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- PDB-8ym5: Structure of Caspase-8/cFLIP death effector domain assembly -

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基本情報

登録情報
データベース: PDB / ID: 8ym5
タイトルStructure of Caspase-8/cFLIP death effector domain assembly
要素
  • CASP8 and FADD-like apoptosis regulator subunit p43
  • Caspase-8
キーワードAPOPTOSIS / FADD / Caspase-8 / cFLIP / death effector domain
機能・相同性
機能・相同性情報


negative regulation of myoblast fusion / skeletal myofibril assembly / caspase-8 / death effector domain binding / FasL/ CD95L signaling / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation ...negative regulation of myoblast fusion / skeletal myofibril assembly / caspase-8 / death effector domain binding / FasL/ CD95L signaling / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / TRAIL-activated apoptotic signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / TRIF-mediated programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / regulation of necroptotic process / Caspase activation via Death Receptors in the presence of ligand / positive regulation of extracellular matrix organization / positive regulation of macrophage differentiation / self proteolysis / positive regulation of glomerular mesangial cell proliferation / response to cobalt ion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / skeletal muscle tissue regeneration / CLEC7A/inflammasome pathway / negative regulation of necroptotic process / response to anesthetic / negative regulation of hepatocyte apoptotic process / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of hepatocyte proliferation / natural killer cell activation / negative regulation of cellular response to transforming growth factor beta stimulus / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / negative regulation of cardiac muscle cell apoptotic process / execution phase of apoptosis / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / response to testosterone / : / B cell activation / positive regulation of proteolysis / macrophage differentiation / response to tumor necrosis factor / extrinsic apoptotic signaling pathway via death domain receptors / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cellular response to nitric oxide / cysteine-type peptidase activity / cellular response to epidermal growth factor stimulus / cellular response to dexamethasone stimulus / regulation of cytokine production / protein maturation / proteolysis involved in protein catabolic process / T cell activation / enzyme activator activity / positive regulation of interleukin-1 beta production / negative regulation of extrinsic apoptotic signaling pathway / Regulation of NF-kappa B signaling / apoptotic signaling pathway / cellular response to estradiol stimulus / Regulation of TNFR1 signaling / wound healing / NOD1/2 Signaling Pathway / protein processing / positive regulation of neuron projection development / Regulation of necroptotic cell death / cellular response to insulin stimulus / cellular response to mechanical stimulus / positive regulation of NF-kappaB transcription factor activity / positive regulation of neuron apoptotic process / response to estradiol / lamellipodium / peptidase activity / heart development / cell body / protease binding / scaffold protein binding / angiogenesis / cellular response to hypoxia / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / cytoskeleton / positive regulation of ERK1 and ERK2 cascade
類似検索 - 分子機能
Caspase-8 / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. ...Caspase-8 / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
類似検索 - ドメイン・相同性
CASP8 and FADD-like apoptosis regulator / Caspase-8
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.09 Å
データ登録者Lin, S.-C. / Yang, C.-Y.
資金援助 台湾, 1件
組織認可番号国
Other government 台湾
引用ジャーナル: Nat Commun / 年: 2024
タイトル: Reverse hierarchical DED assembly in the cFLIP-procaspase-8 and cFLIP-procaspase-8-FADD complexes.
著者: Chao-Yu Yang / Yi-Chun Tseng / Yi-Fan Tu / Bai-Jiun Kuo / Li-Chung Hsu / Chia-I Lien / You-Sheng Lin / Yin-Ting Wang / Yen-Chen Lu / Tsung-Wei Su / Yu-Chih Lo / Su-Chang Lin /
要旨: cFLIP, a master anti-apoptotic regulator, targets the FADD-induced DED complexes of procaspase-8 in death receptor and ripoptosome signaling pathways. Several tumor cells maintain relatively high ...cFLIP, a master anti-apoptotic regulator, targets the FADD-induced DED complexes of procaspase-8 in death receptor and ripoptosome signaling pathways. Several tumor cells maintain relatively high levels of cFLIP in achieving their immortality. However, understanding the three-dimensional regulatory mechanism initiated or mediated by elevated levels of cFLIP has been limited by the absence of the atomic coordinates for cFLIP-induced DED complexes. Here we report the crystal plus cryo-EM structures to uncover an unconventional mechanism where cFLIP and procaspase-8 autonomously form a binary tandem DED complex, independent of FADD. This complex gains the ability to recruit FADD, thereby allosterically modulating cFLIP assembly and partially activating caspase-8 for RIPK1 cleavage. Our structure-guided mutagenesis experiments provide critical insights into these regulatory mechanisms, elucidating the resistance to apoptosis and necroptosis in achieving immortality. Finally, this research offers a unified model for the intricate bidirectional hierarchy-based processes using multiprotein helical assembly to govern cell fate decisions.
