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- PDB-7udg: Integrin alpha IIB beta3 complex with lotrafiban -

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基本情報

登録情報
データベース: PDB / ID: 7udg
タイトルIntegrin alpha IIB beta3 complex with lotrafiban
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
Lotrafiban / 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: 2.80006901797 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19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)302,63440
ポリマ－297,4068
非ポリマー5,22832
水12,394688
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)151,39319
ポリマ－148,7034
非ポリマー2,69015
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)151,24121
ポリマ－148,7034
非ポリマー2,53817
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)256.760, 144.170, 104.550
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
#11: 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 , 6種, 714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: 9 / 由来タイプ: 合成 / 式: SO4
#9: 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: 10 / 由来タイプ: 合成 / 式: Ca
#10: 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
#12: 化合物 ChemComp-MWI / Lotrafiban / [(2S)-7-([4,4'-bipiperidine]-1-carbonyl)-4-methyl-3-oxo-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-2-yl]acetic acid / SB-214857


分子量: 428.525 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C23H32N4O4 / タイプ: SUBJECT OF INVESTIGATION
#13: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Cl
#14: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 688 / 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: 3.25 Å3/Da / 溶媒含有率: 62.19 %
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, pH 8.9

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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: 0.996 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015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: 0.996 Å / 相対比: 1
反射解像度: 2.8→50 Å / Num. obs: 183986 / % possible obs: 99.6 % / 冗長度: 5 % / Biso Wilson estimate: 73.7470023912 Å2 / CC1/2: 0.983 / Net I/σ(I): 4.66
反射 シェル解像度: 2.8→2.87 Å / Num. unique obs: 13682 / CC1/2: 0.141

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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: 2.80006901797→49.1441518768 Å / SU ML: 0.501160464347 / 交差検証法: FREE R-VALUE / σ(F): 1.12852072606 / 位相誤差: 27.9506718708
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.234941078932 3805 2.06860932913 %
Rwork0.212865903006 180135 -
obs0.213321122371 183940 99.6165677397 %
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: 103.318110988 Å2
精密化ステップサイクル: LAST / 解像度: 2.80006901797→49.1441518768 Å
タンパク質核酸リガンド溶媒全体
原子数20715 0 317 688 21720
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006193923501421709
X-RAY DIFFRACTIONf_angle_d0.60495621996829498
X-RAY DIFFRACTIONf_chiral_restr0.04381798357363281
X-RAY DIFFRACTIONf_plane_restr0.003941724613013815
X-RAY DIFFRACTIONf_dihedral_angle_d11.671545648612915
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.83550.3854211083881410.3998409658976750X-RAY DIFFRACTION99.5809248555
2.8355-2.87280.4108774582631360.3828849801926652X-RAY DIFFRACTION99.7355274758
2.8728-2.91220.3948928103831430.3774710981466668X-RAY DIFFRACTION99.6488661302
2.9122-2.95380.3382332989941440.3644072244256647X-RAY DIFFRACTION99.5018315018
2.9538-2.99780.3883138950061370.3632368670866673X-RAY DIFFRACTION99.6050899517
2.9978-3.04470.3679076119831380.3556913299196631X-RAY DIFFRACTION99.6173657101
3.0447-3.09460.3609097424031410.3509197063896749X-RAY DIFFRACTION99.6240601504
3.0946-3.14790.3170537876991400.3248135161726626X-RAY DIFFRACTION99.6025320183
3.1479-3.20520.3415238595151420.3099588900936681X-RAY DIFFRACTION99.5913005401
3.2052-3.26680.3282792460031450.2950444658156672X-RAY DIFFRACTION99.7512437811
3.2668-3.33350.3494449842521400.2827685083996661X-RAY DIFFRACTION99.444363211
3.3335-3.40590.3052246773611360.270353396526684X-RAY DIFFRACTION99.736765136
3.4059-3.48520.2557486417261430.248864592876685X-RAY DIFFRACTION99.5480390728
3.4852-3.57230.2501969372921420.2428235874416658X-RAY DIFFRACTION99.6191034281
3.5723-3.66880.2546995914771400.2366794513596614X-RAY DIFFRACTION99.469808542
3.6688-3.77680.241474195811420.2198606616796736X-RAY DIFFRACTION99.6956080591
3.7768-3.89860.2335333716781430.2094025900956653X-RAY DIFFRACTION99.6042796424
3.8986-4.03790.2008589522931390.1909011298916662X-RAY DIFFRACTION99.6337532962
