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- PDB-8dgp: 14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) peptide -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 8dgp
タイトル14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) peptide
要素
  • 14-3-3 protein epsilon
  • Phosphorylated PEAK3 (pS69) peptide
キーワードSIGNALING PROTEIN
機能・相同性
機能・相同性情報


regulation of heart rate by hormone / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / regulation of potassium ion transmembrane transport ...regulation of heart rate by hormone / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / regulation of potassium ion transmembrane transport / protein phosphatase inhibitor activity / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of calcium ion export across plasma membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of heart rate by cardiac conduction / intracellular potassium ion homeostasis / phosphoserine residue binding / Regulation of HSF1-mediated heat shock response / Activation of BAD and translocation to mitochondria / protein localization to nucleus / regulation of cytosolic calcium ion concentration / HSF1 activation / potassium channel regulator activity / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / calcium channel inhibitor activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / signaling adaptor activity / substantia nigra development / Transcriptional and post-translational regulation of MITF-M expression and activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / protein sequestering activity / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / hippocampus development / phosphoprotein binding / mitochondrial membrane / cerebral cortex development / histone deacetylase binding / neuron migration / Regulation of PLK1 Activity at G2/M Transition / MHC class II protein complex binding / melanosome / intracellular protein localization / MAPK cascade / cellular response to heat / scaffold protein binding / protein phosphatase binding / transmembrane transporter binding / intracellular signal transduction / cadherin binding / protein heterodimerization activity / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / signal transduction / RNA binding / extracellular exosome / identical protein binding / nucleus / membrane / cytosol / cytoplasm
類似検索 - 分子機能
14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein ...14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
14-3-3 protein epsilon
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: 2.7 Å
データ登録者Roy, M.J. / Hardy, J.M. / Lucet, I.S.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)APP1144149 オーストラリア
引用ジャーナル: Nat Commun / 年: 2023
タイトル: Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling.
著者: Roy, M.J. / Surudoi, M.G. / Kropp, A. / Hou, J. / Dai, W. / Hardy, J.M. / Liang, L.Y. / Cotton, T.R. / Lechtenberg, B.C. / Dite, T.A. / Ma, X. / Daly, R.J. / Patel, O. / Lucet, I.S.
履歴
登録2022年6月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年6月7日Provider: repository / タイプ: Initial release
改定 1.12023年7月12日Group: Data collection / Database references / カテゴリ: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
改定 1.22023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
改定 1.32024年10月23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: 14-3-3 protein epsilon
B: 14-3-3 protein epsilon
C: 14-3-3 protein epsilon
D: 14-3-3 protein epsilon
E: Phosphorylated PEAK3 (pS69) peptide
F: Phosphorylated PEAK3 (pS69) peptide
G: Phosphorylated PEAK3 (pS69) peptide
H: Phosphorylated PEAK3 (pS69) peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)128,20913
ポリマ－127,7968
非ポリマー4125
水2,306128
1
A: 14-3-3 protein epsilon
B: 14-3-3 protein epsilon
E: Phosphorylated PEAK3 (pS69) peptide
F: Phosphorylated PEAK3 (pS69) peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)64,3109
ポリマ－63,8984
非ポリマー4125
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-59 kcal/mol
Surface area23500 Å2
手法PISA
2
C: 14-3-3 protein epsilon
D: 14-3-3 protein epsilon
G: Phosphorylated PEAK3 (pS69) peptide
H: Phosphorylated PEAK3 (pS69) peptide


分子量 (理論値)分子数
合計 (水以外)63,8984
ポリマ－63,8984
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-32 kcal/mol
Surface area22660 Å2
手法PISA
単位格子
Length a, b, c (Å)155.532, 155.532, 58.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w

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要素

#1: タンパク質
14-3-3 protein epsilon / 14-3-3E


分子量: 29454.133 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: YWHAE / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): C41 / 参照: UniProt: P62258
#2: タンパク質・ペプチド
Phosphorylated PEAK3 (pS69) peptide


