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- PDB-7ue0: Integrin alpha IIB beta3 complex with fradafiban -

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基本情報

登録情報
データベース: PDB / ID: 7ue0
タイトルIntegrin alpha IIB beta3 complex with fradafiban
要素
  • 10E5 Fab heavy chain
  • 10E5 Fab light chain
  • Integrin alpha-IIb heavy chain
  • Isoform Beta-3C of Integrin beta-3
キーワードCELL ADHESION/INHIBITOR / Complex / Inhibitor / BLOOD CLOTTING / CELL ADHESION / CELL ADHESION-INHIBITOR complex
機能・相同性
機能・相同性情報


tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / negative regulation of low-density lipoprotein receptor activity / fibrinogen binding / alphav-beta3 integrin-PKCalpha complex / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / mesodermal cell differentiation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / glycinergic synapse / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / alphav-beta3 integrin-IGF-1-IGF1R complex / cell-substrate junction assembly / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte migration / Molecules associated with elastic fibres / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / microvillus membrane / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / activation of protein kinase activity / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / Integrin signaling / positive regulation of endothelial cell migration / cell-matrix adhesion / substrate adhesion-dependent cell spreading / Signal transduction by L1 / integrin-mediated signaling pathway / response to activity / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / wound healing / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / platelet aggregation / VEGFA-VEGFR2 Pathway / cell-cell adhesion / ruffle membrane / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants
類似検索 - 分子機能
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1.
類似検索 - ドメイン・相同性
Fradafiban / Integrin beta-3 / Integrin alpha-IIb
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 2.74196193977 Å
データ登録者Lin, F.-Y. / Zhu, J. / Zhu, J. / Springer, T.A.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL-103526 米国
引用ジャーナル: Cell / 年: 2022
タイトル: A general chemical principle for creating closure-stabilizing integrin inhibitors.
著者: Lin, F.Y. / Li, J. / Xie, Y. / Zhu, J. / Huong Nguyen, T.T. / Zhang, Y. / Zhu, J. / Springer, T.A.
履歴
登録2022年3月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年8月17日Provider: repository / タイプ: Initial release
改定 1.12023年3月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
改定 1.22023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.32024年10月2日Group: Structure summary / カテゴリ: struct / Item: _struct.title

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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: Integrin alpha-IIb heavy chain
B: Isoform Beta-3C of Integrin beta-3
C: Integrin alpha-IIb heavy chain
D: Isoform Beta-3C of Integrin beta-3
E: 10E5 Fab heavy chain
F: 10E5 Fab light chain
H: 10E5 Fab heavy chain
L: 10E5 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)302,43141
ポリマ－297,4068
非ポリマー5,02533
水5,134285
1
A: Integrin alpha-IIb heavy chain
B: Isoform Beta-3C of Integrin beta-3
H: 10E5 Fab heavy chain
L: 10E5 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)151,40321
ポリマ－148,7034
非ポリマー2,70017
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Integrin alpha-IIb heavy chain
D: Isoform Beta-3C of Integrin beta-3
E: 10E5 Fab heavy chain
F: 10E5 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)151,02820
ポリマ－148,7034
非ポリマー2,32516
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)258.282, 145.023, 104.986
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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要素

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タンパク質 , 2種, 4分子 ACBD

#1: タンパク質 Integrin alpha-IIb heavy chain


分子量: 49515.965 Da / 分子数: 2 / 断片: UNP Residues 32-488 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGA2B, GP2B, ITGAB
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P08514
#2: タンパク質 Isoform Beta-3C of Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


分子量: 52087.902 Da / 分子数: 2 / 断片: UNP Residues 27-498 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGB3, GP3A
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P05106

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抗体 , 2種, 4分子 EHFL

#3: 抗体 10E5 Fab heavy chain


分子量: 23766.473 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Mus musculus (ハツカネズミ)
#4: 抗体 10E5 Fab light chain


分子量: 23332.686 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Mus musculus (ハツカネズミ)

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糖 , 4種, 6分子

#5: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#12: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 7種, 312分子

#8: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 6 / 由来タイプ: 合成 / 式: SO4
#9: 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: 1 / 由来タイプ: 合成 / 式: C3H8O3
#10: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Ca
#11: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#13: 化合物 ChemComp-MWX / Fradafiban / [(3S,5S)-5-{[(4'-carbamimidoyl[1,1'-biphenyl]-4-yl)oxy]methyl}-2-oxopyrrolidin-3-yl]acetic acid / フラダフィバン


分子量: 367.398 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C20H21N3O4 / タイプ: SUBJECT OF INVESTIGATION
#14: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#15: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 285 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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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: 3.31 Å3/Da / 溶媒含有率: 62.79 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.9
詳細: 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl

