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- PDB-8aj8: Structure of p110 gamma bound to the p84 regulatory subunit -

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基本情報

登録情報
データベース: PDB / ID: 8aj8
タイトルStructure of p110 gamma bound to the p84 regulatory subunit
要素
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
  • Phosphoinositide 3-kinase regulatory subunit 6
キーワードSIGNALING PROTEIN / PI3K / PIK3CG / PIK3R6 / phosphoinositide 3-kinase / p110 / p84
機能・相同性
機能・相同性情報


G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / regulation of natural killer cell mediated cytotoxicity / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-4-phosphate 3-kinase / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex / phosphatidylinositol 3-kinase complex, class IB / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol 3-kinase complex, class IA ...G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / regulation of natural killer cell mediated cytotoxicity / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-4-phosphate 3-kinase / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex / phosphatidylinositol 3-kinase complex, class IB / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / positive regulation of T cell differentiation / 1-phosphatidylinositol-3-kinase activity / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / immune system process / positive regulation of MAP kinase activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / endocytosis / positive regulation of angiogenesis / chemotaxis / cell migration / phospholipase C-activating G protein-coupled receptor signaling pathway / angiogenesis / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / G protein-coupled receptor signaling pathway / inflammatory response / protein serine kinase activity / ATP binding / membrane / plasma membrane / cytoplasm
類似検索 - 分子機能
Phosphoinositide 3-kinase regulatory subunit 5/6 / Phosphoinositide 3-kinase gamma adapter protein p101 subunit / PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. ...Phosphoinositide 3-kinase regulatory subunit 5/6 / Phosphoinositide 3-kinase gamma adapter protein p101 subunit / PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform / Phosphoinositide 3-kinase regulatory subunit 6
類似検索 - 構成要素
生物種Sus scrofa (ブタ)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 8.5 Å
データ登録者Burke, J.E. / Williams, R.L. / Zhang, X.
資金援助 英国, カナダ, 2件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MC_U105184308 英国
Canadian Institutes of Health Research (CIHR)168998 カナダ
引用ジャーナル: Cell Rep / 年: 2023
タイトル: Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs.
著者: Manoj K Rathinaswamy / Meredith L Jenkins / Benjamin R Duewell / Xuxiao Zhang / Noah J Harris / John T Evans / Jordan T B Stariha / Udit Dalwadi / Kaelin D Fleming / Harish Ranga-Prasad / ...著者: Manoj K Rathinaswamy / Meredith L Jenkins / Benjamin R Duewell / Xuxiao Zhang / Noah J Harris / John T Evans / Jordan T B Stariha / Udit Dalwadi / Kaelin D Fleming / Harish Ranga-Prasad / Calvin K Yip / Roger L Williams / Scott D Hansen / John E Burke /
要旨: Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled ...Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled receptors (GPCRs) and Ras. Using a combination of X-ray crystallography, hydrogen deuterium exchange mass spectrometry (HDX-MS), electron microscopy, molecular modeling, single-molecule imaging, and activity assays, we identify molecular differences between p110γ-p84 and p110γ-p101 that explain their differential membrane recruitment and activation by Ras and GPCRs. The p110γ-p84 complex is dynamic compared with p110γ-p101. While p110γ-p101 is robustly recruited by Gβγ subunits, p110γ-p84 is weakly recruited to membranes by Gβγ subunits alone and requires recruitment by Ras to allow for Gβγ activation. We mapped two distinct Gβγ interfaces on p101 and the p110γ helical domain, with differences in the C-terminal domain of p84 and p101 conferring sensitivity of p110γ-p101 to Gβγ activation. Overall, our work provides key insight into the molecular basis for how PI3Kγ complexes are activated.
履歴
登録2022年7月27日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年3月22日Provider: repository / タイプ: Initial release
改定 1.12024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
B: Phosphoinositide 3-kinase regulatory subunit 6
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
D: Phosphoinositide 3-kinase regulatory subunit 6
E: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
F: Phosphoinositide 3-kinase regulatory subunit 6
G: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
H: Phosphoinositide 3-kinase regulatory subunit 6


分子量 (理論値)分子数
合計 (水以外)846,4038
ポリマ－846,4038
非ポリマー00
水00
1
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
B: Phosphoinositide 3-kinase regulatory subunit 6


分子量 (理論値)分子数
合計 (水以外)211,6012
ポリマ－211,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
D: Phosphoinositide 3-kinase regulatory subunit 6


分子量 (理論値)分子数
合計 (水以外)211,6012
ポリマ－211,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
F: Phosphoinositide 3-kinase regulatory subunit 6


分子量 (理論値)分子数
合計 (水以外)211,6012
ポリマ－211,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
H: Phosphoinositide 3-kinase regulatory subunit 6