分子量: 2494.931 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#3: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H6O2
#4: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 3 / 由来タイプ: 合成 / 式: SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 128 / 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: 2.75 Å3/Da / 溶媒含有率: 55.23 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 9.35
詳細: 2M ammonium sulfate, 0.1 M sodium bicine pH 9.35, 5% (v/v) 2-methyl-2,4,-pentandiol (MPD)

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データ収集

回折平均測定温度: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年3月15日
放射モノクロメーター: M / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9537 Å / 相対比: 1
反射解像度: 2.69→49.18 Å / Num. obs: 38786 / % possible obs: 99.6 % / 冗長度: 13.9 % / Biso Wilson estimate: 48.69 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.256 / Rrim(I) all: 0.266 / Net I/σ(I): 9.71
反射 シェル解像度: 2.69→2.86 Å / 冗長度: 13.6 % / Rmerge(I) obs: 1.786 / Num. unique obs: 82902 / CC1/2: 0.546 / Rrim(I) all: 1.854 / % possible all: 97.7

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation3.7 Å49.18 Å
Translation3.7 Å49.18 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDS20161205データ削減
Aimless0.5.21データスケーリング
PHASER2.8.3位相決定
PDB_EXTRACT3.27データ抽出
Coot0.9.8.1モデル構築
精密化構造決定の手法: 分子置換
開始モデル: 2BR9

