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- PDB-7tct: Integrin alaphIIBbeta3 complex with UR2922 -

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基本情報

登録情報
データベース: PDB / ID: 7tct
タイトルIntegrin alaphIIBbeta3 complex with UR2922
要素
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Integrin alpha-IIb heavy chain
  • Isoform Beta-3C of Integrin beta-3
キーワードBLOOD CLOTTING/INHIBITOR / Complex / Inhibitor / BLOOD CLOTTING (凝固・線溶系) / 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 / 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 / maintenance of postsynaptic specialization structure / fibrinogen binding / 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 / regulation of release of sequestered calcium ion into cytosol / angiogenesis involved in wound healing / Elastic fibre formation / cell-substrate junction assembly / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of cell adhesion mediated by integrin / 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 / cell adhesion mediated by integrin / Syndecan interactions / negative chemotaxis / 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 / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / 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 / 着床 / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / Signal transduction by L1 / response to activity / 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 / 凝固・線溶系 / 血小板 / ruffle membrane / VEGFA-VEGFR2 Pathway / 細胞接着 / 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様ドメイン / 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 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
Chem-I1F / 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: 2.501 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2021年12月28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: Fab heavy chain
F: Fab light chain
H: Fab heavy chain
L: Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)302,72939
ポリマ－297,4068
非ポリマー5,32331
水17,979998
1
A: Integrin alpha-IIb heavy chain
B: Isoform Beta-3C of Integrin beta-3
H: Fab heavy chain
L: Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)151,52420
ポリマ－148,7034
非ポリマー2,82116
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: Fab heavy chain
F: Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)151,20519
ポリマ－148,7034
非ポリマー2,50215
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)259.160, 143.840, 104.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 Fab heavy chain / Fragment antigen-binding


分子量: 23766.473 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#4: 抗体 Fab light chain / Fragment antigen-binding


分子量: 23332.686 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)

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糖 , 4種, 6分子

#5: 多糖 beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-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オリゴ糖 / 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
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/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)][b-D-Manp]{}[(6+1)][b-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オリゴ糖 / 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 beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-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オリゴ糖 / 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
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/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)][b-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 / N-アセチルグルコサミン


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, 1023分子

#8: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Ca
#9: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン / 硫酸塩


分子量: 96.063 Da / 分子数: 8 / 由来タイプ: 合成 / 式: SO4
#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-I1F / {5-[N-(4-carbamimidoylbenzoyl)-4-nitro-L-phenylalanyl]-4,5,6,7-tetrahydro-2H-pyrazolo[4,3-c]pyridin-2-yl}acetic acid


分子量: 519.509 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C25H25N7O6 / タイプ: SUBJECT OF INVESTIGATION
#13: 化合物 ChemComp-CL / CHLORIDE ION / クロリド / 塩化物


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


分子量: 18.015 Da / 分子数: 998 / 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: 3.32 Å3/Da / 溶媒含有率: 62.96 %
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: 1.0332 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2011年6月23日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.0332 Å / 相対比: 1
反射解像度: 2.5→50 Å / Num. obs: 134985 / % possible obs: 99.4 % / 冗長度: 4.7 % / Biso Wilson estimate: 42.4032868899 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.61
反射 シェル解像度: 2.5→2.57 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 9487 / % possible all: 95.4

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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
PDB_EXTRACT3.27データ抽出
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: 3NIG

