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- PDB-7u9v: Integrin alpha IIB beta3 complex with BMS4-1 -

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基本情報

登録情報
データベース: PDB / ID: 7u9v
タイトルIntegrin alpha IIB beta3 complex with BMS4-1
要素
  • 10E5 Fab heavy chain
  • 10E5 light chain
  • Integrin alpha-IIb
  • Integrin beta-3
キーワードBLOOD CLOTTING/INHIBITOR / Complex / Inhibitor / BLOOD CLOTTING / BLOOD CLOTTING-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 / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization ...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 / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / blood coagulation, fibrin clot formation / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / glycinergic synapse / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / positive regulation of bone resorption / filopodium membrane / extracellular matrix binding / negative regulation of low-density lipoprotein particle clearance / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / regulation of bone resorption / positive regulation of leukocyte migration / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of fibroblast migration / integrin complex / heterotypic cell-cell adhesion / positive regulation of smooth muscle cell migration / smooth muscle cell migration / Molecules associated with elastic fibres / negative chemotaxis / positive regulation of cell-matrix adhesion / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / cell adhesion mediated by integrin / p130Cas linkage to MAPK signaling for integrins / positive regulation of osteoblast proliferation / cellular response to insulin-like growth factor stimulus / protein disulfide isomerase activity / regulation of postsynaptic neurotransmitter receptor internalization / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / wound healing / cellular response to mechanical stimulus / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell-cell adhesion / MAP2K and MAPK activation / platelet activation / platelet aggregation / VEGFA-VEGFR2 Pathway / ruffle membrane / integrin binding / cellular response to xenobiotic stimulus / positive regulation of fibroblast proliferation
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 tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Chem-M6K / : / 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: 2.25492157575 Å
データ登録者Zhu, J. / Lin, F.-Y. / 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11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
改定 1.42024年11月6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: Integrin alpha-IIb
B: Integrin beta-3
C: Integrin alpha-IIb
D: Integrin beta-3
E: 10E5 Fab heavy chain
F: 10E5 light chain
H: 10E5 Fab heavy chain
L: 10E5 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)300,98142
ポリマ－295,7188
非ポリマー5,26334
水20,2671125
1
A: Integrin alpha-IIb
B: Integrin beta-3
H: 10E5 Fab heavy chain
L: 10E5 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)150,56620
ポリマ－147,8594
非ポリマー2,70716
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Integrin alpha-IIb
D: Integrin beta-3
E: 10E5 Fab heavy chain
F: 10E5 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)150,41522
ポリマ－147,8594
非ポリマー2,55518
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)257.796, 143.887, 104.678
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 / GPalpha IIb / GPIIb / Platelet membrane glycoprotein IIb


分子量: 49228.625 Da / 分子数: 2 / 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 Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


分子量: 51958.789 Da / 分子数: 2 / 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: 23339.062 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 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


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, 1153分子

#8: 化合物
ChemComp-SO4 / SULFATE ION


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


分子量: 40.078 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Ca
#10: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Mn
#12: 化合物 ChemComp-M6K / (4-{[(5S)-3-(4-carbamimidoylphenyl)-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperazin-1-yl)acetic acid


分子量: 345.396 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C17H23N5O3 / タイプ: SUBJECT OF INVESTIGATION
#13: 化合物 ChemComp-CL / CHLORIDE ION


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: 1125 / 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
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: 3.28 Å3/Da / 溶媒含有率: 62.53 %
結晶化温度: 297 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 11-13% 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: 0.97934 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 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: 0.97934 Å / 相対比: 1
反射解像度: 2.25→50 Å / Num. obs: 348261 / % possible obs: 97.7 % / 冗長度: 10.9 % / Biso Wilson estimate: 49.3472589724 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.166 / Net I/σ(I): 4.15
反射 シェル解像度: 2.25→2.31 Å / Num. unique obs: 25565 / CC1/2: 0.136 / % possible all: 96.9