履歴
登録2024年3月8日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年10月30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
C: Caspase-8
B: Caspase-8
D: Caspase-8
H: CASP8 and FADD-like apoptosis regulator subunit p43
G: CASP8 and FADD-like apoptosis regulator subunit p43
F: CASP8 and FADD-like apoptosis regulator subunit p43
K: CASP8 and FADD-like apoptosis regulator subunit p43
I: CASP8 and FADD-like apoptosis regulator subunit p43
J: CASP8 and FADD-like apoptosis regulator subunit p43
A: Caspase-8


分子量 (理論値)分子数
合計 (水以外)217,52510
ポリマ－217,52510
非ポリマー00
水8,431468
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration, light scattering
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)82.147, 166.224, 179.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
Caspase-8 / CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3- ...CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3-like protease / FADD-like ICE / FLICE / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH


分子量: 22339.715 Da / 分子数: 4 / 変異: F122G, L123G / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CASP8, MCH5 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q14790, caspase-8
#2: タンパク質
CASP8 and FADD-like apoptosis regulator subunit p43 / cFLIP


分子量: 21361.031 Da / 分子数: 6 / 変異: H7G / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CFLAR, CASH, CASP8AP1, CLARP, MRIT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O15519
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 468 / 由来タイプ: 天然 / 式: H2O
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: 2.82 Å3/Da / 溶媒含有率: 56.32 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1 M MES pH 6.5, 0.08 M sodium chloride, 0.2 M Potassium Thiocyanate, 10 % PEG 4000, 0.01 M TCEP

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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: NSRRC / ビームライン: BL13B1 / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年6月5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: 2.09→50 Å / Num. obs: 143558 / % possible obs: 98.6 % / 冗長度: 3.7 % / Biso Wilson estimate: 30.46 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.459
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.09-2.163.50.279137070.9360.9830.1710.3281.07195.1
2.16-2.253.70.23142260.9590.9890.1390.2691.08399.2
2.25-2.353.90.189143820.9760.9940.110.2191.09199.5
2.35-2.483.90.144144000.9850.9960.0850.1681.0799.6
2.48-2.633.90.111143870.9910.9980.0650.1291.08199.6
2.63-2.843.80.083144210.9940.9990.0490.0961.0999.5
2.84-3.123.80.061144260.9960.9990.0370.0721.06899.5
3.12-3.573.80.046145060.9970.9990.0280.0541.06699.2
3.57-4.53.60.041144820.9960.9990.0250.0481.05398.6
4.5-503.60.032146210.9980.9990.020.0381.05296.4

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487: ???)精密化
HKL-2000データスケーリング
HKL-2000データ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.09→32.88 Å / SU ML: 0.22 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.32 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2313 7322 5.11 %
Rwork0.1937 --
obs0.1957 143410 98.49 %
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
精密化ステップサイクル: LAST / 解像度: 2.09→32.88 Å