3nig


解像度: 2.501→49.28 Å / SU ML: 0.32 / 交差検証法: FREE R-VALUE / σ(F): 1.99 / 位相誤差: 23.87 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2271 2000 1.48 %
Rwork0.1951 132972 -
obs0.1955 134972 99.38 %
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: 176.57 Å2 / Biso mean: 62.6399 Å2 / Biso min: 16.12 Å2
精密化ステップサイクル: final / 解像度: 2.501→49.28 Å
タンパク質核酸リガンド溶媒全体
原子数20708 0 326 998 22032
Biso mean--79.47 46.03 -
残基数----2701
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00421748
X-RAY DIFFRACTIONf_angle_d0.55529533
X-RAY DIFFRACTIONf_chiral_restr0.0433278
X-RAY DIFFRACTIONf_plane_restr0.0043826
X-RAY DIFFRACTIONf_dihedral_angle_d8.75512948
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 (%)
2.5012-2.56370.39321360.3415900295
2.5637-2.6330.33011400.30959386100
2.633-2.71050.30571430.28859505100
2.7105-2.7980.29841420.26249407100
2.798-2.8980.25411430.24699474100
2.898-3.0140.27921420.23289481100
3.014-3.15110.27661430.22469508100
3.1511-3.31720.25731430.20959467100
3.3172-3.5250.24251430.19359556100
3.525-3.79710.24471430.18069535100
3.7971-4.1790.17741450.15989575100
4.179-4.78330.16251430.13939590100
4.7833-6.02470.181460.15869649100
6.0247-49.280.19641480.1759983798
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)
11.38380.51510.53330.853-0.18671.29880.05330.18240.0894-0.1667-0.09460.3465-0.0105-0.20650.00440.35060.06960.06450.19360.01170.271246.117788.791138.8074
21.4103-0.23920.05751.06560.34170.99910.1199-0.07140.03170.2941-0.19170.22450.1517-0.201-0.03170.4501-0.01480.15050.09080.01110.24544.255492.48763.2507
30.9463-0.41710.05061.2348-0.06271.22830.0959-0.2094-0.23260.4402-0.0433-0.30270.33710.16570.89050.59620.15120.0465-0.07380.17490.199167.09980.236755.226
40.68570.13120.20160.58650.25790.5312-0.06250.0569-0.1408-0.0708-0.0791-0.11070.29680.1403-0.10320.47280.18850.1276-0.05650.06580.241660.582782.416341.3571
51.03970.7837-0.38080.6509-0.52281.22950.04710.171-0.0109-0.06620.1273-0.61860.34271.0220.00010.65290.2131-0.12071.2935-0.07460.9704113.322297.94842.7705
61.02740.75020.36042.61880.54581.18940.1587-0.17040.25150.3208-0.1163-0.0049-0.17320.3458-0.0030.5014-0.03540.10590.01430.02550.256467.5748115.765963.6563
70.5394-0.2136-0.48080.25430.23760.4258-0.02810.1055-0.17680.2456-0.0166-0.27390.38630.6296-0.00440.62220.0929-0.10330.8213-0.04440.771797.0368103.557956.2812
80.0760.0228-0.00030.0588-0.06670.08680.01760.0636-0.1271-0.2026-0.1841-0.56460.41090.12880.00010.87530.23430.07891.25980.04351.0196114.882586.976218.6823
91.5726-0.1456-0.18190.71520.32041.2601-0.2778-0.17350.14820.14980.08-0.1909-0.04190.5489-0.03880.2577-0.0099-0.03640.45290.05470.384889.901595.8419125.7651
102.00470.1999-0.03510.8131-0.11731.1524-0.25370.5181-0.2091-0.17620.0142-0.12150.26980.44390.00760.3959-0.03640.1140.53580.0230.358587.683685.3789107.8554
112.1049-0.1004-0.0631.61360.20772.06-0.4016-0.0046-0.5517-0.06050.0972-0.0130.61880.0806-0.04280.42960.01710.17810.26010.05590.382972.223778.8367126.9439
120.12140.10250.07830.12880.00430.1684-0.5591-0.0359-0.66360.03790.15560.80770.4389-0.5625-0.00020.9123-0.36430.20051.10640.05460.941814.349169.357142.2259
130.4688-0.15860.11910.34070.00420.81480.21060.21110.19740.09960.07360.27590.0449-0.6340.00680.4756-0.1405-0.12410.85020.14010.565530.164693.7917114.5711
141.4286-0.32670.91841.3697-0.24712.07410.01080.28690.2835-0.1054-0.1298-0.0062-0.286-0.0507-0.01490.3444-0.0546-0.04340.47640.09230.38360.6476103.24101.3183
150.23120.0698-0.40210.029-0.14830.7768-0.27580.1595-0.1183-0.2741-0.02-0.01761.1746-0.5167-0.02550.6983-0.3047-0.05090.91120.03290.537735.67285.957108.0534