分子量 (理論値)分子数
合計 (水以外)211,6012
ポリマ－211,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)322.347, 166.598, 255.794
Angle α, β, γ (deg.)90.000, 114.024, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "A"
d_2ens_1chain "C"
d_3ens_1chain "E"
d_4ens_1chain "G"
d_1ens_2chain "B"
d_2ens_2chain "D"
d_3ens_2chain "F"
d_4ens_2chain "H"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLULYSA1 - 995
d_21ens_1GLULYSC1 - 995
d_31ens_1GLULYSE1 - 995
d_41ens_1GLULYSG1 - 995
d_11ens_2SERGLNB1 - 558
d_21ens_2SERGLND1 - 558
d_31ens_2SERGLNF1 - 558
d_41ens_2SERGLNH1 - 558

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.999994641788, -0.00202890867663, 0.00256903197895), (0.00201541818863, 0.999984224711, 0.00524293995871), (-0.0025796288981, -0.00523773419215, 0.999982955682)4.95692737026, 81.9467022275, 20.2094895081
2given(-0.995672539242, 0.0197712490206, -0.0908035919576), (-0.00743073228929, -0.990915633154, -0.134279530047), (-0.0926335728442, -0.133023703467, 0.986774399495)-0.673712310169, 44.0792667864, 5.91278487541
3given(-0.993187016113, 0.0291504406243, -0.112826427915), (-0.0117837846656, -0.98836712914, -0.151629681969), (-0.11593400469, -0.149267109058, 0.98197690233)5.49955990194, -39.9096304752, 25.6942608986
4given(0.999135295165, 0.028569246637, 0.0302069545246), (-0.0280296683355, 0.999442522789, -0.0181378426221), (-0.0307082993351, 0.0172754678251, 0.999379086515)4.70405349802, 83.9980144973, 20.7170008013
5given(-0.996118787943, 0.0285196090499, -0.0832705962959), (-0.021185572691, -0.995924583074, -0.0876663922966), (-0.0854314451335, -0.085562005167, 0.992663392825)-0.00433677885863, 44.4443405396, 5.31732223578
6given(-0.996163452997, 0.00828033799606, -0.0871195208647), (0.00345975470992, -0.991008858394, -0.13375153338), (-0.0874437248199, -0.133539801508, 0.98717815839)5.03388012802, -40.8766576239, 23.6002091712

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要素

#1: タンパク質
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform / PI3-kinase subunit gamma / PI3K-gamma / PI3Kgamma / PtdIns-3-kinase subunit gamma / ...PI3-kinase subunit gamma / PI3K-gamma / PI3Kgamma / PtdIns-3-kinase subunit gamma / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit gamma / PtdIns-3-kinase subunit p110-gamma / p110gamma / Phosphoinositide-3-kinase catalytic gamma polypeptide / Serine/threonine protein kinase PIK3CG / p120-PI3K


分子量: 126830.812 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Sus scrofa (ブタ) / 遺伝子: PIK3CG
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: O02697, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, phosphatidylinositol-4-phosphate 3-kinase, non-specific serine/threonine protein kinase
#2: タンパク質
Phosphoinositide 3-kinase regulatory subunit 6 / Phosphoinositide 3-kinase gamma adapter protein of 87 kDa / p84 PI3K adapter protein / p84 PIKAP / ...Phosphoinositide 3-kinase gamma adapter protein of 87 kDa / p84 PI3K adapter protein / p84 PIKAP / p87 PI3K adapter protein / p87PIKAP


分子量: 84769.906 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Pik3r6
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q3U6Q4

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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: 3.71 Å3/Da / 溶媒含有率: 66.81 %
結晶化温度: 290 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: Optimized crystals were grown from a crystallization solution containing 16% EDO_P8K (20% w/v PEG 8000, 40% v/v ethylene glycol), 0.06 M amino acids (0.2 M sodium L-glutamate, 0.2 M DL- ...詳細: Optimized crystals were grown from a crystallization solution containing 16% EDO_P8K (20% w/v PEG 8000, 40% v/v ethylene glycol), 0.06 M amino acids (0.2 M sodium L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine, 0.2 M DL-serine), 0.08 M buffer 2 pH7.5 (0.5 M HEPES, 0.5 M MOPS), 0.4 M Na/K phosphate pH 6.3.
PH範囲: 6.3-7.5

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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: ESRF / ビームライン: ID29 / 波長: 0.9762 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2008年8月15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: 0.9762 Å / 相対比: 1
反射解像度: 8.5→90.3 Å / Num. obs: 10835 / % possible obs: 99.9 % / 冗長度: 5.8 % / Biso Wilson estimate: 484.61 Å2 / CC1/2: 0.99 / CC star: 0.129 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.066 / Rrim(I) all: 0.129 / Rsym value: 0.122 / Net I/σ(I): 6.8
反射 シェル解像度: 8.5→8.89 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1187 / CC1/2: 0.9 / Rpim(I) all: 0.228 / Rrim(I) all: 0.463 / Rsym value: 0.39

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.1_4122精密化
MOSFLM7.0.3データ削減
SCALA6データスケーリング
PHASER2.8.3位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7MEZ

