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- PDB-9b9f: Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3... -

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基本情報

登録情報
データベース: PDB / ID: 9b9f
タイトルZebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII
要素
  • Transforming growth factor beta receptor type-1
  • Transforming growth factor beta receptor type-2
  • Transforming growth factor beta receptor type-3
  • Transforming growth factor beta-3
  • Transforming growth factor beta-3 triple mutant
キーワードMEMBRANE PROTEIN / Complex / Betaglycan / TGFBR3 / TGFb / TGFBR1 / TGFBR2
機能・相同性
機能・相同性情報


FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGF-beta receptor signaling activates SMADs / TGFBR3 PTM regulation / TGFBR3 regulates TGF-beta signaling / TGFBR3 regulates FGF2 signaling / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown / inferior endocardial cushion morphogenesis ...FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGF-beta receptor signaling activates SMADs / TGFBR3 PTM regulation / TGFBR3 regulates TGF-beta signaling / TGFBR3 regulates FGF2 signaling / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown / inferior endocardial cushion morphogenesis / bronchus morphogenesis / mammary gland morphogenesis / detection of hypoxia / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / frontal suture morphogenesis / extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / TGFBR2 MSI Frameshift Mutants in Cancer / embryonic neurocranium morphogenesis / miRNA transport / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / type III transforming growth factor beta receptor binding / aorta morphogenesis / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / Langerhans cell differentiation / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / ventricular compact myocardium morphogenesis / cardiac left ventricle morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / secondary palate development / trophoblast cell migration / positive regulation of mesenchymal stem cell proliferation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / endocardial cushion fusion / positive regulation of T cell tolerance induction / membranous septum morphogenesis / TGFBR3 regulates TGF-beta signaling / lung lobe morphogenesis / positive regulation of tight junction disassembly / positive regulation of NK T cell differentiation / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / positive regulation of vasculature development / response to laminar fluid shear stress / somite development / neuron fate commitment / activin receptor complex / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / pharyngeal system development / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / transforming growth factor beta receptor activity, type III / activin binding / regulation of epithelial to mesenchymal transition / regulation of stem cell proliferation / coronary artery morphogenesis / angiogenesis involved in coronary vascular morphogenesis / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / germ cell migration / filopodium assembly / mammary gland development / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / activin receptor signaling pathway / glycosaminoglycan binding / cell-cell junction organization / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of stem cell differentiation / response to cholesterol / embryonic cranial skeleton morphogenesis / I-SMAD binding / transforming growth factor beta binding / collagen fibril organization / kinase activator activity / digestive tract development / aortic valve morphogenesis / negative regulation of chondrocyte differentiation / sprouting angiogenesis / face morphogenesis / atrioventricular valve morphogenesis / endothelial cell activation / anterior/posterior pattern specification
類似検索 - 分子機能
Transforming growth factor beta-3 / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / : / : / ZP-N domain / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. ...Transforming growth factor beta-3 / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / : / : / ZP-N domain / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Transforming growth factor beta receptor III / Transforming growth factor beta-3 proprotein / TGF-beta receptor type-1 / TGF-beta receptor type-2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Danio rerio (ゼブラフィッシュ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å
データ登録者Wieteska, L. / Taylor, A.B. / Hinck, A.P.
資金援助 米国, European Union, 3件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM058670 米国
H2020 Marie Curie Actions of the European Commission893196European Union
National Institutes of Health/Office of the DirectorOD030374 米国
引用ジャーナル: Nat Commun / 年: 2025
タイトル: Structures of TGF-β with betaglycan and signaling receptors reveal mechanisms of complex assembly and signaling.
著者: Łukasz Wieteska / Alexander B Taylor / Emma Punch / Jonathan A Coleman / Isabella O Conway / Yeu-Farn Lin / Chang-Hyeock Byeon / Cynthia S Hinck / Troy Krzysiak / Rieko Ishima / Fernando ...著者: Łukasz Wieteska / Alexander B Taylor / Emma Punch / Jonathan A Coleman / Isabella O Conway / Yeu-Farn Lin / Chang-Hyeock Byeon / Cynthia S Hinck / Troy Krzysiak / Rieko Ishima / Fernando López-Casillas / Peter Cherepanov / Daniel J Bernard / Caroline S Hill / Andrew P Hinck /
要旨: Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development, tissue homeostasis and fertility ...Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development, tissue homeostasis and fertility in adults. It functions by enabling binding of the three TGF-β isoforms to their signaling receptors and is additionally required for inhibin A (InhA) activity. Despite its requirement for the functions of TGF-βs and InhA in vivo, structural information explaining BG ligand selectivity and its mechanism of action is lacking. Here, we determine the structure of TGF-β bound both to BG and the signaling receptors, TGFBR1 and TGFBR2. We identify key regions responsible for ligand engagement, which has revealed binding interfaces that differ from those described for the closely related co-receptor of the TGF-β family, endoglin, thus demonstrating remarkable evolutionary adaptation to enable ligand selectivity. Finally, we provide a structural explanation for the hand-off mechanism underlying TGF-β signal potentiation.
履歴
登録2024年4月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年3月12日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Transforming growth factor beta-3
B: Transforming growth factor beta-3 triple mutant
C: Transforming growth factor beta receptor type-1
D: Transforming growth factor beta receptor type-2
E: Transforming growth factor beta receptor type-3
F: Transforming growth factor beta-3
G: Transforming growth factor beta-3 triple mutant
H: Transforming growth factor beta receptor type-1
I: Transforming growth factor beta receptor type-2
J: Transforming growth factor beta receptor type-3