160.3926-0.0723-0.11060.26790.30980.35940.01330.0101-0.10140.1358-0.14040.13540.13350.2258-0.00010.5755-0.1808-0.05360.71740.06090.559632.681588.2464126.1321
170.21630.15840.07290.15550.10780.0937-0.0587-0.0609-0.2840.3899-0.00450.10010.61710.091800.9516-0.13430.18010.7779-0.02380.821921.489977.7572155.9035
180.11610.108-0.23750.2176-0.17060.49910.08940.5453-0.0774-0.1291-0.04770.14380.0469-0.01680.07050.5077-0.11150.17041.54830.00510.6867118.871582.685981.9622
190.4607-0.211-0.05310.24510.11130.1592-0.0850.6545-0.0199-0.14450.0435-0.07560.0110.17991.00980.2926-0.25660.12641.34810.2060.6283111.433191.648986.9574
200.207-0.07220.08370.08750.04530.1167-0.07991.04850.0408-0.2021-0.0419-0.0467-0.02870.0816-0.06210.4367-0.13960.1331.49720.16080.5221113.10789.496486.5885
210.02230.00640.01480.01440.00960.02560.36540.1178-0.0542-0.22410.28430.08780.09660.08190.00080.71310.16520.09432.1457-0.0110.7105130.012184.164271.8601
220.0164-0.0280.00010.08540.03910.03630.04880.35860.2489-0.28790.073-0.4727-0.1581-0.30740.00010.7318-0.1180.12541.86860.17261.1079153.556784.279477.3083
230.1099-0.1234-0.18580.15320.22040.32390.1620.27580.0606-0.032-0.2157-0.1554-0.0208-0.3387-0.01750.4778-0.1896-0.00571.64780.19230.9349145.308278.513183.9041
240.1110.0398-0.0150.25020.14340.17930.19710.3602-0.2353-0.675-0.089-0.371-0.4256-0.17110.00190.683-0.001-0.0451.7640.16661.0759149.680182.109580.5536
250.003-0.00450.00130.0077-0.00190.0538-0.22060.15130.0895-0.1926-0.4556-0.1446-0.2162-0.2891-0.00010.7591-0.06880.03941.8544-0.19731.1286150.085375.246974.445
260.21870.14040.20010.82780.61380.51280.1071-0.13620.1225-0.03920.359-0.3108-0.06070.27230.97210.4431-0.2316-0.07621.37560.34260.8866130.0331102.8076100.6072
271.5047-1.1869-0.45052.48250.56370.8005-0.19280.13240.51530.08580.092-0.268-0.04290.4707-0.18660.3232-0.2269-0.06661.1920.25240.7497120.895898.3125103.8072
280.1155-0.0009-0.10760.04050.02920.1162-0.1254-0.22430.1618-0.03420.1138-0.3926-0.06530.2224-0.00010.4892-0.1822-0.00551.17070.21760.7285123.426797.568298.8691
290.1119-0.0084-0.1420.1340.11770.2669-0.08740.12920.1221-0.10590.0332-0.1128-0.0632-0.0576-0.0810.3804-0.1337-0.00491.38270.11061.1412145.447897.174699.4231
301.0091-0.96680.50913.9432-0.78490.2852-0.07080.89560.4769-1.0234-0.3664-0.59340.22930.0287-0.01960.6789-0.20680.24831.83390.33311.134152.615491.62479.646
310.15430.0872-0.02390.0495-0.01370.0037-0.06490.12620.0407-0.17520.03350.01610.0026-0.0404-0.11961.1597-0.07940.38461.9330.84211.5616153.4192104.220574.7927
320.0906-0.4927-0.23463.26980.66751.22120.21860.34420.2252-0.60720.0331-0.3086-0.2557-0.14390.04350.5232-0.16530.08651.57010.37591.202144.99593.515187.6912
330.00420.0277-0.00450.1535-0.02230.0024-0.02770.34750.0818-0.79520.1995-0.4426-0.43680.013-0.07481.1433-0.05910.40022.52420.52051.2098154.461997.18270.4459
340.018-0.0160.01840.0314-0.01350.0182-0.19480.58270.0523-0.72240.0883-0.04530.10870.2748-0.00070.99690.04530.40482.03180.33991.869160.485598.998180.6636
350.47520.1810.16170.567-0.36050.6969-0.0806-0.341-0.240.2244-0.07140.0280.1731-0.3182-0.00010.46070.11830.15560.6595-0.04910.484918.882695.29983.8595
360.10430.06230.06420.03950.03010.11050.1083-0.66160.04710.2773-0.2203-0.0872-0.19670.041800.54480.14540.12980.7751-0.04250.461124.007795.730189.0138
370.4243-0.06010.12190.2414-0.17690.1457-0.044-0.40170.04180.17150.15120.18080.0045-0.352-0.00110.43810.08420.19270.7749-0.02950.503912.657893.844884.7725
380.0534-0.0069-0.03620.04910.07670.21970.0777-0.2355-1.0420.0694-0.06860.35810.9610.3206-0.00370.88020.25550.13240.83730.21371.3513-16.00180.751792.1895
390.1950.0123-0.19350.1188-0.15760.3675-0.197-0.6708-0.44880.2582-0.150.41340.44580.0536-0.00010.67320.19090.18460.74660.12351.0972-12.057386.911489.9737
