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- PDB-7uko: Integrin alaphIIBbeta3 complex with sibrafiban (Mn) -

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基本情報

登録情報
データベース: PDB / ID: 7uko
タイトルIntegrin alaphIIBbeta3 complex with sibrafiban (Mn)
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 / 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 ...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 / 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 / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / 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 / Molecules associated with elastic fibres / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / smooth muscle cell migration / microvillus membrane / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / fibronectin binding / ECM proteoglycans / positive regulation of T cell migration / positive regulation of bone resorption / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / platelet aggregation / ruffle membrane / VEGFA-VEGFR2 Pathway / cell-cell adhesion / 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 / regulation of protein localization
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 Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / 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 2. / EGF-like domain signature 1.
類似検索 - ドメイン・相同性
: / sibrafiban (active form) / 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: 2.604 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4月1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

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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)302,46038
ポリマ－297,4068
非ポリマー5,05430
水12,917717
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)151,43320
ポリマ－148,7034
非ポリマー2,73016
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)151,02618
ポリマ－148,7034
非ポリマー2,32314
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)258.388, 144.599, 104.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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: 合成
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: 合成
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: 合成
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, 741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: 5 / 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: 8 / 由来タイプ: 合成 / 式: Ca
#10: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#11: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 6 / 由来タイプ: 天然 / 式: Mn
#13: 化合物 ChemComp-XQS / sibrafiban (active form) / ({1-[N-(4-carbamimidoylbenzene-1-carbonyl)-L-alanyl]piperidin-4-yl}oxy)acetic acid / Ro-44-3888 / Ro-44-3888


分子量: 376.407 Da / 分子数: 2 / 由来タイプ: 天然 / 式: C18H24N4O5 / タイプ: SUBJECT OF INVESTIGATION / コメント: 阻害剤*YM
#14: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#15: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 717 / 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: 3.29 Å3/Da / 溶媒含有率: 62.65 %
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-D / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年10月25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: 2.5→50 Å / Num. obs: 135279 / % possible obs: 99.3 % / 冗長度: 4.6 % / Biso Wilson estimate: 70.6181325213 Å2 / CC1/2: 0.233 / Net I/σ(I): 6.74
反射 シェル解像度: 2.5→2.56 Å / Num. unique obs: 9924 / CC1/2: 0.11

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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