分子量 (理論値)分子数
合計 (水以外)170,89910
ポリマ－170,89910
非ポリマー00
水00
1
A: Transforming growth factor beta-3
B: Transforming growth factor beta-3 triple mutant
C: Transforming growth factor beta receptor type-1
D: Transforming growth factor beta receptor type-2
E: Transforming growth factor beta receptor type-3


分子量 (理論値)分子数
合計 (水以外)85,4495
ポリマ－85,4495
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: Transforming growth factor beta-3
G: Transforming growth factor beta-3 triple mutant
H: Transforming growth factor beta receptor type-1
I: Transforming growth factor beta receptor type-2
J: Transforming growth factor beta receptor type-3


分子量 (理論値)分子数
合計 (水以外)85,4495
ポリマ－85,4495
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)195.136, 200.923, 47.436
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
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 301 through 324 or resid 326...
d_2ens_1(chain "B" and (resid 301 through 324 or resid 326...
d_3ens_1(chain "F" and (resid 301 through 324 or resid 326...
d_4ens_1(chain "G" and (resid 301 through 324 or resid 326...
d_1ens_2(chain "C" and (resid 31 through 89 or resid 92 through 107))
d_2ens_2chain "H"
d_1ens_3chain "D"
d_2ens_3chain "I"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAPHEPHEAA301 - 3241 - 24
d_12ens_1GLNGLNLEULEUAA326 - 38926 - 89
d_13ens_1TYRTYRGLYGLYAA391 - 39391 - 93
d_14ens_1THRTHRSERSERAA395 - 41295 - 112
d_21ens_1ALAALAPHEPHEBB301 - 3241 - 24
d_22ens_1GLNGLNLEULEUBB326 - 38926 - 89
d_23ens_1TYRTYRGLYGLYBB391 - 39391 - 93
d_24ens_1THRTHRSERSERBB395 - 41295 - 112
d_31ens_1ALAALAPHEPHEFF301 - 3241 - 24
d_32ens_1GLNGLNLEULEUFF326 - 38926 - 89
d_33ens_1TYRTYRGLYGLYFF391 - 39391 - 93
d_34ens_1THRTHRSERSERFF395 - 41295 - 112
d_41ens_1ALAALAPHEPHEGG301 - 3241 - 24
d_42ens_1GLNGLNLEULEUGG326 - 38926 - 89
d_43ens_1TYRTYRGLYGLYGG391 - 39391 - 93
d_44ens_1THRTHRSERSERGG395 - 41295 - 112
d_11ens_2ALAALALYSLYSCC31 - 895 - 63
d_12ens_2SERSERILEILECC92 - 10766 - 81
d_21ens_2ALAALAILEILEHH31 - 1075 - 81
d_11ens_3VALVALPHEPHEDD45 - 1495 - 109
d_21ens_3VALVALPHEPHEII45 - 1495 - 109