400.0839-0.04390.00760.04280.04530.1175-0.10030.0456-0.5020.10070.11880.21931.10990.32970.00351.14950.02090.16360.93540.42431.6108-17.60875.504796.1118
410.7580.0364-0.1460.008-0.0170.53-0.04880.1411-0.1145-0.1402-0.16530.4041-0.0273-0.6022-0.00380.40460.04460.10170.6867-0.15750.67356.160294.674865.7946
420.6622-0.08970.47561.20.61651.1437-0.2405-0.0762-0.51480.38440.08360.1240.35520.06680.17350.40020.06640.26050.70890.23190.9657-20.260493.022988.1516
430.1315-0.23590.05940.89420.58892.0754-0.06210.3219-0.85840.2518-0.06780.57790.6269-0.72620.19420.4235-0.00640.24680.93320.04780.9926-30.071194.693785.6715
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 67 )A1 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 296 )A68 - 296
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 373 )A297 - 373
4X-RAY DIFFRACTION4chain 'A' and (resid 374 through 453 )A374 - 453
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 111 )B1 - 111
6X-RAY DIFFRACTION6chain 'B' and (resid 112 through 339 )B112 - 339
7X-RAY DIFFRACTION7chain 'B' and (resid 340 through 431 )B340 - 431
8X-RAY DIFFRACTION8chain 'B' and (resid 432 through 466 )B432 - 466
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 92 )C1 - 92
10X-RAY DIFFRACTION10chain 'C' and (resid 93 through 304 )C93 - 304
11X-RAY DIFFRACTION11chain 'C' and (resid 305 through 453 )C305 - 453
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 53 )D1 - 53
13X-RAY DIFFRACTION13chain 'D' and (resid 54 through 121 )D54 - 121
14X-RAY DIFFRACTION14chain 'D' and (resid 122 through 339 )D122 - 339
15X-RAY DIFFRACTION15chain 'D' and (resid 340 through 403 )D340 - 403
16X-RAY DIFFRACTION16chain 'D' and (resid 404 through 432 )D404 - 432
17X-RAY DIFFRACTION17chain 'D' and (resid 433 through 471 )D433 - 471
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 17 )E1 - 17
19X-RAY DIFFRACTION19chain 'E' and (resid 18 through 64 )E18 - 64
20X-RAY DIFFRACTION20chain 'E' and (resid 65 through 112 )E65 - 112
21X-RAY DIFFRACTION21chain 'E' and (resid 113 through 125 )E113 - 125
22X-RAY DIFFRACTION22chain 'E' and (resid 126 through 151 )E126 - 151
23X-RAY DIFFRACTION23chain 'E' and (resid 152 through 171 )E152 - 171
24X-RAY DIFFRACTION24chain 'E' and (resid 172 through 205 )E172 - 205
25X-RAY DIFFRACTION25chain 'E' and (resid 206 through 219 )E206 - 219
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 18 )F1 - 18
27X-RAY DIFFRACTION27chain 'F' and (resid 19 through 75 )F19 - 75
28X-RAY DIFFRACTION28chain 'F' and (resid 76 through 102 )F76 - 102
29X-RAY DIFFRACTION29chain 'F' and (resid 103 through 113 )F103 - 113
30X-RAY DIFFRACTION30chain 'F' and (resid 114 through 144 )F114 - 144
31X-RAY DIFFRACTION31chain 'F' and (resid 145 through 155 )F145 - 155
32X-RAY DIFFRACTION32chain 'F' and (resid 156 through 174 )F156 - 174
33X-RAY DIFFRACTION33chain 'F' and (resid 175 through 197 )F175 - 197
34X-RAY DIFFRACTION34chain 'F' and (resid 198 through 214 )F198 - 214
35X-RAY DIFFRACTION35chain 'H' and (resid 1 through 64 )H1 - 64
36X-RAY DIFFRACTION36chain 'H' and (resid 65 through 83 )H65 - 83
37X-RAY DIFFRACTION37chain 'H' and (resid 84 through 125 )H84 - 125
38X-RAY DIFFRACTION38chain 'H' and (resid 126 through 168 )H126 - 168
39X-RAY DIFFRACTION39chain 'H' and (resid 169 through 190 )H169 - 190
40X-RAY DIFFRACTION40chain 'H' and (resid 191 through 219 )H191 - 219
41X-RAY DIFFRACTION41chain 'L' and (resid 1 through 113 )L1 - 113
42X-RAY DIFFRACTION42chain 'L' and (resid 114 through 188 )L114 - 188
43X-RAY DIFFRACTION43chain 'L' and (resid 189 through 214 )L189 - 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

他の情報も見る