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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: APS / ビームライン: 23-ID-B / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年2月23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: 2.65→50 Å / Num. obs: 114346 / % possible obs: 99.4 % / 冗長度: 3.4 % / Biso Wilson estimate: 75.3661647178 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.88
反射 シェル解像度: 2.65→2.72 Å / Num. unique obs: 8404 / CC1/2: 0.125

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3t3p

3t3p


解像度: 2.74196193977→42.8207985844 Å / SU ML: 0.416742498305 / 交差検証法: FREE R-VALUE / σ(F): 1.33442233697 / 位相誤差: 28.2694309669
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.252991046836 1994 1.97224612524 %
Rwork0.225170134893 99109 -
obs0.225716024498 101103 97.21722742 %
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: 93.4762453242 Å2
精密化ステップサイクル: LAST / 解像度: 2.74196193977→42.8207985844 Å
タンパク質核酸リガンド溶媒全体
原子数20715 0 303 285 21303
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0053565024498821710
X-RAY DIFFRACTIONf_angle_d0.53009812856629475
X-RAY DIFFRACTIONf_chiral_restr0.04192037948883280
X-RAY DIFFRACTIONf_plane_restr0.003623922033053818
X-RAY DIFFRACTIONf_dihedral_angle_d11.752371122312919
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.742-2.81050.3847628315331320.3652999011876552X-RAY DIFFRACTION90.9016727866
2.8105-2.88650.3612203887661360.3595241116736792X-RAY DIFFRACTION94.5802047782
2.8865-2.97140.3604230450321390.3470155103086895X-RAY DIFFRACTION95.7527906344
2.9714-3.06730.3258076301171400.3323681812396941X-RAY DIFFRACTION96.2353900516
3.0673-3.17690.3264360219311400.3207627328336987X-RAY DIFFRACTION96.8473977443
3.1769-3.3040.3428464986131420.2927267163727040X-RAY DIFFRACTION97.6080456646
3.304-3.45440.2858254123111430.2691506833277105X-RAY DIFFRACTION98.2380048794
3.4544-3.63640.2729014810751440.2473476338357133X-RAY DIFFRACTION98.5108975227
3.6364-3.86410.2636321077271450.2414106036337200X-RAY DIFFRACTION99.0960604425
3.8641-4.16220.2373237367311450.2117179740987249X-RAY DIFFRACTION99.5154777927
4.1622-4.58060.236554866191450.1895884784327210X-RAY DIFFRACTION98.9772574351
4.5806-5.24240.2223737243431470.1825890310827289X-RAY DIFFRACTION99.2790387183
5.2424-6.6010.2516330042411470.2019886689197314X-RAY DIFFRACTION98.7819409506
6.601-42.82079858440.1906036218461490.1790118389217402X-RAY DIFFRACTION96.5971600358
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)
12.82063640015-0.545804313559-1.863321671111.896597128121.374036665852.973506429880.103178682720.219867962880.175534669029-0.280541708081-0.0825027654640.311552493561-0.0837505789974-0.352822172037-0.03531823223790.4753698634430.009755878661350.006432944236690.3717128568360.05220665780150.48874785443742.447811401693.965083067842.7322536212
22.58374909281-0.929750967575-0.3111783782761.849976390530.2792736617381.449364858140.0902200268334-0.171882613875-0.1293993162360.365358132007-0.1268388725620.2213048103890.211424515613-0.1623874286370.03017845899580.564127068376-0.0437944178910.1213871854130.3568111249220.02221710360150.4847814928945.686427286892.413570897263.266222704
31.83449939490.4483937957580.7291238033882.03432035120.7327095460543.35412037190.0238744719710.0101856601338-0.2112033065680.07548786454690.0499916444691-0.09132400614680.2721762074920.132087672664-0.06365164298360.4666002477280.08691727748140.05510154734380.3073083189610.03684541811410.43479375843664.453069471484.190748713847.9490407122
42.170508002160.473774064243-0.7920873363860.2911211176830.6633640347272.9398509121-0.169252406706-0.1103227349860.1925079310170.2110933049430.643403836536-0.6677419404220.3476590569091.43021262467-0.3542302786710.6420614409090.140136749521-0.07322615766611.34780717486-0.201758453771.08144701858113.49198696101.5128363343.6729314583
52.402222975780.6783931700420.1735719312683.466079947410.5521144334021.518742101680.00436997557013-0.01694012562380.2829869908730.05834045802260.0354057719858-0.00187526648581-0.237366945315-0.0290835935134-0.034858029060.5744721285090.03396309549340.0487667689060.3132105422930.0271837883340.4248752480565.7466875996119.55034923462.1368160993
61.577690515130.131163529056-0.2016215985790.76218948950.5016259742731.714504074840.0345985603347-0.0859757899189-0.1647236942660.3582080242710.163164034135-0.4001816124820.352222638020.561579033138-0.1864789751690.6851852424290.0672992846476-0.1012086648430.616765360493-0.03744915848120.74857364752286.705489482108.68650860266.7300420584