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.852921964177, -0.346336071214, -0.390609074139), (-0.336889307008, -0.206414208009, 0.918639629863), (-0.398785302949, 0.915119937772, 0.0593782927061)238.507682365, 34.0205392465, 59.5016392445
2given(-0.918986062343, 0.162150377349, -0.359404886369), (0.213889791669, -0.560735024602, -0.799892110978), (-0.331233715433, -0.811962737637, 0.480625361846)149.449665352, 34.8997139007, 53.3594041238
3given(0.888452670137, -0.0419196508605, 0.457049883271), (0.318308074576, -0.661139477068, -0.679392788836), (0.330653629324, 0.749091005642, -0.574047770382)-85.9228035203, 20.897355036, -22.20958426
4given(-0.913827737441, 0.111427334984, -0.390516088404), (0.256395674676, -0.587423140258, -0.767590588984), (-0.314928760661, -0.80157220717, 0.508234072451)151.588898309, 30.8365170567, 50.9848093384
5given(-0.889766345197, 0.198726069608, -0.410881735069), (0.223912080387, -0.594399248568, -0.77236837944), (-0.397717526911, -0.779228774212, 0.484379279313)147.195334278, 34.3794171559, 58.301224277

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要素

#1: タンパク質 Transforming growth factor beta-3 / TGF-beta-3


分子量: 12734.504 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: TGFB3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P10600
#2: タンパク質 Transforming growth factor beta-3 triple mutant / TGF-beta-3


分子量: 12586.247 Da / 分子数: 2 / Mutation: R325E,Y390A,R394E / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TGFB3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P10600
#3: タンパク質 Transforming growth factor beta receptor type-1 / TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ...TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ALK-5 / ALK5 / Serine/threonine-protein kinase receptor R4 / SKR4 / TGF-beta type I receptor / Transforming growth factor-beta receptor type I / TGF-beta receptor type I / TbetaR-I


分子量: 9474.826 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: TGFBR1, ALK5, SKR4 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P36897, receptor protein serine/threonine kinase
#4: タンパク質 Transforming growth factor beta receptor type-2


分子量: 12926.812 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: TGFBR2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P37173
#5: タンパク質 Transforming growth factor beta receptor type-3 / Transforming growth factor beta receptor type 3 precursor


分子量: 37727.000 Da / 分子数: 2 / Mutation: C150G,C277G / 由来タイプ: 組換発現
由来: (組換発現) Danio rerio (ゼブラフィッシュ)
遺伝子: tgfbr3, si:ch73-18k18.1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A0A0H3UK16
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: 2.72 Å3/Da / 溶媒含有率: 54.79 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.2 M lithium sulfate, 0.1 M tris pH 8.5, 30 %(w/v) polyethylene glycol 4000