7mez


解像度: 8.5→90.29 Å / SU ML: 1.2545 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 38.6969
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3399 1084 10 %
Rwork0.2795 9751 -
obs0.2857 10835 97.6 %
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: 545.97 Å2
精密化ステップサイクル: LAST / 解像度: 8.5→90.29 Å
タンパク質核酸リガンド溶媒全体
原子数50008 0 0 0 50008
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003851076
X-RAY DIFFRACTIONf_angle_d0.634969220
X-RAY DIFFRACTIONf_chiral_restr0.04227916
X-RAY DIFFRACTIONf_plane_restr0.00588768
X-RAY DIFFRACTIONf_dihedral_angle_d10.683219152
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.0813187226868
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.100133135077
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.0957579923772
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.117716413945
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.11339534884
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.114664888476
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
8.5-8.890.36041310.31311187X-RAY DIFFRACTION96.84
8.89-9.350.34031370.29011219X-RAY DIFFRACTION98.47
9.35-9.940.32151350.25341219X-RAY DIFFRACTION98.47
9.94-10.70.29741350.24681220X-RAY DIFFRACTION98.26
10.71-11.780.29461350.24221210X-RAY DIFFRACTION97.82
11.78-13.480.30611380.25781229X-RAY DIFFRACTION97.57
13.49-16.960.3381370.28241223X-RAY DIFFRACTION97.42
16.97-90.290.41221360.33281244X-RAY DIFFRACTION96.17
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)
13.158314941721.60281079137-0.385818351421.81086363436-2.349170337321.97313882658-0.1470089449590.3488900183680.7439198286580.03391067580610.200744815260.5454738067410.6331956309140.2851671821123.61670256035E-55.487047510920.1536636441710.2074934230914.53250518447-0.7086636248695.2698184690834.7056773346-6.1258708123466.7501442754
27.632011208572.016292920972.06635000222-0.5214703806811.063763490194.81273155612-1.946862899940.604667810491-1.664029613841.1335631331.73133979717-0.418142934013-0.521476147788-1.245668431930.0001600902645315.481933509010.755549716971-0.4282469000965.171228866390.3063491168566.0950748547554.9824969793-1.8010661550210.2018361738
32.668602353141.50813747851-0.5412310936321.19435535807-1.748624408611.616193830760.6904488850090.714773598566-0.376719176843-0.205653489199-0.396790645342-0.4455570283620.813218715777-0.9165564785242.78189583259E-55.48761175133-0.118757014248-0.09927440167675.02731177473-0.8077063710865.5682091544839.846252266576.240927313686.9010091646
46.003320728440.05386310180461.25119651334-1.987791826391.35260838372-0.158240763188-0.04396934530822.0026699185-0.582292970499-0.2696173799230.7187362968350.517862908715-0.572111566039-1.044466991610.0004994201262836.491066114680.5100124839110.02969468869447.454925581360.01412646806864.9326658587359.895509794180.471600589829.1931047138
52.892999076091.606304250131.835945996721.05017020709-1.191203825153.280477351550.283444203269-1.15019400516-0.1665365018780.0660982861194-0.121549892418-1.11769598214-0.6424030335650.392126281823.10978590633E-55.039427144661.025692819930.1959033619775.761374998060.107503824075.60412637952-41.411501225940.928449800169.3800204751
610.92111163862.406093454461.912844671846.00880914535-0.8562485180692.94663628684-1.437819461410.8853336069360.0819994724615-1.153875061951.071636980753.17897624874-0.7520343352960.2523556028880.0003420437130345.481605453140.436469246941.137400665364.62132747739-0.09935564917275.7296211477-55.673986636344.17886515810.9010826558
71.846981305773.198766771490.9445829798710.275328374397-0.131879935093-0.3339522310750.121014661217-1.05661760363-0.416545070176-0.2886026064160.0404224172035-1.05235034987-0.254848840038-0.5401186534861.25801398017E-55.362017429621.2816012975-0.589424779787.12838019310.1571267470856.7348312012-36.6794630081-44.385170753988.1320885219
86.18088811582-0.6077974206251.81491567582-2.26344984858-1.44671110141.244535218150.187602976182-0.3962615791670.981035866594-0.560616440259-0.258706410144-0.536543332262-0.09524966840941.281534591510.0001096990406366.14259399173-0.00144363924162-0.3440754485266.54881684473-0.1483609542385.11713790748-50.6410069962-40.265844232929.1037506669
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
11(chain 'A' and resid 36 through 1086)AA36 - 10781 - 995
22(chain 'B' and resid 3 through 756)BB3 - 7561 - 558
33(chain 'C' and resid 36 through 1086)CC36 - 10781 - 995
44(chain 'D' and resid 3 through 756)DD3 - 7561 - 558
55(chain 'E' and resid 36 through 1086)EE36 - 10781 - 995
66(chain 'F' and resid 3 through 756)FF3 - 7561 - 558
77(chain 'G' and resid 36 through 1086)GG36 - 10781 - 995
88(chain 'H' and resid 3 through 756)HH3 - 7561 - 558

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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