4.0379-4.19950.1878785193181400.1850031986296647X-RAY DIFFRACTION99.6330005872
4.1995-4.39050.1994818612131430.1683503139866696X-RAY DIFFRACTION99.5487627365
4.3905-4.62180.1867109998691430.1579939855146652X-RAY DIFFRACTION99.7797356828
4.6218-4.91110.1670423963361400.1599659479796647X-RAY DIFFRACTION99.6330005872
4.9111-5.28990.2005754574941430.157465936566724X-RAY DIFFRACTION99.6517196343
5.2899-5.82150.1921892875871420.1734124784596641X-RAY DIFFRACTION99.6913580247
5.8215-6.66210.2065993094841370.1860699759066708X-RAY DIFFRACTION99.7377240274
6.6621-8.38680.1997214911811440.1730651172746653X-RAY DIFFRACTION99.6773720487
8.3868-49.14415187680.195070874771410.16205689026665X-RAY DIFFRACTION99.3431615823
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)
16.92616771254-2.2328391209-2.166311596565.889648841331.938559120096.222239739160.0722427725960.3691245129320.188691712051-0.515735970171-0.07393392442470.191064727726-0.109861706791-0.368909810442-0.0238112447550.4949837458230.0128313727369-0.03073193304330.3637725267450.09068692093190.41150614720146.519661753589.873713231838.5645518541
21.9798466682-0.0252723719879-0.6878221268872.789734325520.6265761905132.539812229490.164072769013-0.04563613694780.1272751821520.350085252007-0.2258286901260.3977457905420.0465981331545-0.3379539937660.08150099424940.576256583183-0.01343984802980.1247495109360.4815148320070.008319538870390.65802295337437.45502524797.196170845559.1707241606
32.61267827011-0.816905603341-0.5332227983472.613914066340.5456909082111.914197231370.0151013485788-0.406427350185-0.2474699658110.701547490892-0.0654081056440.3195745164820.7115228597-0.24077302284-0.01182584824890.838731995466-0.02232625746440.07948923486680.4371136967470.09065247945540.51555963415955.146961178685.493076244965.9803220711
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52.754769126650.612329938373-0.3195077736793.6710490150.6444605918893.15661130370.0429018691959-0.149044785293-0.3810300861040.4903936251390.00484448879773-0.3357430771020.7845756650650.00467042154836-0.1700577241530.6077085973770.08316397552190.002748126647390.3760897628190.02538923434770.46352463284963.24501275781.180482128244.5814887887
63.19153255044-0.3356016345771.308196026723.62239182415-0.1714925463244.08427440898-0.01726975318420.138664212855-0.3304527601850.112329196508-0.00726568931262-0.1549106356090.2963554407240.02400415447310.01471580339590.5289315871040.02956946137440.08412952203380.3873678220080.0153787797780.44984881038759.16407309282.04043338340.3656118711
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143.838317535340.2779298871280.8466964030093.426401664880.4002898239045.0457548819-0.3553756165730.065663233375-0.644905290508-0.145055261240.169696927872-0.05114721206320.8052832850570.01756084727840.08253072115510.6575407413330.01541265245250.175919914320.478380560958-0.0006433354282740.49200127013173.470137466679.8495740152128.029561121
152.871156513391.32616881252-2.125684538321.4862521966-1.36511519374.0355495575-0.4396943504250.9552208355550.144532895151-0.3239424911210.4605860655030.4435094888440.463671490026-1.28408250518-0.09328197913080.992843264086-0.367908165201-0.08627034602611.491039073520.05566567258190.89394876215730.633710077888.1739477682116.7899741
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174.05387920264-0.5342840085761.366435295721.60050850832-0.1367332323583.79652570842-0.1927938052120.7129353027860.340161720991-0.5438108433690.218249405660.118162060869-0.111016774731-0.620398248025-0.06241659505730.786210558922-0.184648582157-0.02421504253740.9868490072570.1772405403980.52375490998359.8851834499100.365135483103.0256777
186.064622869012.72420585841-5.975893721522.56163535535-2.972060141815.87331027311-0.3119950317870.977115119883-0.2000885638-0.3933859833940.416957122740.03774837243670.494634296591-0.753971776925-0.004603850202791.01778175011-0.304754092233-0.151188271541.527102215130.00334818084230.78584202583642.759990236390.2881692965105.542884333
194.681172551711.20402672805-2.801645620554.95674852499-0.4529805951149.12663063589-0.562203741180.888641328649-0.31328286578-0.308383171507-0.03254882023980.06492495037580.509544512753-0.4747542652260.6542719463230.886927855898-0.321699934449-0.09276642794181.172979389050.06953653911850.80298009622831.868446525683.9323512584117.713894127