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243.791101388782.382762870710.6377554783594.540019911211.364587169193.657153321610.1405514198431.74949097815-0.5862909969390.541349379950.892899920437-1.293934122390.253109482492-0.095447421481-0.6508241057522.146910729231.060162556080.2450709975053.217999091650.119938923951.6524611643157.76193976286.846458890878.9561637369
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260.1928157402380.00749277330429-0.3908607385791.21430743821-0.2086979244530.776446022816-0.501973793866-1.04564753178-0.0760413447119-0.2441239156140.64413097457-0.4139896950510.1129875014150.4755951579850.1355510429471.905735085210.7973836709640.03501071863392.606196555510.05625893796961.48551232736153.57152631984.383830509281.3631958007
270.25623118293-0.0569960265435-0.04121465045120.273800050436-0.1741409926650.11516627784-0.110136206867-0.5863401917710.509685679647-0.232541345639-0.3402438035890.115731206299-0.218610236615-0.5263025616630.5666891321591.902198637560.511353141082-0.01704216145692.17789188186-0.3038260695251.48648615794150.89898801876.916620724875.8300392313
281.52851570481-0.2076135469531.155558740631.206253652530.1377588847821.23149861155-0.1327178107620.113256902310.446613963319-0.0635518978367-0.0601231013322-0.702915760589-0.008133029478040.4558457408560.1616625058670.78760670503-0.09583763816050.198061019431.324981166870.008451096118491.21150534402124.342657576100.304042827102.130857613
290.4238507884740.319871958101-0.3529267359610.17989363728-0.223638976850.234448834280.5368474684881.24860308635-0.344417353017-1.04969670455-0.863412605452-0.2006659706760.3314792828171.636518549680.2435433043311.26143855190.8192339864330.4481941146472.965739636120.03398368093061.33013911677152.46580449393.710640398184.1019614981
300.7586171310470.1953148073940.4235239548190.605868069014-0.5515113059131.013108890.1774563377631.42660836053-0.298898834614-0.426801116074-0.2646182902530.244042067542-0.8692777731841.45148269654-0.01577750418171.547286058680.198661239190.3029747307832.387360700620.3846256414041.58040929432151.13927962297.26135652287.0871206298
310.2164904230010.047287096745-0.3762442885910.0322441340508-0.1287700011950.710572547813-0.106702637462-0.2306401280510.162141424048-1.028263188250.398612618913-0.4702367595620.183253016978-0.194668534674-0.09837017426592.02054370733-0.01699682868990.7857700554781.76554450510.6460044137012.30443592485154.205641767106.45825592775.4436687087
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330.1659646239610.2293833342240.07937231977390.4978860255290.1916122997790.270380924527-0.277126374562-0.9152679572050.530623058872-1.041462924360.212536040303-0.328917200921-0.6623696255960.2936045739590.07527535173711.66871992383-0.04388320920920.8909111971162.537465703630.4329022111281.88602904369155.45758243999.541254440970.9349348673
341.69533896342-0.1220906642510.003920925715281.48565946637-0.4165941015590.6857022738770.262131788068-0.656241827813-0.39801286369-0.49621597002-0.919471818057-0.8471570900990.3829898360171.247738923860.6934523271931.37821114221-0.1185554313380.2814372058932.348881364840.07057408624591.67844092023161.532092943101.34617546681.2172893467
351.37738141960.42971550171-0.1413668118971.70809557882-0.3560331969822.26569361146-0.453028590777-0.4624766875730.0223290488920.5429790942890.3724860329860.1741919221630.303576007271-0.2305583957070.04436326105340.8766737871790.08975558668240.1247034706771.01844681168-0.06183985345160.88745528234317.658403530192.751244672684.4587805943
361.942294406110.441836200937-0.3680443733751.6631372482-1.111828061240.7768673507220.0491973784546-0.495764962381-0.2730220863270.590022192070.1081955993540.0422346238152-0.05957894972610.138308564582-0.1832560449350.8615678075860.04251186237770.1340464749610.8839494721-0.1213931023520.84336583239917.60716683397.639770085684.2759396482
370.990971813972-0.1883630954360.6252266750230.8524608046270.3348393850361.450191158710.01154138625620.08711494406040.1470801265310.491621793308-0.3867288049460.8312720035220.557838586122-0.07705631725490.4375746400210.767292451538-0.07868087344050.09462427673151.096258941310.2342112320781.98087505849-24.062893362882.229327127294.2216630306
