408923-0.03221015971660.002584472291550.09593864412030.001802663310580.16485403445711.87449856498.0323984069823.251408881
66.578244956232.60854501224-1.90001391856.05465789075-1.854215779956.656732655430.274596129714-0.116037810363-0.03697207261860.854748489053-0.6182340699790.6160208876720.208388012092-1.050070155810.2776686720310.347686344488-0.1390696586590.02350723496020.321815357787-0.09603477324940.3332174295771.26922119242-1.3613232076839.4172218532
71.53818711527-0.535392418042-0.9602777252835.21932269813-4.801056143538.3064155273-0.146986886912-0.1919402683860.2843143426570.2342534624820.218698263662-0.18548981035-0.54282202358-0.0543771248589-0.07816629140630.143908637845-0.0293323531097-0.02157481054840.110680187219-0.05799999171480.161195245656.6686652802313.282880916732.7882543725
82.2211616922-2.007023853170.3376296970859.72111621689-0.2685560009031.67987028893-0.05726482922840.0180688183213-0.1902852214730.003098072997760.09286970512380.0860656151292-0.04540881514420.00812829264049-0.05505067690430.00627966274536-0.01951796468230.02240054511640.1342550762450.01084998876660.08938244962423.709067923220.83635836541320.3924240755
93.620849357231.220352812612.185759693241.234237519480.6044445524832.762206674370.0801496754734-0.197524668855-0.2722388453440.10396805560.203467248764-0.5050096061440.442313076680.18329002511-0.1505750176990.4602016708460.176599886462-0.02833346104740.384664586812-0.04213053892640.20035241373418.8541309003-10.298300172637.5879735557
106.10995151261-0.0802215107428-0.09853908419110.9255352250940.3087289249483.021895258110.07534259330730.2694375516510.482664868295-0.134173275889-0.03189046781970.0620027117447-0.550698922814-0.33371735906-0.071280225240.3228121337870.0384156666431-0.0789901614879-0.00113530573745-0.05686463659250.26662365010518.44767754323.720220797671.0007754252
112.91659578143-0.957893911097-1.008969441711.310236802450.5552929734794.163066202330.008697999856920.1192160797040.1133466124780.0189300921118-0.07044197666260.0457481032575-0.358543291832-0.2851556254910.0596091304690.1052357277930.03801198210170.0009940255116310.0487489097221-0.001002418511320.13241891453218.0543551846-3.9611876565667.6861824609
123.41111452107-2.302984408640.1478898629343.048501866270.2787876627933.66563362227-0.322684626222-0.646509679697-0.3572529271520.2248726912540.1961963274820.426473211883-0.119455187692-0.3009133753780.07293193524690.2222857633250.06629075725590.05100776568940.1997903911510.006903278761870.13072687062419.1019825057-10.422757403383.4060490082
132.6261212582-0.5368496192-1.098941979811.03190452098-0.5898133783732.657120937970.04535936441340.2848086549020.0574995796039-0.0461794724583-0.03733819461130.00832561601992-0.0721841889859-0.1409177274350.01688551813460.1190613434330.009148326102050.01552997680320.0487008109257-0.001373185501840.10252027613228.367668907-8.6052194878265.2179115012
143.704804259753.166561331630.5000160836484.901200546070.8954747976653.460445282850.04988496875630.00711623296727-0.1448556834240.303933904492-0.0791775720715-0.2787481360090.6076084391140.483799866936-0.003964427129420.06842629832250.121162361790.06435521086090.1929760785920.04975781118080.30862250700312.9976380414.584241661768.6792506859
150.457444300309-0.08683298598710.3041869701083.868628232540.6283434923014.58616627972-0.01727194860680.0646646190412-0.0412776110327-0.220984511977-0.08161199610390.07279386042340.3811672811050.05741884841610.09525513480510.0897628593660.02508308118720.01821168102790.0890719908797-0.0153699646050.1207872899553.8107647623518.815232614366.3806404873