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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: 2.25492157575→44.9513141354 Å / SU ML: 0.308512027275 / 交差検証法: FREE R-VALUE / σ(F): 1.32534210003 / 位相誤差: 25.7412311523
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.225954331894 1999 1.09875009619 %
Rwork0.203441484638 179935 -
obs0.203690326129 181934 99.2212126831 %
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: 77.5097266604 Å2
精密化ステップサイクル: LAST / 解像度: 2.25492157575→44.9513141354 Å
タンパク質核酸リガンド溶媒全体
原子数20715 0 307 1125 22147
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006012587052221759
X-RAY DIFFRACTIONf_angle_d0.54435152989529555
X-RAY DIFFRACTIONf_chiral_restr0.04238067955853285
X-RAY DIFFRACTIONf_plane_restr0.00364850558343828
X-RAY DIFFRACTIONf_dihedral_angle_d11.825268416612962
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25492157575-2.31130.3699750518811340.37046435267912004X-RAY DIFFRACTION93.8021638331
2.3113-2.37380.3543337381091410.34454420733712727X-RAY DIFFRACTION98.9770017691
2.3738-2.44360.3393821234861420.32137369226912753X-RAY DIFFRACTION99.4140775576
2.4436-2.52250.2860234098841410.30245755009912755X-RAY DIFFRACTION99.490819318
2.5225-2.61270.3197679311531420.28630337693112822X-RAY DIFFRACTION99.4782074893
2.6127-2.71730.2960802632011420.26232291286112764X-RAY DIFFRACTION99.7141311906
2.7173-2.84090.2704562682541440.24573447712112899X-RAY DIFFRACTION99.8545398867
2.8409-2.99070.2378780719111430.23001917629112898X-RAY DIFFRACTION99.8621640248
2.9907-3.1780.2441027771521430.22206749327712890X-RAY DIFFRACTION99.9309921791
3.178-3.42330.2348340506871440.20316297775712937X-RAY DIFFRACTION99.977071232
3.4233-3.76760.2033206063591440.18338288703812962X-RAY DIFFRACTION99.9847421422
3.7676-4.31240.1981219887811450.17034609922213039X-RAY DIFFRACTION99.9772503223
4.3124-5.43170.1922533320021450.15398863959213095X-RAY DIFFRACTION99.8190591074
5.4317-44.95131413540.1869657878161490.17586007938413390X-RAY DIFFRACTION98.7815555231
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)
15.76115261666-1.53868092805-1.373942219364.124333232681.266381737574.117767443850.05097254961040.2395256627830.170861374301-0.346963950434-0.1216021662040.125052837834-0.0525768531097-0.313960157740.07024495882820.3132965246530.01169710637690.02708657375370.2728522216860.07590438266980.23879868363646.733675030189.696999247338.7059194298
21.369470726970.0476841259476-0.1442468898771.162373048740.1645858120291.102228780330.0810730098081-0.1153177397570.05241239388430.297455543002-0.1492615641120.2447631729220.142681660423-0.2040226763450.06525198276530.44036019997-0.03146343574610.1282539016920.289336621310.00345073763990.36947357045444.219697821992.605819440761.8271300771
31.553469397570.5327065487650.3673418034131.978298948090.4984789650152.009119726110.00277467342903-0.0429963416101-0.2082182497910.1437537939180.0544049698655-0.1578172319220.300448798090.117554441148-0.03521423455860.3850606685380.08233509970970.07804410376260.2424673559240.04074525438530.30119264528564.216611988783.151008714347.6759050374
45.76652163069-2.14981576798-2.7063942583.087965072210.689227218272.4312953273-0.5484733683280.678153910432-0.9040234406620.1094155201150.349425000237-0.7062550856690.9852798205931.914456576350.4406846245790.9481527020740.563737289097-0.03159344008252.21391948345-0.289044558671.33358818807122.72322368685.81348900734.8769093817
56.65193911361-3.89080998027-4.75251798534.232888918383.312873462615.544799151160.344605734006-0.06844877978690.7110437668820.01991128976710.42364629591-0.833124526914-0.1766288299041.29621556199-0.6143322148430.463466349279-0.0225410157358-0.04548051095641.13851662972-0.156776106240.899963650467106.701264917110.00678879649.2547394946
61.400556540390.5329750221560.2305305947531.951491993530.5364028961951.232721348850.0715090646532-0.07698670516150.2100394127590.154590549165-0.0198081221949-0.027605565616-0.2219215932450.0598839868345-0.05366758805750.4507583195350.004178575874570.07173393814550.2310010282580.01071302069720.33722008139166.6201445178117.02143794963.5635802185