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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: 24-ID-C / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年3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: 0.97918 Å / 相対比: 1
反射解像度: 3→139.98 Å / Num. obs: 38615 / % possible obs: 100 % / 冗長度: 13.4 % / Biso Wilson estimate: 105.95 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.045 / Net I/σ(I): 10.5
反射 シェル解像度: 3→3.16 Å / 冗長度: 13.9 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5562 / CC1/2: 0.407 / Rpim(I) all: 1.427 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21_5207精密化
autoPROCデータ削減
Aimless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 / 解像度: 3→63.35 Å / SU ML: 0.4918 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 34.5241
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2779 2011 5.22 %
Rwork0.2353 36497 -
obs0.2375 38508 99.86 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 156.18 Å2
精密化ステップサイクル: LAST / 解像度: 3→63.35 Å
タンパク質核酸リガンド溶媒全体
原子数11078 0 0 0 11078
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003911334
X-RAY DIFFRACTIONf_angle_d0.732715402
X-RAY DIFFRACTIONf_chiral_restr0.06271754
X-RAY DIFFRACTIONf_plane_restr0.0041978
X-RAY DIFFRACTIONf_dihedral_angle_d15.31234163
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.81756078523
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.491682567932
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.875006761952
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.798432985765
ens_3d_2DDX-RAY DIFFRACTIONTorsion NCS0.509781700708
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.42711390.39052535X-RAY DIFFRACTION99.78
3.08-3.160.38691500.36442589X-RAY DIFFRACTION99.89
3.16-3.250.38171290.34622526X-RAY DIFFRACTION99.74
3.25-3.360.39841470.32632579X-RAY DIFFRACTION99.82
3.36-3.480.35571370.31082541X-RAY DIFFRACTION99.81
3.48-3.620.32951460.26032594X-RAY DIFFRACTION99.78
3.62-3.780.30391370.25322576X-RAY DIFFRACTION99.96
3.78-3.980.32561430.2542607X-RAY DIFFRACTION99.93
3.98-4.230.24051430.22542576X-RAY DIFFRACTION99.93
4.23-4.550.21561390.18732591X-RAY DIFFRACTION99.85
4.55-5.010.21871440.18832634X-RAY DIFFRACTION100
5.01-5.740.27261500.2132643X-RAY DIFFRACTION100
5.74-7.230.31741470.26732677X-RAY DIFFRACTION99.89
7.23-63.350.25321600.21082829X-RAY DIFFRACTION99.7
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)
18.44613167159-0.44514466242-8.24238489769.36860470141-0.127256675488.177879681210.210702040801-0.153932255363-2.202301338571.30683650658-0.7040131057150.724471035764-1.00713656538-0.4602119487430.7248434593771.45109493731-0.0443714673615-0.1849650769611.210716133520.02474585740940.990259581336105.14138544215.408327080351.0295687199
29.00487814309-1.65496992173-0.3504852867014.264202158452.55180172343.336429784380.187808161873-3.580143945222.447938340714.27802153414-0.04109681263020.557386607763-2.334447199862.103612481770.1902273220471.39197661163-0.312315027168-0.1684578229911.63133371144-0.1083433591531.01907139066107.95138532321.913919122157.0956857102
35.424257298151.40762613748-2.415428453122.69708903190.1371960681643.370295932570.0689735920742-0.4998682584770.1220854261410.509804116546-0.142470861836-0.2133744912590.02334635849650.201235529241-0.02782114649691.175127271510.0170650833031-0.02332160663971.12862381264-0.03000535871220.756626882065105.44661867527.082398063244.4137401458
42.29440554262-0.8758400714163.330031730183.15577679283-0.6566274348165.639963906891.54541978632-0.6345925698511.098600168611.68200724099-0.356358705404-1.09743184856-1.321658816820.1362744129050.2994183352661.750573442780.05516815838790.2457046726832.263884916260.144195483951.59766060362121.90845756235.514811297455.1682098664
56.023953515661.423093101585.946808448062.433089688061.356160101825.86897528173-0.2914121369460.579297533319-3.81613455366-0.6283172218321.09605063771-3.72624757205-0.1677103148551.86890013717-0.3153409059731.30839951841-0.269472955451-0.01726105842871.322727422020.004378071550681.31438632826109.03392750821.947969330241.2285912365