XDS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: 2.604→49.287 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.74 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2388 1998 1.67 %
Rwork0.2141 117876 -
obs0.2145 119874 99.3 %
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 max: 178.6 Å2 / Biso mean: 67.2307 Å2 / Biso min: 24.49 Å2
精密化ステップサイクル: final / 解像度: 2.604→49.287 Å
タンパク質核酸リガンド溶媒全体
原子数20715 0 301 717 21733
Biso mean--64.11 47.96 -
残基数----2702
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00721714
X-RAY DIFFRACTIONf_angle_d0.60329479
X-RAY DIFFRACTIONf_chiral_restr0.0443280
X-RAY DIFFRACTIONf_plane_restr0.0043821
X-RAY DIFFRACTIONf_dihedral_angle_d12.65112936
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6042-2.66930.38191380.3406812297
2.6693-2.74140.33471410.32558345100
2.7414-2.82210.34051430.32478402100
2.8221-2.91320.3051430.29918383100
2.9132-3.01730.29081430.28078421100
3.0173-3.13810.2581410.25698406100
3.1381-3.28090.29131430.24958398100
3.2809-3.45380.27821430.23418418100
3.4538-3.67010.22891440.20218440100
3.6701-3.95340.21541420.19458444100
3.9534-4.3510.20041450.17328481100
4.351-4.98010.18971430.1597849499
4.9801-6.27240.19121450.1892849099
6.2724-49.2870.2191440.181863297
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)
10.7384-0.39470.3531.20550.02531.14240.01560.1594-0.0423-0.08180.03430.21970.2134-0.32720.00030.35910.00740.0470.23620.04650.32249.246286.771738.2865
20.55320.41420.04030.77490.16240.5760.18730.11690.4191-0.22410.01140.1558-0.3663-0.2017-0.00070.33840.04970.03110.3650.0160.469137.256699.957145.8032
31.6760.03640.07171.2819-0.20621.00150.0859-0.07220.06720.2317-0.150.34720.1468-0.23320.00220.3414-0.01960.12440.2171-0.01610.377638.808696.98760.6083
41.5688-0.1689-0.71941.94650.49882.02710.0086-0.1885-0.19460.3548-0.0226-0.00460.42030.096-0.02350.390.01760.03070.11950.05370.26959.51787.135463.9649
51.0730.50370.08871.45160.61361.70140.0020.0529-0.17530.05510.0198-0.03680.29250.041-0.00030.35670.04960.06440.13740.03840.284462.440882.417145.5007
61.31660.4668-0.47680.11180.0881.3935-0.0549-0.0440.23340.08250.5198-0.65390.23461.280.0190.53340.1469-0.0541.3218-0.18640.9005113.4822101.173143.5715
71.58630.47630.19461.92450.49170.93530.038-0.15740.20620.14390.0025-0.1053-0.17690.1246-0.00350.38550.01310.05410.17980.00930.313568.3083117.725163.574
80.2992-0.44930.0581.0580.36570.6507-0.02560.1210.0218-0.05530.0936-0.20520.29940.738100.60570.1326-0.00961.0516-0.07880.8058105.061199.344642.5907
92.27390.3309-0.94291.23040.17880.8934-0.0514-0.1692-0.03160.02670.0157-0.12480.15330.556600.34190.02140.040.5553-0.02630.392787.673594.9238132.2383
102.13950.50980.42510.958-0.46061.5258-0.13670.3534-0.1198-0.3213-0.0303-0.25950.21620.49870.00040.44260.02670.17040.6436-0.01890.428991.781389.4954107.7469
112.058-0.22330.16561.6150.04812.059-0.1909-0.1116-0.3476-0.11580.1109-0.1540.47120.0609-0.00420.4550.01490.1240.33530.01590.362373.839979.5282126.0886
121.14020.1337-0.74560.6602-0.33162.0468-0.16860.57290.0803-0.07110.25250.37240.338-1.1129-0.00430.6044-0.2532-0.03461.01040.01760.545531.056488.4759117.019
132.1325-0.30350.48861.0045-0.55852.406-0.13070.29770.3377-0.15270.09040.011-0.1307-0.2118-0.0120.4578-0.09990.01010.48420.08620.364963.8244102.0302102.0247
140.86650.1998-1.16140.7822-0.0380.8093-0.2920.5139-0.2581-0.0460.17760.09720.5063-0.478500.6618-0.2412-0.01250.9370.04240.589336.146886.265112.9487