207.543713200456.117738564495.925216818155.02454329474.810199804724.65616530829-0.235592555887-0.23185824544-1.382778438111.01595356583-0.2167408527020.4857598923990.928036674949-1.475491794050.6980905073351.38495486867-0.1549550355730.2738046312761.32796356274-0.09436766365911.3113312890121.416828986777.7034819223156.77268909
214.43358958224-2.786915672131.254611258534.523764737650.9475745693917.723257909240.4381840671920.4296446611540.220922830959-0.761636746517-0.231407566317-0.07313132928921.08387776516-0.308300457343-0.2167886748111.18667233875-0.1633359183810.381978259141.45025301914-0.005954516199540.903756038089113.57927302789.729511212185.8023336819
226.90455368967-2.43442803822-4.101611917092.121722175511.392543524223.29837161830.3842756765140.9784923928150.215485432082-0.376766420677-0.236048795134-0.3983239467050.763165668766-0.2687932781560.01237971293941.31359889108-0.08755499431150.3033648940281.57733104434-0.003644200033710.903989040994117.45374854688.591191689983.4552816946
234.848680053013.23477101032-0.06378482939027.451122126724.851510604144.517276964990.6302177688561.69485773525-0.196674217924-0.2709901439280.585295257778-2.70289409020.5812262299941.21871951163-1.071415622711.634484190560.7804129583820.2258393164892.971249784990.2812595027532.18534286764157.09040560686.589655617978.450080626
246.344611930732.71772471439-0.2471113589647.506668275814.703083410794.57717058261.129896877690.6739520082570.224469154884-0.696933679877-0.593606105308-0.688798158010.253980541097-0.0425426733956-0.2021997088781.519957684710.5322594473190.1521275724132.025930264720.288655061691.2804904933143.39828223683.415145666380.1619475071
250.1012226323140.3053408115860.5498835062294.352415092561.146983350433.893884847460.8256062758581.5738849117-0.490100872699-0.376486270963-0.680472236634-0.5158712557461.017405163531.59926603922-0.6474631534611.761988057920.8735743657930.1038857140913.23571871461-0.02586815652561.96581576782159.08854056181.627209361984.5687647501
260.684353843023-1.0304442971-1.335905602841.832111967792.063858560422.773796435110.4375027298331.19098315518-0.31012422713-0.538404989094-0.541850066898-0.4590073723650.09067744607510.7014694143880.008230771719091.747644507010.971895038205-0.2617896061543.10036079142-0.351066789341.84042843176150.15261043476.669866068875.1788520678
274.23786728524-1.591655076981.833639753162.2546653236-0.2767180380342.03533668068-0.1892511824540.3383122954420.729356700072-0.2657467423550.0137077397561-0.7534582963570.02781074883940.7085494592280.1229412049680.853281156158-0.1690343016190.2405631230631.438173892550.02552590806481.21226602545123.55415756199.6893803036101.613452084
285.785316003760.956316038152-2.523480501531.07544848550.5431049189372.09632189574-0.134010719779-0.572096829885-0.129631609231-0.773020555737-0.219609544037-0.674458204120.2744871113312.299701341670.7424915489251.54996586070.2669449747350.5785818910592.556922172920.6820292143361.81036280791151.754271497.12462393682.7106468533
295.944525672191.37421831861-3.375632997010.843488556790.6117773871688.26849913676-0.2630738374680.4839310062460.00288644988871-0.9802403111820.174626339371-0.669060779791-0.3536811948421.380283885470.2430681706791.38002426611-0.008808304014140.5001648560562.211490379130.4552972881721.79535473087153.57796169498.204594590179.0553946078
307.14001808852-3.89366799604-4.683700647673.354804114324.996422164168.29495561426-1.26802610502-1.53213511677-0.490524666561.830045183590.735314270430.5723101652881.576018249030.02664744185870.2230727359151.39494257710.03656165116220.3494704246681.184882457620.09654033813650.93427888017314.950604770189.651608745988.9026504057
318.02154599787-5.14289749958-5.280218286337.950277349845.193191460584.23001456667-0.463320926999-1.45799539107-0.4659037071151.490539323720.276540612116-0.4624758749871.79010845530.628911260815-0.2595324470611.09708451102-0.0326100011652-0.03237796059421.10137273684-0.003634341265330.86022101822825.223172098889.195301976681.846099326
325.177306718521.589264682691.807790865136.08448132064-0.1443905646117.88296872298-0.0924951876385-1.004789727990.1420408150810.8106043044030.05890994818470.280789731745-0.4021486456860.0193316288979-0.05294895842210.6606623868380.03899446680490.1923498604810.898043863602-0.07314644531970.57514219458919.804126169699.640384968682.8688562018
336.523581464510.169862602693-4.303624475981.91990574049-1.69889757985.171637716380.0154926780772-0.675333725446-0.01043870262590.5062002767690.2039381045310.409791690672-0.357280356165-0.262462258344-0.4479212855380.8431421053680.03189036769340.2125790183891.008410305970.01700292475780.8611183631412.557657196894.180347280383.8702468162