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106.168041177831.49350216449-2.930009121351.705995103040.0274959050094.04808491824-0.269592467085-0.336527946473-0.0863989839078-0.02261392657510.0376216248911-0.2893231966690.1728540755910.841872186750.2280770792680.3296181176030.03539595081690.01216694589680.572203465317-0.02956463394450.34811935717187.127017118593.7142420837131.718494692
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122.75393049463-0.2481662403370.4751816006972.39816679261-0.1153557460873.64529791509-0.268165969459-0.00429973717892-0.508996302479-0.132946712180.1229757841-0.06271999401060.7321511584280.08788311352280.104197657920.531380605396-0.0003797417003270.1932451069880.4120982570450.02629489546510.40559007143473.371676891178.8624036508125.811140034
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142.52032742433-0.3320055675380.3460298086420.942819293048-0.5317753075462.89515462216-0.1288388613920.6323586112560.394125777676-0.1988874311690.1415688876180.103514826101-0.0651244121502-0.351012070487-0.04566248702150.498686352456-0.144812074073-0.0111113569190.6963057388830.1445726060610.42198345717561.3705085587102.30707979299.9303072188
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164.614782122030.723099535697-2.435790380553.23132666374-0.898391628827.03352269899-0.1120419602410.22363509702-0.06559392270780.3511656085260.04133338218660.288539178907-0.0136844848814-0.01156021732440.1435848260720.610434226817-0.196446496239-0.03471834357860.7812203661960.09662244322410.54628570115733.171992214188.1994000422125.050180421
172.284353091582.921718654042.27374221014.806966909645.178212173687.09241754805-0.153684462127-0.064841022494-0.2051172844350.284261144988-0.315016468540.116436769480.932085995529-1.310081316360.1487655453751.05923493232-0.3083059886730.226797006991.00616884741-0.1360640920880.95772529227721.59167274378.1264608229154.83671244
184.47752397191-2.69518873473-1.773229680522.373668063741.907675706992.68124904470.2600369584210.8272279247170.195976625877-0.510127041372-0.287204816897-0.2710716111620.903797922915-0.1151496845210.01782558958591.08328700493-0.118909905990.292213644231.241949768220.04098991457930.725587904311115.98262907988.873628168284.8157113916
197.329576781132.388260983151.14097444745.998375224744.021447965294.809960136420.5034568367161.74383085444-0.036729171044-0.5466579817920.675136585296-2.222619407140.2140459993911.13789672846-0.9844440533541.440728647970.5203536323170.155865421172.171575000860.1195152930541.74649691742157.61359139786.626484215978.611153594
208.152957506260.4919867099070.7942331687248.239570374012.328343318674.590598566650.5039542395090.906222725356-0.3889912860530.189695098754-0.261777405185-1.221051731680.8649034389530.157859196757-0.2042680627071.437003024630.2777420964010.09583095643361.248320488060.1691856392111.20983259597144.83750016178.87685710880.4208698918
215.053055993513.956970637312.273442095515.316315996375.202769098946.373435785281.020145864251.484085455630.608415903901-0.808870826969-0.7367168011840.167404079434-0.399998723938-0.245231243209-0.1137673687521.291354450110.6825389989070.3508246361851.84843794020.3616606873341.21691073416143.6642795387.738264859479.9798887967
225.061939747171.97977577859-0.8460923613913.873821708973.333827388424.482496226220.5842746500130.528679369377-0.8934258406190.1441260838670.197640378264-1.405265225930.8382530272111.23485069873-1.131473160181.599806423970.8967212697860.02787865571892.389645018720.05913514137351.64389077614163.24478896480.231255858286.1328673465
232.088075458250.932340702858-1.112140041813.537789185872.626225018323.714892758730.2749526710231.19217705783-0.258253303821-0.0590274456652-0.123914483433-0.8792375466590.1404517401420.324630384397-0.3295777066071.286588036840.458515685538-0.151487970621.69474416001-0.115916046171.58797796567150.79812971876.63023655675.316993211
242.075396890550.06329273100530.7694822710150.116841064742-0.2512169340471.6072539052-0.1973001820390.04104613666540.63333753219-0.024420727893-0.0888843954182-0.5957926537120.07006298517820.6468398537680.2957111844690.566131225254-0.1008810204830.1722817733581.247789856570.04759293155771.09212527773126.12784216799.3045026694101.60657133