タンパク質核酸リガンド溶媒全体
原子数14421 0 0 468 14889
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00814564
X-RAY DIFFRACTIONf_angle_d1.14319496
X-RAY DIFFRACTIONf_dihedral_angle_d6.081926
X-RAY DIFFRACTIONf_chiral_restr0.0512262
X-RAY DIFFRACTIONf_plane_restr0.0082479
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.110.34082260.26674052X-RAY DIFFRACTION89
2.11-2.140.24492200.23974338X-RAY DIFFRACTION96
2.14-2.160.27282270.23324470X-RAY DIFFRACTION97
2.16-2.190.2672280.2184480X-RAY DIFFRACTION99
2.19-2.220.26132410.21314517X-RAY DIFFRACTION99
2.22-2.250.27422530.21414528X-RAY DIFFRACTION100
2.25-2.280.24732450.19954571X-RAY DIFFRACTION99
2.28-2.320.23862410.19544525X-RAY DIFFRACTION100
2.32-2.350.24192300.20264556X-RAY DIFFRACTION99
2.35-2.390.25072420.19714548X-RAY DIFFRACTION100
2.39-2.430.23842390.19664558X-RAY DIFFRACTION99
2.43-2.480.25982430.20764577X-RAY DIFFRACTION100
2.48-2.530.22292370.20294502X-RAY DIFFRACTION100
2.53-2.580.24052810.20454545X-RAY DIFFRACTION99
2.58-2.630.2492730.20794540X-RAY DIFFRACTION100
2.63-2.690.23092750.2014531X-RAY DIFFRACTION100
2.69-2.760.27262500.20614544X-RAY DIFFRACTION99
2.76-2.840.22222670.20164563X-RAY DIFFRACTION99
2.84-2.920.26232370.20994558X-RAY DIFFRACTION99
2.92-3.010.25952470.21134565X-RAY DIFFRACTION100
3.01-3.120.24672340.21854593X-RAY DIFFRACTION99
3.12-3.250.26882250.20644614X-RAY DIFFRACTION99
3.25-3.390.22552420.20474591X-RAY DIFFRACTION99
3.39-3.570.23742510.19784578X-RAY DIFFRACTION99
3.57-3.80.212570.18064570X-RAY DIFFRACTION99
3.8-4.090.20232490.16564579X-RAY DIFFRACTION98
4.09-4.50.18752370.15634596X-RAY DIFFRACTION98
4.5-5.150.21052640.16424596X-RAY DIFFRACTION98
5.15-6.480.23932210.20214612X-RAY DIFFRACTION97
6.48-32.880.20822400.18674691X-RAY DIFFRACTION95
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)
17.0357-0.12511.28042.63570.1583.81860.1129-0.4690.1710.0388-0.06890.3034-0.0097-0.5494-0.05170.18410.02850.01180.16030.0190.1887.1366133.685482.0272
22.19811.2314-0.28531.6272-0.78062.4304-0.03280.20790.0365-0.15160.05260.03870.00880.0407-0.0190.18510.01550.00040.1898-0.00480.17615.5371131.116376.796
34.9636-1.55470.4962.441-0.39041.4929-0.0869-0.4003-0.59450.13740.22570.28960.3429-0.1063-0.12770.2527-0.0241-0.00980.29760.02160.208112.76122.489890.0558
41.74121.27680.5296.28721.76423.01140.1186-0.29470.16520.4786-0.20390.1176-0.258-0.13490.04470.3094-0.0346-0.01750.3028-0.05680.300625.3423141.505194.1979
59.04972.1626-1.28566.3861-1.11174.1413-0.30770.61640.9448-0.46360.19230.0328-0.6740.11930.15290.5701-0.0279-0.01680.44250.00310.467829.6661152.316987.2497
63.0897-0.345-0.54542.0697-1.59784.90180.0658-0.2750.09620.2515-0.173-0.1798-0.25540.35520.0860.2718-0.0449-0.03140.2664-0.03910.266433.094140.992190.3297
77.6202-2.0416-1.28858.97821.67657.55150.0917-0.3959-0.9340.8491-0.0788-0.13960.98630.9750.00990.28760.0379-0.0660.4181-0.00060.321331.8699129.169398.1031
81.60691.70250.65225.7601-0.27462.24550.05370.05890.040.2601-0.0412-0.21620.06070.11370.00310.1394-0.0006-0.00370.19030.02660.229331.14142.078866.6928
92.5836-1.04060.09672.1868-1.47222.64990.01460.6230.0138-0.1784-0.14350.0396-0.17950.23480.06390.1786-0.0317-0.00230.29810.01590.232535.4201148.698160.4785