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558.77814568036-0.235472136662-0.339115418875.39771360852-0.673187480952.61328022136-0.560499972591-0.02936277760940.783545240943-0.408467376063-0.472800283196-1.85099775503-2.29793623775-2.357710122630.7851332262011.297427656630.0762197937457-0.09902408320331.0912592583-0.1366664361441.1254151406168.866386177221.61801097395.41765447871
565.68759756693-3.550052202383.536403533665.31367092302-4.422032045314.79008787244-0.436427618023-2.516762821922.53723679879-0.34397563519-0.149201399402-0.140883389849-0.37402182958-1.65333418953-0.4122329118991.24502083886-0.167565591450.05975643139731.329804888810.07196630998980.77596525853884.272385355514.527499242210.306705806
573.49630294015-3.884183588882.697843605364.67301219337-4.97640179176.177264024840.0751985301431.263978386041.59064022996-0.201779390179-1.53749203056-1.252795647720.464820207451.289964937250.1099895415041.30146480433-0.037865344522-0.06839695037431.24675237846-0.01179013891611.0078844003484.410322479415.997561871613.6813741778
583.710555150944.878668669610.2945534156567.361730519422.345546488273.883338543810.14067537591-1.01430077381-0.646349281315-0.4878238402550.5889913634220.860253939237-0.111611641626-1.199545385880.2554029338391.88387863131-0.264326145151-0.04879139891421.240277815650.1970780305990.74582605176281.653458003922.84000447990.533101600066
592.4168632377-0.734423206299-2.458833215352.55215966095-2.027170576548.14537144022-0.07659197987890.586071240657-1.03169210306-2.27060140427-1.72074464438-0.3135737397730.2087711405610.3412788175111.603742323331.631915027060.00757095902390.1641990558761.3323023707-0.2284118469921.1964555921484.686443850716.4710492220.00678797587058
608.01214485062-2.662843674230.885131528163.36327421844-4.066724226075.948816450840.174692283939-0.156768728334-1.11080212572-1.27854049063-1.738761690641.98396336626-0.6011159192220.6658943864810.5353747863111.40759982440.0505874742271-0.03601386466371.56876955785-0.2670398493951.4897060498480.15806614266.421149315863.5521769433
612.830240190134.543706103053.098721660078.313220976295.414570554843.67281382685-0.743291971176-1.034397156310.128712785674-0.941537629451-1.14584752080.207236369351-0.36981620697-1.782663162981.279200056051.32401383602-0.1741931699970.1291798584181.12229328574-0.09050714500160.97535200257294.242612848113.48237285546.26697879433
623.592511338154.758150891381.612878173486.955952414690.9901276852642.106953557-1.4009047243-0.399681717976-0.712172992283-0.744497285790.809145980515-0.958691837191-1.210866863820.1766035056551.29584781241.06562508074-0.01411427866270.002287092601051.56158230891-0.06577215226551.0470674280887.469695648512.49755715267.53287122657
635.23174163226-4.561744499090.08313388779614.171044391730.6044236706637.704268452510.5680113375461.77933957572-3.06649410796-0.977428308831-0.01084580910540.9480661880920.505186601524-2.30668268616-0.3786380337791.45888369731-0.249043243824-0.06699532654310.923479300546-0.1383299903411.3449488169175.80797577857.774665469817.69512647418
643.286299855481.457342663074.89722569554-1.07994610003-0.2033364590033.573391206010.3180654035650.461023236775-1.087867650470.01382338627680.834425097554-0.256541701797-0.346946640062-0.639165101375-0.3969708164561.173271012270.05999900136960.09261824898911.942902342240.160522011982.445104010213.3494786052829.37559816421.35743806008
652.89066133569-0.4927194303831.974767981543.209152780430.7142564188362.056231643810.6907037199681.59228891327-0.157637737819-0.435386611001-0.2669973872820.364259780832-0.0206763870951-0.137682411703-0.387486916281.49054484280.1469900192760.01140953801242.380041963540.2870721340072.09784841819-0.13321464304926.7426767877-5.1956825277
661.135678179452.18171531174-0.197428429398.39680589789-0.1967442176692.36326770751-0.3504546470090.156401326627-0.360855908083-0.1065558041810.934803563529-0.776756575478-0.0350879637177-0.11450611793-0.4955032412851.222029597810.1706571899580.1047890151651.81690538440.09534628230991.9617374325426.640714031233.717755532911.537941529