160.9242102924820.6763823879081.082787930532.685102293130.7818322118053.397671676850.0976683054089-0.1297970902-0.02234997489230.258079990156-0.0820521096216-0.01872688931480.188860349326-0.05869799387060.009877984340410.08326376975380.0450147383306-0.000485099783150.06845787444-0.00502751011320.1096291734056.7785401374128.496595662874.161434625
178.705072533513.405230781731.045852202329.124912063851.398460005574.99201947389-0.2309368266410.9469246276180.674735638561-1.24430722620.3454933330440.706041696377-1.25462758869-0.302223386194-0.06444853421740.3762322178350.306151934246-0.09707081712130.2472057156480.0727737495750.311328302183-17.774139242216.072363945915.8837871448
182.935825012831.47281059081-0.7490093972121.834149709120.054755971823.48697731491-0.06499995510910.1577482163790.01483766102880.03975907109280.03897616319640.2616665823440.398572870372-0.8772817195450.01086466135850.03371470089210.002670085800280.01023208333240.24484233154-0.02756125136510.164836718169-22.280477909-5.7600919753922.7250514297
192.926583233532.254968443770.07230827737261.12489529141-0.3444707638693.628263299320.0463583509652-0.412394697795-0.1413431566760.807278394755-0.113107898977-0.1488498508060.290213648336-0.07271527129590.0381599835584-0.1205432269720.02477062163650.05699913249710.1472839176460.01019344592670.145712526027-12.6207346585-4.4582320816530.491433929
201.382981164741.825641903760.6286783426482.08839793638-0.6258778841653.23185807091-0.0896876289410.1573271625840.227617914718-0.1385603084510.1508564676430.104151836999-0.1120501633910.056710786761-0.01650415294680.06292897798190.0439552022914-0.006149790330410.09108330365250.04524710577490.166866620786-7.390451282449.4030630972416.5048377405
212.075635621120.491104514421-0.2233525494131.63675979302-1.74129443722.15581876082-0.05722008763260.0924761537712-0.2747623788-0.4182913045460.169785209335-0.1273097504140.347262067449-0.178341928509-0.08813117406140.0364254273444-0.000193943571501-0.007431151965670.1564226128410.004644587878080.109659185262-7.64304759941-3.3014090266221.858212293
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 306 through 322 )
2X-RAY DIFFRACTION2chain 'B' and (resid 323 through 371 )
3X-RAY DIFFRACTION3chain 'B' and (resid 372 through 420 )
4X-RAY DIFFRACTION4chain 'B' and (resid 421 through 438 )
5X-RAY DIFFRACTION5chain 'B' and (resid 439 through 455 )
6X-RAY DIFFRACTION6chain 'B' and (resid 456 through 465 )
7X-RAY DIFFRACTION7chain 'B' and (resid 466 through 496 )
8X-RAY DIFFRACTION8chain 'B' and (resid 497 through 528 )
9X-RAY DIFFRACTION9chain 'B' and (resid 529 through 549 )
10X-RAY DIFFRACTION10chain 'A' and (resid 307 through 341 )
11X-RAY DIFFRACTION11chain 'A' and (resid 342 through 407 )
12X-RAY DIFFRACTION12chain 'A' and (resid 408 through 438 )
13X-RAY DIFFRACTION13chain 'A' and (resid 439 through 545 )
14X-RAY DIFFRACTION14chain 'C' and (resid 306 through 341 )
15X-RAY DIFFRACTION15chain 'C' and (resid 342 through 438 )
16X-RAY DIFFRACTION16chain 'C' and (resid 439 through 546 )
17X-RAY DIFFRACTION17chain 'D' and (resid 307 through 321 )
18X-RAY DIFFRACTION18chain 'D' and (resid 322 through 371 )
19X-RAY DIFFRACTION19chain 'D' and (resid 372 through 437 )
20X-RAY DIFFRACTION20chain 'D' and (resid 438 through 496 )
21X-RAY DIFFRACTION21chain 'D' and (resid 497 through 545 )

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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。

-
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