107.45752.5878-0.29714.83760.71292.23180.1677-0.2852-0.51660.4078-0.1982-0.6649-0.04190.98650.0480.2457-0.0232-0.02620.44170.05510.264543.1926141.707474.2758
115.2522-1.4064-1.06583.24660.61183.7442-0.07110.02230.39280.4643-0.1123-0.3718-0.44020.62160.13370.3186-0.0987-0.09340.32260.02630.345841.9346157.053172.1156
122.4881-1.6291.26628.4407-2.50985.9906-0.4201-0.69450.46921.37290.26080.403-0.2576-0.4192-0.06350.68670.07450.11470.5741-0.13230.489225.9941166.121982.1392
133.15160.20220.9883.79480.18654.377-0.16440.05730.38610.7140.2092-0.219-0.63260.0640.05070.4927-0.0412-0.08210.3689-0.02770.440134.079168.854974.6652
148.03523.4263.94474.97532.11631.9855-0.9860.65191.6617-0.86530.10090.6505-1.6458-0.3470.65760.55070.06810.02560.42560.09260.562-15.013158.510388.5893
153.5717-1.5718-0.82543.252-1.84892.2487-0.4217-0.41960.58380.39810.5322-0.319-0.35790.1788-0.03810.331-0.0236-0.010.2038-0.08080.4106-3.9991150.017297.592
164.14560.5995-1.57893.2570.27512.91140.0514-0.07480.0419-0.4564-0.127-0.2876-0.03670.21150.12620.24490.04130.06750.2956-0.02260.268-1.3485143.834588.3808
176.91972.51523.57422.89784.77167.922-0.27481.27460.743-0.81940.1389-0.4058-0.54251.37080.10660.33890.040.05680.43210.0520.3688-8.3271148.96685.3054
182.9539-0.0038-0.00623.4180.10793.28780.08680.30380.2102-0.0869-0.08840.13740.0375-0.08960.02160.26260.05040.03840.2212-0.01240.2622-16.6217148.592694.8904
194.3375-2.22680.41373.2402-3.20064.62730.2083-0.4854-0.17170.90430.02070.8974-0.1875-0.1474-0.11680.55320.02450.13360.5793-0.09730.4446-23.2425145.6398103.9801
206.14290.16292.36372.63771.30825.3228-0.0106-0.70030.22370.1417-0.00390.0631-0.05850.091-0.01440.2459-0.03920.03920.2763-0.02240.2497-2.895141.0283106.4763
216.09741.5394-2.57124.7692.45323.26440.1348-0.47540.1985-0.3729-0.0837-0.4962-0.43270.50530.03950.49630.00030.00810.857-0.06360.546113.8719140.9694103.027
222.8587-0.5631-1.33913.09180.46736.5697-0.026-0.5732-0.03820.13170.009-0.14040.22760.65590.01860.239-0.0182-0.00270.3499-0.01270.20834.3232134.3368105.7556
239.15064.88482.66437.17581.96613.57360.459-0.86150.10440.1985-0.49330.11340.3484-0.3518-0.01520.3057-0.03520.04910.2717-0.00490.2455-8.5972131.8031112.5864
249.63040.7629-0.94158.0216-2.56932.4616-0.24841.2623-0.3797-1.23910.2545-1.1919-0.27940.474-0.23420.6374-0.00190.14510.76760.14130.62725.0384168.198719.047
253.4343-3.36161.7044.3131-0.6272.0475-0.1289-1.2037-0.02030.37540.0921-0.47650.2729-0.09230.02850.3905-0.09350.00260.52850.20470.550912.7808167.224827.9297
260.67310.3676-0.62120.2467-0.10021.61810.20250.6069-0.6445-0.2853-0.00180.15850.1799-0.8448-0.05120.51560.019-0.03190.60530.16560.69576.2825169.787516.908
275.8219-0.76530.59379.0653-2.2594.29690.32380.9244-0.3328-0.5249-0.26320.23330.52630.3447-0.13210.5696-0.08480.01640.57690.05860.457416.0586169.298314.2605
283.1109-1.4999-1.32412.9663-1.42849.3250.340.30850.25-0.5518-0.00030.5235-0.1295-0.5742-0.35930.3526-0.0952-0.02230.440.22130.509616.9243178.018320.9824
294.72362.9310.58593.7771-1.50664.53780.0189-0.1985-0.01480.5608-0.3508-0.113-0.39650.66110.16120.3956-0.0926-0.03140.450.17150.494524.5124174.307129.3765