150.43170.38960.26960.45310.25090.1224-0.188-0.02550.07450.07110.1906-0.02890.4484-0.4884-00.8624-0.24830.20671.0186-0.19340.997221.751978.7274154.7436
160.0092-0.0292-0.03140.00960.0111-0.00470.59550.2146-0.7472-0.6478-0.4673-0.27970.7207-0.09260.00161.3790.07910.26960.99830.07690.9178119.981981.490187.6867
170.06260.04340.01370.01110.0060.0050.08660.79140.0811-0.547-0.21410.1008-0.27340.4599-0.00011.8589-0.12710.32141.1287-0.02750.8155117.171484.607278.9617
180.2686-0.1580.22770.52260.15790.3260.3043-0.37910.2647-0.9994-0.2826-0.32121.08740.05680.03020.8899-0.21790.28771.05870.05320.7266112.191792.815988.5942
190.0314-0.02620.02030.03170.00210.04920.40550.35180.28-0.262-0.35310.25180.5685-0.62650.00021.1054-0.13380.29051.1743-0.00710.7358111.322695.171380.076
200.7999-0.69220.48120.7265-0.25780.28930.01760.45310.0885-0.701-0.0667-0.24750.9163-0.15360.00051.0749-0.13650.38151.06340.01080.6985115.368289.766788.5618
21-0.00590.013-0.02050.03060.01480.0204-0.0510.5051-0.28920.01260.0871-0.20680.12050.04170.00021.80360.2340.45741.46630.00150.8667128.773286.040473.0071
220.05230.02990.0254-0.00910.01770.02830.4936-0.26050.2081-0.1405-0.1189-0.7395-0.1821.10940.00011.14620.0180.1221.8616-0.19211.6029154.571885.39773.7592
230.00690.01570.01990.04360.0465-0.0113-0.27050.4910.00960.56930.0148-0.9856-0.01610.4628-0.00021.650.28040.05311.89420.11681.3379147.98984.959678.8309
240.0146-0.00270.0188-0.0025-0.0050.01420.3830.14820.2020.07240.594-0.37890.13140.0810.00031.3440.42690.03481.52460.06511.4195151.330976.453485.1816
250.0114-0.0116-0.00560.1191-0.04780.0250.24230.217-0.011-0.0201-0.1331-0.00690.0964-0.0503-0.00031.09040.11410.01291.56460.08021.5513151.911583.569191.3549
260.0106-0.0138-0.04660.01950.03930.11730.57150.0241-0.5361-0.71110.3614-0.081-0.1210.82070.00011.27240.42830.19611.93490.03511.3057145.894988.471679.8922
270.006-0.00380.00130.0039-0.00570.0042-0.03940.13870.09840.07970.0567-0.14670.0107-0.117701.54430.30160.15532.2410.20831.8985165.572878.632385.6266
280.0511-0.01040.0003-0.0020.00040.00060.0528-0.13150.09640.0809-0.2402-0.6198-0.07150.1482-0.00021.74010.85030.04212.5041-0.15441.3687150.863776.54479.2637
290.01250.006-0.00890.008-0.00030.00290.03610.07420.0912-0.0746-0.1463-0.06970.092-0.1491-01.82770.1703-0.04091.7081-0.37531.5172141.432674.189374.1225
300.0003-0.0046-0.00210.0020.0019-0.0002-0.2250.07170.2927-0.031-0.43510.01-0.0508-0.265101.1422-0.02080.08321.4413-0.05031.8882160.522280.016175.5329
310.00750.009-0.02760.0139-0.08170.1086-0.1744-0.0017-0.0594-0.19690.1973-1.0742-0.21030.6183-0.00260.5218-0.06780.11421.1920.03651.3477131.3559104.0224100.8222
320.0867-0.05860.14780.2186-0.1740.1545-0.38180.10310.7494-0.0158-0.251-0.67310.28280.4126-0.00090.4644-0.10530.1160.9961-0.00870.9833121.5742104.4304101.1061
330.5193-0.30990.18190.230.07820.531-0.0607-0.2290.46930.0957-0.2156-0.73290.11650.5065-0.00040.5918-0.02550.1991.0584-0.06760.9604123.527197.5969102.822
340.7137-0.07180.05960.5085-0.44810.491-0.06540.25050.1886-0.2556-0.3264-0.0950.24430.5969-0.09680.31090.0440.36051.77360.23381.56146.774198.701199.9757
350.02110.0545-0.04490.3089-0.02890.15370.29290.401-0.4487-0.9828-0.1586-0.10560.21280.07590.02981.53880.56020.66642.15040.22671.7067157.15389.861972.6969
360.0142-0.0083-0.08340.0843-0.06770.0664-0.08490.25690.1525-0.8080.1475-1.22180.22430.6146-0.00011.53630.00640.39971.53750.38921.5733152.6847101.155682.2757
370.01960.12850.08870.16350.13010.08520.28650.1708-0.3531-0.9504-0.16290.0661-0.45580.27850.00011.0230.00240.20471.42820.28831.4338146.354295.091788.3419