2br9


解像度: 2.7→49.18 Å / SU ML: 0.3637 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 23.6838
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.233 1985 5.15 %
Rwork0.1874 36526 -
obs0.1898 38511 99.28 %
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: 60.89 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→49.18 Å
タンパク質核酸リガンド溶媒全体
原子数7505 0 23 128 7656
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00617642
X-RAY DIFFRACTIONf_angle_d0.770910362
X-RAY DIFFRACTIONf_chiral_restr0.04371199
X-RAY DIFFRACTIONf_plane_restr0.00691330
X-RAY DIFFRACTIONf_dihedral_angle_d3.71791080
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.41031330.30242379X-RAY DIFFRACTION90.39
2.76-2.840.30291510.25192550X-RAY DIFFRACTION100
2.84-2.920.27131410.21982632X-RAY DIFFRACTION100
2.92-3.020.24521300.21622612X-RAY DIFFRACTION100
3.02-3.130.2531480.21122580X-RAY DIFFRACTION100
3.13-3.250.26991870.20612574X-RAY DIFFRACTION100
3.25-3.40.2861200.23612657X-RAY DIFFRACTION100
3.4-3.580.24831170.18032587X-RAY DIFFRACTION100
3.58-3.80.21121570.16572624X-RAY DIFFRACTION100
3.8-4.090.19341270.15472648X-RAY DIFFRACTION100
4.09-4.510.18311370.15632650X-RAY DIFFRACTION100
4.51-5.160.20851550.16822621X-RAY DIFFRACTION100
5.16-6.50.2821370.21192680X-RAY DIFFRACTION100
6.5-49.180.19771450.16432732X-RAY DIFFRACTION99.55
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)
13.3055577018-1.269209561611.745684603977.775069381390.4651286891551.595313100470.168731906479-0.372467129115-0.09638272401650.229465819593-0.1187522621160.311859967943-0.0498007271502-0.392710059856-0.1036065386780.381145977085-0.05571493609050.01043999701060.4214988804930.03504615956130.197158602907-83.979960383448.38012914212.36112511721
21.402104447830.363264344895-1.750471219030.5008450599810.9744600505936.616333483060.04119867398810.093600389463-0.0231866224494-0.274773890729-0.06724077463750.0450283692393-0.407138405350.278811780108-0.03983261254080.3910944251910.00999342033644-0.06221397679690.3946563319170.04205118042710.209085455764-70.834746008556.1068853731-16.1229713004
33.57511816507-0.6813724807371.316752404822.50050717725-0.0460471703572.19583859831-0.0933699413028-0.02697286820410.136121583132-0.1146819141150.01712990177-0.259367675451-0.1472908042780.2531596242580.07763062893370.343693812392-0.0540196425785-0.003957516255030.31973040278-0.03808092955420.196634042871-62.316278797962.28167917930.913322483379
46.609016266192.138947574971.927485304955.304175086351.706545622323.37476666511-0.588755862325-0.975493113936-0.9461390640230.390199293366-0.148986111644-0.1926582924231.013286130050.4389158710210.0887388829830.4551573778160.1495296072590.01968299021520.3311159939230.07279035911030.354831280595-53.516124145949.02824301755.58945123838
57.856808899911.933093135920.7368230966715.88547002934-0.2476832157783.1566409441-0.1803974718950.25792161736-0.0754764287268-0.2028672573880.1466666563570.342363839208-0.218492336056-0.1933362514150.006467249066640.419867155822-0.0308651908029-0.02101227830630.391725433241-0.01347720236950.208426514544-76.196871154244.340677605-32.8199204179
62.838104481150.305966161519-2.372590688152.28270006182-0.05167049423218.0800042598-0.317335353232-0.160819746511-0.6160346772930.19584443994-0.1941404588-0.2290337532940.517191206181-0.02941915859410.0669601033010.443489084706-0.00896135885991-0.08256409992520.3930766630740.0113948674560.299497091493-80.163095518433.085995738-14.8796378186
72.57427368252-0.0133650845007-1.274908464562.274645035751.071257677237.41939991325-0.178706942797-0.120433937261-0.1089463202320.200469638864-0.3095506332060.3367531677480.141652427254-0.5833683621310.09614252097410.365483240047-0.08122643855-0.003175649527960.2925647091490.03249999938840.366648105523-89.694032449835.3791657627-13.522140591
83.986901765911.494260580671.013166337344.31005265148-1.259894022231.4946290646-0.1511750977550.287785147958-0.578751093560.013302402969-0.150928478799-0.0612998616267-0.358943970324-0.085913631471-0.002961146437230.418049924408-0.0132521395382-0.07151131481460.301400539078-0.08334395300070.327751444424-83.157302412627.7500200258-30.4604733778