301.79240.7355-0.71851.9277-0.78461.52150.2020.0760.2704-0.039-0.1444-0.0764-0.44630.3866-0.00420.4557-0.1067-0.0220.44390.17430.592913.1326180.84129.3299
311.7577-0.00531.91581.3861-0.10476.4807-0.04620.21250.1984-0.00650.44920.2573-0.6802-0.8806-0.38320.313-0.116-0.03060.37560.19740.5187-4.1057163.605439.5855
325.26932.4177-0.48671.57560.31730.8435-0.02690.9745-0.0404-0.005-0.0476-0.18470.3182-0.17080.10260.4244-0.0672-0.0340.48580.07920.3977-4.2812159.538332.8141
332.93641.37730.62290.67910.63362.8882-0.03850.31240.3481-0.30510.10170.1688-0.0982-0.2963-0.02590.322-0.0752-0.06890.38220.20320.4542-3.7177171.072428.3805
344.2633-1.18813.36882.0727-1.25598.99640.0457-0.27980.26690.1244-0.357-0.2287-0.0337-0.58630.36050.3002-0.03890.02780.32940.06570.4279-6.0124173.71341.717
350.1727-0.4370.34153.3235-4.47796.56130.10670.0350.78810.50020.2550.2567-0.7204-0.147-0.17970.4645-0.00860.02680.23130.1440.6764-0.3307183.240538.4917
367.1818-0.81284.30836.59910.02832.63340.06510.7481.0402-1.78090.5341-0.2939-0.4786-0.1427-0.44220.7809-0.09210.18131.10990.30960.5957-5.0685167.11056.0653
379.27023.99670.02956.38081.54343.68590.1358-0.49390.44530.7767-0.0672-0.48860.31210.68220.09760.33470.06270.00090.420.07890.3675-6.7449155.757415.5448
380.088-0.1942-0.2281.068-0.37992.16940.11011.1272-0.4442-1.1257-0.0366-0.28530.2484-0.5969-0.20560.6569-0.04780.07770.6275-0.060.402-12.8235150.17785.7318
392.2784-2.05461.88476.1155-1.42877.4045-0.25932.04870.2409-1.3745-0.0994-1.1036-0.3390.68840.16210.80850.00160.18340.82580.05930.4421-9.3628158.83381.7862
404.07320.5620.76183.773-0.50786.61480.27980.5653-0.3576-0.5332-0.1720.61480.5825-0.3920.01680.39160.0332-0.07950.34330.05540.3987-16.4652163.18449.7575
413.8898-2.49782.15486.1285-0.60774.397-0.1838-0.0449-0.14610.214-0.0268-0.5659-0.179-0.11480.22430.3205-0.0346-0.04810.39780.20650.4263-9.2097169.167817.2677
421.70041.3963-0.0474.1196-1.02180.58880.1473-0.05490.52210.33730.04240.8203-0.2449-0.3856-0.20190.38910.0318-0.01310.36580.03450.4898-21.9022167.562115.825
439.1068-0.99375.93234.0423-1.29734.1430.11340.06290.6319-0.0596-0.1397-0.2430.23190.22060.00770.28570.00670.02340.31930.02640.3233-15.5749151.762723.49
444.77330.548-0.01251.94691.61385.17870.31290.4579-0.1758-0.72-0.1740.3960.85390.1433-0.30260.5070.1264-0.13560.5284-0.02450.322-7.4073139.873228.6269
453.1378-0.85231.45382.21590.14423.20530.16290.3604-0.4937-0.2107-0.1552-0.18570.52240.92140.05070.46880.12160.00420.4409-0.01940.2911-9.152139.851619.0802
462.4829-2.0505-2.37973.89691.42282.4919-0.14450.8075-0.5275-0.2899-0.02290.59850.5798-0.82230.01070.4507-0.0624-0.05240.4248-0.07090.3145-21.1718139.887218.0929
474.56163.85214.27895.22345.11998.40470.16590.0992-0.54020.33130.05370.00660.84560.1536-0.19750.41310.0112-0.03270.2714-0.00540.2857-17.3674141.474231.658
489.1485-0.98965.69133.3817-0.71854.11560.052-0.37721.16550.1904-0.18460.4329-0.2597-1.03660.02470.2743-0.05710.02820.33090.01470.3382-24.9079149.680928.5791
494.5668-1.21580.48174.72530.26363.875-0.17890.28950.018-0.2720.3484-0.0709-0.770.4706-0.18370.4331-0.0906-0.03560.5405-0.0850.2744-6.41134.4726-1.0614