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 301 through 309 )AA301 - 3091 - 9
22chain 'A' and (resid 310 through 315 )AA310 - 31510 - 15
33chain 'A' and (resid 316 through 368 )AA316 - 36816 - 68
44chain 'A' and (resid 369 through 376 )AA369 - 37669 - 76
55chain 'A' and (resid 377 through 385 )AA377 - 38577 - 85
66chain 'A' and (resid 386 through 412 )AA386 - 41286 - 112
77chain 'B' and (resid 301 through 309 )BB301 - 3091 - 9
88chain 'B' and (resid 310 through 320 )BB310 - 32010 - 20
99chain 'B' and (resid 321 through 328 )BB321 - 32821 - 28
1010chain 'B' and (resid 329 through 337 )BB329 - 33729 - 37
1111chain 'B' and (resid 338 through 368 )BB338 - 36838 - 68
1212chain 'B' and (resid 369 through 377 )BB369 - 37769 - 77
1313chain 'B' and (resid 378 through 385 )BB378 - 38578 - 85
1414chain 'B' and (resid 386 through 392 )BB386 - 39286 - 92
1515chain 'B' and (resid 393 through 412 )BB393 - 41293 - 112
1616chain 'C' and (resid 31 through 59 )CC31 - 591 - 29
1717chain 'C' and (resid 60 through 70 )CC60 - 7030 - 40
1818chain 'C' and (resid 71 through 80 )CC71 - 8041 - 50
1919chain 'C' and (resid 81 through 94 )CC81 - 9451 - 64
2020chain 'C' and (resid 95 through 107 )CC95 - 10765 - 77
2121chain 'D' and (resid 45 through 58 )DD45 - 581 - 14
2222chain 'D' and (resid 59 through 65 )DD59 - 6515 - 21
2323chain 'D' and (resid 66 through 81 )DD66 - 8122 - 37
2424chain 'D' and (resid 82 through 91 )DD82 - 9138 - 47
2525chain 'D' and (resid 92 through 113 )DD92 - 11348 - 69
2626chain 'D' and (resid 114 through 123 )DD114 - 12370 - 79
2727chain 'D' and (resid 124 through 130 )DD124 - 13080 - 86
2828chain 'D' and (resid 131 through 138 )DD131 - 13887 - 94
2929chain 'D' and (resid 139 through 149 )DD139 - 14995 - 105
3030chain 'E' and (resid 30 through 203 )EE30 - 2031 - 142
3131chain 'E' and (resid 204 through 241 )EE204 - 241143 - 180
3232chain 'E' and (resid 242 through 315 )EE242 - 315181 - 254
3333chain 'E' and (resid 316 through 359 )EE316 - 359255 - 298
3434chain 'F' and (resid 301 through 309 )FF301 - 3091 - 9
3535chain 'F' and (resid 310 through 315 )FF310 - 31510 - 15
3636chain 'F' and (resid 316 through 356 )FF316 - 35616 - 56
3737chain 'F' and (resid 357 through 376 )FF357 - 37657 - 76
3838chain 'F' and (resid 377 through 392 )FF377 - 39277 - 92
3939chain 'F' and (resid 393 through 401 )FF393 - 40193 - 101
4040chain 'F' and (resid 402 through 412 )FF402 - 412102 - 112
4141chain 'G' and (resid 301 through 308 )GG301 - 3081 - 8
4242chain 'G' and (resid 309 through 315 )GG309 - 3159 - 15
4343chain 'G' and (resid 316 through 356 )GG316 - 35616 - 56
4444chain 'G' and (resid 357 through 376 )GG357 - 37657 - 76
4545chain 'G' and (resid 377 through 385 )GG377 - 38577 - 85
4646chain 'G' and (resid 386 through 401 )GG386 - 40186 - 101
4747chain 'G' and (resid 402 through 412 )GG402 - 412102 - 112
4848chain 'H' and (resid 31 through 59 )HH31 - 591 - 29
4949chain 'H' and (resid 60 through 80 )HH60 - 8030 - 50
5050chain 'H' and (resid 81 through 94 )HH81 - 9451 - 62
5151chain 'H' and (resid 95 through 107 )HH95 - 10763 - 75
5252chain 'I' and (resid 45 through 58 )II45 - 581 - 14
5353chain 'I' and (resid 59 through 65 )II59 - 6515 - 21
5454chain 'I' and (resid 66 through 73 )II66 - 7322 - 29
5555chain 'I' and (resid 74 through 81 )II74 - 8130 - 37
5656chain 'I' and (resid 82 through 91 )II82 - 9138 - 47
5757chain 'I' and (resid 92 through 103 )II92 - 10348 - 59
5858chain 'I' and (resid 104 through 108 )II104 - 10860 - 64
5959chain 'I' and (resid 109 through 118 )II109 - 11865 - 74
6060chain 'I' and (resid 119 through 123 )II119 - 12375 - 79
6161chain 'I' and (resid 124 through 130 )II124 - 13080 - 86
6262chain 'I' and (resid 131 through 138 )II131 - 13887 - 94
6363chain 'I' and (resid 139 through 149 )II139 - 14995 - 105
6464chain 'J' and (resid 31 through 91 )JJ31 - 911 - 52
6565chain 'J' and (resid 92 through 233 )JJ92 - 23353 - 174
6666chain 'J' and (resid 234 through 359 )JJ234 - 359175 - 300

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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