255.021974346661.39823437023-2.673493997490.457616920751-0.7200789234332.67550343711-0.207825793459-0.119237256466-0.5025316728-0.9023342548490.428893160604-0.714127976292-0.02834663333851.57265972194-0.09533139846021.547323065360.746353599310.5175816547732.072831014760.3436719286211.51682555794156.61014910689.619390580772.180822693
263.812096254471.46108370912-2.080954909541.444372650461.459985247146.993374241150.274859581191-0.09046639468820.293324747228-0.656355663159-0.0470443400642-0.594563559442-0.2931651217281.5985534944-0.4373127241441.145139156580.2209759356450.2800275991021.68845272670.4110786870861.41863580581150.82265990496.813340986586.900611958
276.36677136452.11126190271-4.256531050371.834167619050.8952124807217.66217050480.09869382907720.4536639057660.478509044697-1.021465961060.250354284143-0.465808252944-0.4933806352270.957676953838-0.170549182761.157894446660.154145718740.5061428150821.531956031790.4484204721921.6000710949151.63595030799.124590504477.7749156778
285.778446994282.19705226116-2.611565999420.883998217301-1.236458275912.515193898720.197613633283-0.0973995917940.102576934186-0.8635244395910.256044637803-1.15254709087-0.272810920672.34744725321-0.2843095084211.141181515720.08734871504960.4049658013611.849316756460.2016271487761.92862701162161.173487222100.93530730581.1316035475
294.66197982773-3.99738713489-5.957346484254.580222590174.239657624748.29582070474-1.08754198655-0.690538562673-0.4589442023241.848259646310.4648946830210.799015222251.40112561079-0.4070635657120.8666706054031.198205400510.113632338290.383017207141.026695628930.04653297766610.72664361398115.014944432389.377476975189.124165163
303.163184736380.788935527599-2.063273961721.75320360431-1.977915088323.84670475040.00641059303754-0.5490095009770.02115326470780.8303172369740.103948278750.3212651551620.00490915616578-0.144857968565-0.1800106430290.6739093678290.05638825211510.1596930878410.737341467367-0.06799031452330.57018147429517.84054815295.906182955183.3238572979
313.718455517052.47024554784.690000059714.120962542343.239939654085.95597625058-0.204013534659-0.759607318656-1.099871980420.498472526127-0.0943324651650.7498070824610.467752023743-0.1376180757210.4817903278540.7107894512280.06728240239090.2597682173761.097731502270.3609789955261.6581689146-20.341211321682.373223849793.1634878788
325.820301019394.110254237444.112295390766.113868211631.235154156166.9128761356-0.366242643276-0.308246964008-2.213962070330.0654521856130.4761578331260.3180299292821.635299762670.580187443296-0.2923575342580.8432537289390.2891698444930.4240782812951.025569166190.2096190768512.23283713921-8.4394300957877.070168086491.2022627977
338.751118885225.837673210415.655054126024.053128491063.623448702273.79501703245-1.02271505361-0.46406941452-0.8966707046530.2028606916540.2337793884971.332774212540.152195736631-0.03223576023070.8064670975590.5718138212670.08810481785060.2461795285550.9569798105770.1811645738311.41844834703-8.7795605361889.273609918390.0235094643
348.10071049963.368291417544.394494807892.918013971552.968337836379.54443670961-0.486489521016-0.346901659375-1.6623044530.0228734302788-0.0352801012592-0.1459940072721.191367425810.3138227895870.1607169690650.615263709228-0.03379573984690.5009120998080.8714557370970.2849057075831.79561316476-13.907025531283.056324724889.7760009711
354.461781779140.8596087841741.663883224071.829247527661.425414811878.889328202190.141418533973-0.731045957738-2.376842179940.47069667218-0.252437972773-0.334296594532.58843396725-0.323319717080.0148165047271.349088367490.07162512105630.4134392231031.099686418190.4601233492652.3401916076-19.220707574472.714372122692.8730058375
367.768040961141.895099663261.55187205720.8382158674972.024460251397.469292525140.261091007374-1.22621496312-1.94610512170.201192804606-0.336685353846-0.3541407547181.96160024436-0.2584167344040.1133248786021.11082525833-0.03056651638120.2604909980321.202499578620.7906971318552.04876578786-13.742505491677.0950262475100.016018072
375.85748054242.234482539860.1246540748523.36950529690.06088894196172.24250899857-0.05256588164550.588498699973-0.218181682771-0.0730883693096-0.2308147578020.75622166191-0.0431294759778-0.7853868267070.2244941267230.393024398220.03602908309270.09931034346480.8396772742-0.1753859555980.742636588367.8928699093495.292808283363.5433262169