502.9365-0.213-0.79152.23741.08543.3575-0.15360.5541-0.021-0.18440.044-0.0923-0.32550.03690.08110.2802-0.0023-0.05230.414-0.10110.2196-13.7282131.4299-0.7967
514.2036-2.4932-1.05313.04590.38881.34390.0178-0.2169-0.37740.1117-0.0730.4177-0.0087-0.57840.15410.4438-0.1025-0.04390.702-0.15410.4944-18.7131122.90315.5851
524.5365-0.38861.94671.37540.23041.88520.08340.106-0.1527-0.02530.03690.0735-0.12460.1254-0.1030.37530.0528-0.01930.6387-0.13040.35157.9443127.407810.1912
533.23020.46720.5082.61840.10333.66150.2879-0.5029-0.96090.19870.10190.19130.51910.0898-0.18940.34840.0421-0.01350.53860.03740.51994.9842116.958514.2181
542.18550.1594-0.29295.7066-1.90852.42220.02810.04760.21660.1811-0.0584-0.0797-0.18690.1324-0.00440.2536-0.0714-0.00350.44020.07540.3073-10.7607153.736251.4585
551.995-0.1581-0.25932.3772-0.64113.04490.12880.02160.18790.0605-0.00280.3042-0.3694-0.2839-0.10320.2629-0.0210.02160.27410.03480.2963-20.5251156.346653.5012
562.5765-1.66830.15242.60990.37422.8696-0.0648-0.1204-0.0110.03990.1396-0.08210.12270.0935-0.04650.174-0.0272-0.0060.2570.04370.2046-8.8849137.870366.9306
576.34320.2364-1.86535.65262.87132.2107-0.08920.4141-0.9052-0.20270.12120.1270.30010.4775-0.11270.39240.0904-0.01570.7244-0.1440.361121.7766124.448122.9931
587.17022.00990.57314.8722-0.55492.95630.0458-0.4852-0.07690.0627-0.1175-0.025-0.67590.56070.07110.36210.0172-0.00870.4797-0.07630.23527.1902139.009927.4784
592.3027-0.35410.68362.50750.11113.4426-0.0610.3611-0.0373-0.1417-0.005-0.090.05570.30170.01620.27310.00130.02820.4962-0.11770.26128.2358128.370826.3752
602.17022.629-0.32345.3376-0.88310.8707-0.14940.4683-0.94570.09860.0849-1.3140.09680.4592-0.0010.44740.06220.05280.6332-0.11370.559537.4563123.935231.863
612.2787-2.127-1.34224.89162.61142.27940.03450.19470.1069-0.1280.0633-0.1135-0.10390.0244-0.04170.2715-0.06050.00120.50390.01870.255833.6109150.117938.3517
625.11841.5557-1.38546.3392-0.63387.5401-0.20940.88931.0572-0.5961-0.11090.7087-1.1488-0.52850.31120.5293-0.055-0.04830.58940.06290.414630.2303152.448631.4723
632.3935-0.0724-0.90181.91691.11693.9949-0.22410.13460.1828-0.29110.3704-0.4816-0.30890.6983-0.12770.2969-0.12430.05250.5704-0.04010.311442.838148.803839.236
643.8653-0.7333-0.02753.0961-0.14362.51230.22440.4849-0.499-0.4308-0.16290.37990.221-0.0269-0.03070.40110.0875-0.11070.342-0.09910.3394-1.5437126.539642.3707
651.9307-0.00340.53982.10130.95293.22870.14670.2958-0.0483-0.2046-0.1064-0.08910.06180.2151-0.01330.27980.0706-0.01180.2985-0.03280.199919.4411127.601553.6774
664.5044-1.8984-0.08333.60690.48532.5115-0.1859-0.18240.11840.14550.0753-0.0645-0.08270.40840.0620.2935-0.0823-0.0540.22750.09560.339928.087166.547650.8312
672.997-0.17231.58651.9787-0.322.10840.0147-0.0291-0.07150.1938-0.11820.0673-0.11680.17720.08270.3666-0.0899-0.02070.3130.06330.420615.4395169.380644.7279
682.2646-0.55960.45922.03460.02583.7494-0.11950.41280.2457-0.3142-0.0933-0.0749-0.2165-0.0810.07950.3844-0.125-0.05550.30770.13780.547827.2657174.066144.6068
691.3097-1.218-0.06611.9139-0.09040.1814-0.3470.13610.99430.21540.0996-0.5353-0.67180.29320.20210.5596-0.1201-0.19480.43330.07240.730332.2156180.584455.0571