380.06210.1230.09680.11430.12710.1105-0.86560.1438-0.092-0.9464-0.1468-0.0653-0.1503-0.1461-0.04521.53770.07330.6252.17420.40331.3399153.767197.110468.4496
39-0-0.03540.0396-0.03910.00780.0272-0.15470.0255-0.1131-0.3912-0.1228-0.91850.77671.11890.00061.4379-0.11460.45452.0290.15171.988160.8146101.93879.4609
400.1963-0.0657-0.02390.1518-0.18520.1390.0259-0.54660.01450.55810.2595-0.2788-0.33140.4928-0.00010.98150.06810.26910.9597-0.02440.671115.287389.7788.6637
410.0687-0.0481-0.00460.0332-0.03750.0431-0.3153-0.23460.07150.2736-0.3655-0.22860.0846-0.0540.00041.2435-0.00530.02160.8489-0.14540.617220.79691.346288.1237
420.0213-0.0221-0.00790.0255-0.00350.0178-0.19910.0972-0.42030.21240.0734-0.49880.55680.5478-0.00040.68750.1986-0.00620.834-0.0590.745829.954289.428876.5722
430.1059-0.10860.00080.18170.0034-0.00880.3048-0.33490.47020.57290.04330.4232-0.3306-0.2070.00250.4990.08530.23540.847-0.13090.702311.967898.880.4431
440.15050.2089-0.01010.2979-0.00010.3238-0.0146-0.0515-0.07490.85060.11570.14460.02380.1526-0.00040.6-0.01770.15360.6614-0.18870.628121.3332103.542880.3077
450.07010.0660.03180.05950.0301-0.00240.4267-0.2765-0.17860.4906-0.2439-0.22240.56020.24510.00020.84350.0022-0.00830.7876-0.20830.599522.5928101.800287.9881
460.11420.1515-0.04310.1784-0.01380.0401-0.0275-0.5927-0.1790.7618-0.03540.02390.3313-0.0745-0.00020.95090.01740.11910.9658-0.18340.741317.864397.33389.7543
470.2624-0.07380.04450.30780.03330.0703-0.2052-0.2492-0.09570.7730.3529-0.11820.50050.1380.00540.5547-0.02270.15940.6114-0.07240.56918.940893.19973.895
480.0694-0.01040.0278-0.0117-0.0080.0095-0.095-0.5628-0.475-0.29681.0513-0.2144-0.3439-0.27980.02160.96340.16290.47631.07030.06810.72015.6893.830297.3388
490.0639-0.021-0.1392-0.0020.08480.2826-0.8384-0.2367-0.34210.28410.17330.7180.6850.06330.05470.5162-0.04560.2370.94360.4661.5548-17.906884.10198.2785
500.1412-0.0249-0.14580.101-0.06270.1729-0.4151-0.3717-0.3828-0.2311-0.14550.26760.28990.22640.00020.67680.05280.18680.99160.251.3528-18.839582.473391.179
510.22860.16230.31250.9541-0.96572.2601-0.2141-0.0669-1.4899-0.15180.11930.67741.64410.6658-0.20490.65980.17970.14620.94160.19121.7637-8.751578.067790.473
520.0356-0.01880.0840.2144-0.45680.9188-0.6419-0.8154-1.29340.1151-0.17950.54430.630.0575-0.03940.5799-0.02510.37260.8670.16671.5378-12.690685.597290.6509
530.0547-0.03550.02150.0037-0.04340.24410.05850.2802-1.10980.4869-0.1653-0.11570.9550.38950.01470.99380.09990.27491.07230.46231.6048-14.913575.856897.8682
540.47930.23810.38470.32350.15850.616-0.05810.73420.2107-0.34630.00140.552-0.3414-1.0347-0.04350.2922-0.02220.09551.0398-0.35550.86780.020697.454764.671
552.3593-1.0934-0.9667-0.0118-0.07490.0466-0.07730.349-0.51980.0059-0.08590.3830.0611-0.384-0.02810.3927-0.05330.12180.7446-0.16950.77422.993593.61469.3861
561.350.74430.42191.3778-0.04161.1476-0.3155-0.0609-0.89950.00020.01820.3855-0.0865-0.1279-0.00150.38930.04130.18010.83030.02941.0849-21.779193.853986.3295
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 39 )A1 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 87 )A40 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 216 )A88 - 216
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 331 )A217 - 331
5X-RAY DIFFRACTION5chain 'A' and (resid 332 through 454 )A332 - 454
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 111 )B1 - 111
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 360 )B112 - 360