387.243963813854.638198066360.4876127795146.089407818232.509208422883.39165347210.0897965115852-0.0143810533542-0.2736147746830.0674552968258-0.4564348142540.6937007812080.326056480462-0.6699454483340.3685435545530.3735576243480.04286977353360.1669688558610.829400108682-0.1079464255790.8302538772117.7852550075995.098199680768.0493037329
397.07608991154-0.909193007743-1.885030767760.495668219426-0.03214338961020.699732186918-0.05687948907210.288226908655-0.716122846719-0.157014834981-0.08893652221890.5878600393990.0436793421485-0.1433295344990.001357514165930.557440587511-0.1558364481230.1395538915471.49217139598-0.5329719182211.46964832865-13.039901557187.783008004468.1236823135
404.70102510007-0.755836010174-1.747401257612.642923184591.749327454052.145237068-0.709091779611-1.01929837174-1.732255847070.779651803210.2499434072250.5926006075481.23994195616-0.5793575865490.5563937501790.8078297410770.05580363351320.471990111611.201424879310.3969947317611.6864136388-22.722274704187.276546257297.0654519364
413.67466608996-0.657869377024-0.6645281020892.297493807951.767289026558.43508310022-0.3951835794810.31470076159-1.53701432570.1896299261280.122524953170.4214101241690.51303604389-0.1611112313090.2900546879710.417591543949-0.0454109961490.206952158431.0238106995-0.02590991533451.44585592082-18.245792347290.061030491581.3350876108
424.11974092207-1.3153368473-2.413275684652.891552813691.18835182666.46672347549-0.439993048004-0.320347682007-1.209144198520.2873201562390.003557175501290.240139360808-0.1719380839880.3862816619310.1898635662510.3772998945590.02026926626820.2653263009110.8797013548870.1164627194651.32530077091-18.952419458994.646634463487.8803311308
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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 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 454 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 47 )
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 111 )
6X-RAY DIFFRACTION6chain 'B' and (resid 112 through 339 )
7X-RAY DIFFRACTION7chain 'B' and (resid 340 through 403 )
8X-RAY DIFFRACTION8chain 'B' and (resid 404 through 431 )
9X-RAY DIFFRACTION9chain 'B' and (resid 432 through 466 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 61 )
11X-RAY DIFFRACTION11chain 'C' and (resid 62 through 281 )
12X-RAY DIFFRACTION12chain 'C' and (resid 282 through 453 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 111 )
14X-RAY DIFFRACTION14chain 'D' and (resid 112 through 339 )
15X-RAY DIFFRACTION15chain 'D' and (resid 340 through 403 )
16X-RAY DIFFRACTION16chain 'D' and (resid 404 through 432 )
17X-RAY DIFFRACTION17chain 'D' and (resid 433 through 471 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 127 )
19X-RAY DIFFRACTION19chain 'E' and (resid 128 through 149 )
20X-RAY DIFFRACTION20chain 'E' and (resid 150 through 165 )
21X-RAY DIFFRACTION21chain 'E' and (resid 166 through 185 )
22X-RAY DIFFRACTION22chain 'E' and (resid 186 through 199 )
23X-RAY DIFFRACTION23chain 'E' and (resid 200 through 219 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 113 )
25X-RAY DIFFRACTION25chain 'F' and (resid 114 through 129 )
26X-RAY DIFFRACTION26chain 'F' and (resid 130 through 144 )
27X-RAY DIFFRACTION27chain 'F' and (resid 145 through 197 )
28X-RAY DIFFRACTION28chain 'F' and (resid 198 through 214 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 17 )
30X-RAY DIFFRACTION30chain 'H' and (resid 18 through 125 )
31X-RAY DIFFRACTION31chain 'H' and (resid 126 through 151 )
32X-RAY DIFFRACTION32chain 'H' and (resid 152 through 168 )
33X-RAY DIFFRACTION33chain 'H' and (resid 169 through 179 )
34X-RAY DIFFRACTION34chain 'H' and (resid 180 through 190 )
35X-RAY DIFFRACTION35chain 'H' and (resid 191 through 205 )
36X-RAY DIFFRACTION36chain 'H' and (resid 206 through 219 )
37X-RAY DIFFRACTION37chain 'L' and (resid 1 through 75 )
38X-RAY DIFFRACTION38chain 'L' and (resid 76 through 102 )
39X-RAY DIFFRACTION39chain 'L' and (resid 103 through 113 )
40X-RAY DIFFRACTION40chain 'L' and (resid 114 through 128 )
41X-RAY DIFFRACTION41chain 'L' and (resid 129 through 144 )
42X-RAY DIFFRACTION42chain 'L' and (resid 145 through 188 )
43X-RAY DIFFRACTION43chain 'L' and (resid 189 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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