348.63249645032.595619485447.751137072155.067125389824.983525081479.83216084887-0.0852399122501-0.600770977347-0.3811096911170.688001669773-0.4518368226121.09877490020.8676620238050.08515232347910.4901599788550.757076912962-0.05731181831680.1450569319341.267563409670.4914479107531.80367902117-20.268667791282.527631182893.0581376782
359.267856355935.715467083854.678497863633.901114891391.620546595546.56790737184-0.28378565664-0.318091717018-2.221549769080.1513811010440.445606172453-0.4565416283041.361302166790.530144386833-0.1377190396920.9309256289060.180795377230.4431699488641.228365559090.3170204892932.24108541739-8.3741916405977.187107284191.0896536779
367.85402824742.936020321464.376102424024.766036813372.256487417818.77907881236-0.736107281722-1.41523171801-0.920086687812-0.0989570961948-0.4289782209870.8087823112510.640604500153-0.3792219986620.9551421065720.757333802682-0.05067386905980.3050624244571.20572647980.2605634235821.59003735622-11.242060585186.333433880589.8080964631
374.448053426440.8025139850471.749124862181.22042901581.305107499079.227092186830.713255763196-0.480309099729-1.684286131370.551225635278-0.694395251236-0.1171706203751.99236798041-0.280246558849-0.0006193878398971.31426639188-0.007341640856080.2451670005291.13999019390.6017128540632.25942904925-16.471502472174.965951313296.3093945785
386.20769231995-0.921459425163-2.88965161828-0.0005065595430180.2441778798711.05996531435-0.1906436700530.577656847439-0.5133698600230.19054304160.1678671598170.4222735271440.142348432377-0.66847676432-0.02321923197120.687779490028-0.01836127665490.1256270727671.09133208352-0.0603400959651.02062319967-1.9300670888893.975480598671.4497734051
395.67684403222-1.28911908744-2.511360000035.302046089413.353269860186.71986116028-0.276767762412-0.312621188701-1.100970382350.531704663973-0.0173456566850.3375354052410.275125995813-0.6244251371180.6472245094390.6515537682590.06732140570130.2138941534211.121022322970.1945664523121.37521755393-22.283594343393.202498516786.9933113468
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 216 )
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 304 )
4X-RAY DIFFRACTION4chain 'A' and (resid 305 through 359 )
5X-RAY DIFFRACTION5chain 'A' and (resid 360 through 392 )
6X-RAY DIFFRACTION6chain 'A' and (resid 393 through 454 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 111 )
9X-RAY DIFFRACTION9chain 'B' and (resid 112 through 339 )
10X-RAY DIFFRACTION10chain 'B' and (resid 340 through 431 )
11X-RAY DIFFRACTION11chain 'B' and (resid 432 through 466 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 61 )
13X-RAY DIFFRACTION13chain 'C' and (resid 62 through 317 )
14X-RAY DIFFRACTION14chain 'C' and (resid 318 through 453 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 156 )
16X-RAY DIFFRACTION16chain 'D' and (resid 157 through 189 )
17X-RAY DIFFRACTION17chain 'D' and (resid 190 through 339 )
18X-RAY DIFFRACTION18chain 'D' and (resid 340 through 365 )
19X-RAY DIFFRACTION19chain 'D' and (resid 366 through 438 )
20X-RAY DIFFRACTION20chain 'D' and (resid 439 through 471 )
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 64 )
22X-RAY DIFFRACTION22chain 'E' and (resid 65 through 127 )
23X-RAY DIFFRACTION23chain 'E' and (resid 128 through 149 )
24X-RAY DIFFRACTION24chain 'E' and (resid 150 through 181 )
25X-RAY DIFFRACTION25chain 'E' and (resid 182 through 199 )
26X-RAY DIFFRACTION26chain 'E' and (resid 200 through 219 )
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 102 )
28X-RAY DIFFRACTION28chain 'F' and (resid 103 through 155 )
29X-RAY DIFFRACTION29chain 'F' and (resid 156 through 214 )
30X-RAY DIFFRACTION30chain 'H' and (resid 1 through 17 )
31X-RAY DIFFRACTION31chain 'H' and (resid 18 through 32 )
32X-RAY DIFFRACTION32chain 'H' and (resid 33 through 83 )
33X-RAY DIFFRACTION33chain 'H' and (resid 84 through 125 )
34X-RAY DIFFRACTION34chain 'H' and (resid 126 through 151 )
35X-RAY DIFFRACTION35chain 'H' and (resid 152 through 168 )
36X-RAY DIFFRACTION36chain 'H' and (resid 169 through 190 )
37X-RAY DIFFRACTION37chain 'H' and (resid 191 through 219 )
38X-RAY DIFFRACTION38chain 'L' and (resid 1 through 155 )
39X-RAY DIFFRACTION39chain 'L' and (resid 156 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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