94.178537440791.47343054166-3.401321365173.35971011898-0.6349680950614.166439435460.1621395438980.36084685318-0.518477544474-0.3142489234320.02159831562210.3204586977630.238770687958-0.3811642401540.2056071714370.5283335702120.0474500104547-0.147739110620.372038829438-0.0996552192780.591462680019-86.849728097219.431608437-28.8743630428
105.84572447163-1.22307680365-0.6685522967163.351583932860.2145769223941.86704203481-0.0479541524482-0.465896034594-1.541180933670.4547246276310.149413031662-0.4527191540810.7849218928540.5725894173480.1854337855650.6024067987940.149840363447-0.1359274994380.419950291557-0.08609868229650.740234766491-74.927189659914.8576649458-26.1636501678
112.235141533491.57847329219-2.608449711346.529450567-1.650049887465.14797629471-0.21196331709-0.708346939406-0.500680248417-0.584237816325-0.278392828183-0.2751571248950.2697155008411.540822519490.3637314903310.5160964865320.137027927781-0.09526630050450.8050026050480.04084370788060.897787440543-64.876595915917.5186784535-25.4939413912
121.099269536981.994903383440.9591112237835.9739608268-1.849645674676.61816175601-0.0882707737911-0.259909189399-0.1535457395341.5490988069-0.2352012833521.575166146570.285939677658-0.0819585803010.4950592647730.67308474671-0.02315784368590.2092106934250.3079725483940.003139486683310.8508831838-56.706456860426.4574292145-1.73172742893
132.42829244422-0.860331742223-0.6464030836296.753946896693.205355322074.3946794068-0.0453511343215-0.127808151918-0.0135485367498-0.07563621158530.02526780493240.381573840715-0.3509549489520.166370322150.1083008052610.406971648839-0.008639198811180.05172168490840.3174185143240.0775953488320.593317963182-47.468790215721.6732346823-16.9644142836
142.3944622035-0.614075745013-0.1807204571777.348694707433.14505170285.20957784538-0.1825820377660.4668859659860.222642148307-0.7052688512170.01001283216280.396768267363-0.2387696249810.0539327761652-0.01805380081130.516191483708-0.06769443666010.1016758546440.3874315817320.09649650810120.575371089072-46.137787147626.4917473793-23.8611124766
152.6924875487-0.26090588217-0.8368663828831.2864152218-0.9267272421546.7271469260.1828269793630.134503092192-0.118207451931-0.153523734802-0.0872216881099-0.446676191015-0.0371338399662-0.246351771997-0.2274998090380.544869404735-0.03576763505940.06071969924710.3462514616910.06198240667010.792623908709-33.310859679533.7733076981-19.9850912338
162.58543089158-0.393462843217-1.46465773493.889036117921.164977621788.100995012040.0100832500384-0.758547064005-0.2833447955670.5176831296290.0160683270273-0.39621066980.1342866003290.845102284733-0.2154902418520.521594030963-0.069116390878-0.0906463747370.5474580053940.1475805328821.01895553787-24.22758921728.0655071875-11.0109657149
176.372907220710.879772556218-0.5143540161885.074049864440.955935514474.80277597904-0.4759189108130.358267543491-0.382651769197-1.363596804460.7379571846650.147437790858-0.1345213495880.261981943754-0.3538489089670.765270978693-0.0912618908659-0.09094107918110.384096969310.05131155848860.864300478944-53.91316966310.573100930748-27.7716388894
185.51963274883-0.853356290159-1.174530614640.170032656850.2896727346830.554159070253-0.1959245730440.449419333118-1.00720854013-0.7061358390530.41694378740.3597834060590.754762034899-0.5738637714650.006346075826790.756732105666-0.351276552771-0.1587793895280.605959268804-0.161571911911.46952108051-59.0694229867-12.4343608485-27.3473935884
191.820587965460.3181696830.1192988112085.36894678892.094917896213.95480491284-0.02911968082-0.281067816843-0.4227158410970.339487061925-0.1775064050141.06635947468-0.196609408232-0.0660329259211-0.2419882433010.6002458042660.005533298024110.1479347477940.3956254753480.2375954508981.07216448653-54.39509359543.91280857258-8.03584631759
201.830615470280.8911441926540.4488414013917.226549950782.876425914923.777878148570.0277191241055-0.1038401831190.2740307833550.4164066126870.03629880210231.45689081149-0.440542336582-0.282613411977-0.1788135200390.6635429338520.07275553710730.3000880462670.3900453070640.3410257631641.31709724211-63.41009875739.47458340618-5.00449419556
212.389216919770.07246020653640.2324140563342.05901826523-1.887934989151.765735492960.3016337402130.153718265461-0.505224570133-0.2088116449550.3604401496440.9857037461460.282886106927-0.349024970491-0.04427485641490.441181657453-0.04340737542730.0411730966830.4426607901180.3063371079431.534836217-60.5887198271-9.60450216697-12.8404040989