383.00416905684-0.519626520343-0.9819364967223.9168557878-0.01024085903013.36856772628-0.863746574316-0.674808203727-0.6027033799590.254423635856-0.1853293192680.3193099588870.8703006974780.6971265167391.089767366810.9056352036040.1049815077340.2285327387231.053927656310.3341961298071.66458773789-15.917754517983.699669901393.2707752963
392.03216369724-0.636713633436-0.8427915708081.80515031743-0.8669161220723.10192650087-0.531946924782-0.717694391788-1.982577423940.07010736920970.173420836534-0.4777992073411.091637584710.2631048543820.3348692435870.9324499986760.08637612483770.2597924254291.04915365750.3534864384111.87252315814-12.561973902479.598033428393.591181565
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411.204561423960.542333253011-0.3116071648151.42926228335-0.02864998541431.35205358143-0.266916961270.386803203419-0.307603745366-0.1989092095880.3092993002140.8689994698770.455578515127-0.662234041296-0.0189405045470.705768708977-0.02950454582810.1111354764561.21454696961-0.207344569611.188723441113.7647411323289.805089753766.282819663
420.964817060055-0.012084419305-0.749506886901-0.005572138427570.1009212875680.483274181110.0902935996720.3655415491060.1089308391860.0790548306158-0.2795510788140.914305590751-0.0692776526181-0.7450465328810.0675453000770.441902669854-0.07653716265020.109657516091.07323872391-0.1869545014411.081710492790.58103192164796.339165285169.9687358425
432.86242757666-0.2205485683711.551424664962.55431826360.1973818993522.46844154991-0.360721487439-0.27464358272-1.452433306820.1615568088790.02029933803850.411075332963-0.183319857179-0.07434019152450.363614118270.5543132320250.01388271060970.2557481444670.9139014303630.133815904291.39692393402-20.356137570893.378360125788.7155608832
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 454 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 111 )
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 311 )
6X-RAY DIFFRACTION6chain 'B' and (resid 312 through 393 )
7X-RAY DIFFRACTION7chain 'B' and (resid 394 through 466 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 67 )
9X-RAY DIFFRACTION9chain 'C' and (resid 68 through 225 )
10X-RAY DIFFRACTION10chain 'C' and (resid 226 through 373 )
11X-RAY DIFFRACTION11chain 'C' and (resid 374 through 453 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 40 )
13X-RAY DIFFRACTION13chain 'D' and (resid 41 through 156 )
14X-RAY DIFFRACTION14chain 'D' and (resid 157 through 339 )
15X-RAY DIFFRACTION15chain 'D' and (resid 340 through 365 )
16X-RAY DIFFRACTION16chain 'D' and (resid 366 through 403 )
17X-RAY DIFFRACTION17chain 'D' and (resid 404 through 432 )
18X-RAY DIFFRACTION18chain 'D' and (resid 433 through 471 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 12 )
20X-RAY DIFFRACTION20chain 'E' and (resid 13 through 25 )
21X-RAY DIFFRACTION21chain 'E' and (resid 26 through 64 )
22X-RAY DIFFRACTION22chain 'E' and (resid 65 through 83 )
23X-RAY DIFFRACTION23chain 'E' and (resid 84 through 127 )
24X-RAY DIFFRACTION24chain 'E' and (resid 128 through 149 )
25X-RAY DIFFRACTION25chain 'E' and (resid 150 through 175 )
26X-RAY DIFFRACTION26chain 'E' and (resid 176 through 199 )
27X-RAY DIFFRACTION27chain 'E' and (resid 200 through 219 )
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 102 )
29X-RAY DIFFRACTION29chain 'F' and (resid 103 through 129 )
30X-RAY DIFFRACTION30chain 'F' and (resid 130 through 144 )
31X-RAY DIFFRACTION31chain 'F' and (resid 145 through 155 )
32X-RAY DIFFRACTION32chain 'F' and (resid 156 through 174 )
33X-RAY DIFFRACTION33chain 'F' and (resid 175 through 197 )
34X-RAY DIFFRACTION34chain 'F' and (resid 198 through 214 )
35X-RAY DIFFRACTION35chain 'H' and (resid 1 through 43 )
36X-RAY DIFFRACTION36chain 'H' and (resid 44 through 125 )
37X-RAY DIFFRACTION37chain 'H' and (resid 126 through 140 )
38X-RAY DIFFRACTION38chain 'H' and (resid 141 through 151 )
39X-RAY DIFFRACTION39chain 'H' and (resid 152 through 219 )
40X-RAY DIFFRACTION40chain 'L' and (resid 1 through 75 )
41X-RAY DIFFRACTION41chain 'L' and (resid 76 through 90 )
42X-RAY DIFFRACTION42chain 'L' and (resid 91 through 113 )
43X-RAY DIFFRACTION43chain 'L' and (resid 114 through 197 )
44X-RAY DIFFRACTION44chain 'L' and (resid 198 through 214 )

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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

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