8X-RAY DIFFRACTION8chain 'B' and (resid 361 through 466 )B361 - 466
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 67 )C1 - 67
10X-RAY DIFFRACTION10chain 'C' and (resid 68 through 281 )C68 - 281
11X-RAY DIFFRACTION11chain 'C' and (resid 282 through 453 )C282 - 453
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 156 )D1 - 156
13X-RAY DIFFRACTION13chain 'D' and (resid 157 through 339 )D157 - 339
14X-RAY DIFFRACTION14chain 'D' and (resid 340 through 432 )D340 - 432
15X-RAY DIFFRACTION15chain 'D' and (resid 433 through 471 )D433 - 471
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 12 )E1 - 12
17X-RAY DIFFRACTION17chain 'E' and (resid 13 through 25 )E13 - 25
18X-RAY DIFFRACTION18chain 'E' and (resid 26 through 60 )E26 - 60
19X-RAY DIFFRACTION19chain 'E' and (resid 61 through 73 )E61 - 73
20X-RAY DIFFRACTION20chain 'E' and (resid 74 through 112 )E74 - 112
21X-RAY DIFFRACTION21chain 'E' and (resid 113 through 122 )E113 - 122
22X-RAY DIFFRACTION22chain 'E' and (resid 123 through 134 )E123 - 134
23X-RAY DIFFRACTION23chain 'E' and (resid 140 through 156 )E140 - 156
24X-RAY DIFFRACTION24chain 'E' and (resid 157 through 165 )E157 - 165
25X-RAY DIFFRACTION25chain 'E' and (resid 166 through 170 )E166 - 170
26X-RAY DIFFRACTION26chain 'E' and (resid 171 through 190 )E171 - 190
27X-RAY DIFFRACTION27chain 'E' and (resid 191 through 199 )E191 - 199
28X-RAY DIFFRACTION28chain 'E' and (resid 200 through 204 )E200 - 204
29X-RAY DIFFRACTION29chain 'E' and (resid 205 through 212 )E205 - 212
30X-RAY DIFFRACTION30chain 'E' and (resid 213 through 219 )E213 - 219
31X-RAY DIFFRACTION31chain 'F' and (resid 1 through 18 )F1 - 18
32X-RAY DIFFRACTION32chain 'F' and (resid 19 through 38 )F19 - 38
33X-RAY DIFFRACTION33chain 'F' and (resid 39 through 102 )F39 - 102
34X-RAY DIFFRACTION34chain 'F' and (resid 103 through 113 )F103 - 113
35X-RAY DIFFRACTION35chain 'F' and (resid 114 through 129 )F114 - 129
36X-RAY DIFFRACTION36chain 'F' and (resid 130 through 155 )F130 - 155
37X-RAY DIFFRACTION37chain 'F' and (resid 156 through 174 )F156 - 174
38X-RAY DIFFRACTION38chain 'F' and (resid 175 through 188 )F175 - 188
39X-RAY DIFFRACTION39chain 'F' and (resid 189 through 214 )F189 - 214
40X-RAY DIFFRACTION40chain 'H' and (resid 1 through 16 )H1 - 16
41X-RAY DIFFRACTION41chain 'H' and (resid 17 through 25 )H17 - 25
42X-RAY DIFFRACTION42chain 'H' and (resid 26 through 32 )H26 - 32
43X-RAY DIFFRACTION43chain 'H' and (resid 33 through 43 )H33 - 43
44X-RAY DIFFRACTION44chain 'H' and (resid 44 through 64 )H44 - 64
45X-RAY DIFFRACTION45chain 'H' and (resid 65 through 73 )H65 - 73
46X-RAY DIFFRACTION46chain 'H' and (resid 74 through 92 )H74 - 92
47X-RAY DIFFRACTION47chain 'H' and (resid 93 through 112 )H93 - 112
48X-RAY DIFFRACTION48chain 'H' and (resid 113 through 122 )H113 - 122
49X-RAY DIFFRACTION49chain 'H' and (resid 123 through 134 )H123 - 134
50X-RAY DIFFRACTION50chain 'H' and (resid 138 through 151 )H138 - 151
51X-RAY DIFFRACTION51chain 'H' and (resid 152 through 171 )H152 - 171
52X-RAY DIFFRACTION52chain 'H' and (resid 172 through 193 )H172 - 193
53X-RAY DIFFRACTION53chain 'H' and (resid 194 through 219 )H194 - 219
54X-RAY DIFFRACTION54chain 'L' and (resid 1 through 18 )L1 - 18
55X-RAY DIFFRACTION55chain 'L' and (resid 19 through 128 )L19 - 128
56X-RAY DIFFRACTION56chain 'L' and (resid 129 through 214 )L129 - 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://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る