221.037569107620.678115785677-0.2001713982631.98218304771-0.3681221716491.533071029730.174548726526-0.00577242227891-0.1710854648910.1173828250980.3787866011150.8345645015860.0798382522119-0.4121345129690.823087125760.579150851816-0.05329195464070.159610813910.3353924181090.2845692008581.56479083451-62.6139128397-13.8010794464-4.45164299466
232.297814890510.177556286739-0.9209536703792.51919691097-1.900318158475.917343020910.175029331284-0.2273792936680.03495986978070.2625193620760.09786728545030.2758567257360.1293397178350.540258325378-0.2523976732430.5045400853930.02793839410210.05667106467010.4320515036320.2177451958861.13803635636-48.1847953354-17.2395657686-3.85593809241
241.82623833729-2.01988097884-2.22756426513.464025585962.483877802357.155621664050.0230405363038-0.05570714190790.167799310408-0.0926728140215-0.0243304933406-0.0265869790579-0.3439319450820.4403460291460.1247086245470.4403611616280.02269145363820.08931536349040.4093611351830.2025701784731.04150647874-40.9347590032-12.0023120163-2.28963767806
258.277416683685.10293879702-4.225983092274.85906714003-1.70067759515.3835097145-0.460827860174-0.901284107276-0.2893909402771.25731254559-0.977499569537-1.78789705399-0.955384895870.9428287329971.078499692960.6013950944870.0471260719046-0.130550762820.5534795618580.04587192526970.727080569111-72.432917657824.9937899869-19.2697437941
269.84772446722-3.43282875305-4.310402244944.26516223975-1.7206698055.27704816276-0.4951023184670.581303242817-1.34409314436-0.8478072825020.188653368137-0.0177719845840.523631683917-0.4733966872270.4920615055790.493447277548-0.03624823662340.01544786560350.405125509244-0.16532663920.315965444595-60.369710998150.0860470597-5.47445288478
275.57117834616-4.33664697929-3.960830813214.173738795745.387991713759.47006896302-0.3281378196790.277158079249-0.09016286216980.3143301585430.983166061382-1.023222210381.1641553558-0.283088774297-0.7520766474190.608437666797-0.0321107151560.1669643373360.4842267902240.07732239272271.24776640148-33.2767625620.5500692272-15.2280642227
280.5446141993291.33151885186-0.8580384977477.244513350731.590683043627.718265142180.867221940909-0.03291644252680.1283512485680.977282061170.424855615686-0.688928991621-0.76379441546-0.13662166833-0.4037517621960.584183956316-0.0841597179476-0.08393434606640.3566159304030.2446822638291.34226374829-46.500227775-4.26080096736-4.70028722634
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 -2 through 38 )AA-2 - 381 - 41
22chain 'A' and (resid 39 through 106 )AA39 - 10642 - 109
33chain 'A' and (resid 107 through 204 )AA107 - 204110 - 207
44chain 'A' and (resid 205 through 233 )AA205 - 233208 - 236
55chain 'B' and (resid 2 through 38 )BD2 - 381 - 37
66chain 'B' and (resid 39 through 73 )BD39 - 7338 - 72
77chain 'B' and (resid 74 through 106 )BD74 - 10673 - 105
88chain 'B' and (resid 107 through 137 )BD107 - 137106 - 136
99chain 'B' and (resid 138 through 162 )BD138 - 162137 - 161
1010chain 'B' and (resid 163 through 204 )BD163 - 204162 - 203
1111chain 'B' and (resid 205 through 234 )BD205 - 234204 - 233
1212chain 'C' and (resid -1 through 17 )CE-1 - 171 - 19
1313chain 'C' and (resid 18 through 73 )CE18 - 7320 - 75
1414chain 'C' and (resid 74 through 138 )CE74 - 13876 - 140
1515chain 'C' and (resid 139 through 187 )CE139 - 187141 - 189
1616chain 'C' and (resid 188 through 234 )CE188 - 234190 - 236
1717chain 'D' and (resid 0 through 33 )DF0 - 331 - 34
1818chain 'D' and (resid 34 through 38 )DF34 - 3835 - 39
1919chain 'D' and (resid 39 through 73 )DF39 - 7340 - 74
2020chain 'D' and (resid 74 through 104 )DF74 - 10475 - 105
2121chain 'D' and (resid 105 through 137 )DF105 - 137106 - 138
2222chain 'D' and (resid 138 through 162 )DF138 - 162139 - 163
2323chain 'D' and (resid 163 through 213 )DF163 - 213164 - 214
2424chain 'D' and (resid 214 through 234 )DF214 - 234215 - 235
2525chain 'E' and (resid 66 through 72 )EG66 - 721 - 7
2626chain 'F' and (resid 65 through 73 )FH65 - 731 - 9
2727chain 'G' and (resid 65 through 72 )GI65 - 721 - 8
2828chain 'H' and (resid 65 through 72 )HJ65 - 721 - 8

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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