706.77740.0815-0.25622.5403-1.26824.2107-0.9201-0.96540.27810.52540.69910.1930.048-0.57030.15050.65930.16770.03350.54250.00620.499.4286174.937363.5817
717.09834.77250.44173.22520.50072.4004-0.6532-0.2077-1.1358-0.1066-0.3887-0.08540.45-0.3771.16520.5936-0.17150.00710.98340.12020.73070.0494166.874158.462
726.291-0.77862.71641.58361.01045.0365-0.2039-0.6360.2867-0.6873-0.0681-0.0025-0.0223-0.23640.17190.46190.0392-0.02280.25730.04330.41825.304177.611454.9423
733.00380.04410.7141.9606-0.40784.4705-0.5435-1.24560.73530.62470.4546-0.0868-0.6573-0.2008-0.14460.81130.2756-0.06780.6766-0.18510.6688.6383184.820366.2932
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'C' and (resid 26 through 68 )
3X-RAY DIFFRACTION3chain 'C' and (resid 69 through 99 )
4X-RAY DIFFRACTION4chain 'C' and (resid 100 through 124 )
5X-RAY DIFFRACTION5chain 'C' and (resid 125 through 138 )
6X-RAY DIFFRACTION6chain 'C' and (resid 139 through 168 )
7X-RAY DIFFRACTION7chain 'C' and (resid 169 through 184 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 25 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 68 )
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 91 )
11X-RAY DIFFRACTION11chain 'B' and (resid 92 through 111 )
12X-RAY DIFFRACTION12chain 'B' and (resid 112 through 123 )
13X-RAY DIFFRACTION13chain 'B' and (resid 124 through 182 )
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 13 )
15X-RAY DIFFRACTION15chain 'D' and (resid 14 through 25 )
16X-RAY DIFFRACTION16chain 'D' and (resid 26 through 40 )
17X-RAY DIFFRACTION17chain 'D' and (resid 41 through 50 )
18X-RAY DIFFRACTION18chain 'D' and (resid 51 through 79 )
19X-RAY DIFFRACTION19chain 'D' and (resid 80 through 91 )
20X-RAY DIFFRACTION20chain 'D' and (resid 92 through 123 )
21X-RAY DIFFRACTION21chain 'D' and (resid 124 through 138 )
22X-RAY DIFFRACTION22chain 'D' and (resid 139 through 168 )
23X-RAY DIFFRACTION23chain 'D' and (resid 169 through 185 )
24X-RAY DIFFRACTION24chain 'H' and (resid 1 through 12 )
25X-RAY DIFFRACTION25chain 'H' and (resid 13 through 24 )
26X-RAY DIFFRACTION26chain 'H' and (resid 25 through 36 )
27X-RAY DIFFRACTION27chain 'H' and (resid 37 through 46 )
28X-RAY DIFFRACTION28chain 'H' and (resid 47 through 61 )
29X-RAY DIFFRACTION29chain 'H' and (resid 62 through 72 )
30X-RAY DIFFRACTION30chain 'H' and (resid 73 through 105 )
31X-RAY DIFFRACTION31chain 'H' and (resid 106 through 118 )
32X-RAY DIFFRACTION32chain 'H' and (resid 119 through 130 )
33X-RAY DIFFRACTION33chain 'H' and (resid 131 through 149 )
34X-RAY DIFFRACTION34chain 'H' and (resid 150 through 161 )
35X-RAY DIFFRACTION35chain 'H' and (resid 162 through 175 )
36X-RAY DIFFRACTION36chain 'G' and (resid 1 through 12 )
37X-RAY DIFFRACTION37chain 'G' and (resid 13 through 24 )
38X-RAY DIFFRACTION38chain 'G' and (resid 25 through 36 )
39X-RAY DIFFRACTION39chain 'G' and (resid 37 through 46 )
40X-RAY DIFFRACTION40chain 'G' and (resid 47 through 61 )
41X-RAY DIFFRACTION41chain 'G' and (resid 62 through 72 )
42X-RAY DIFFRACTION42chain 'G' and (resid 73 through 91 )
43X-RAY DIFFRACTION43chain 'G' and (resid 92 through 105 )
44X-RAY DIFFRACTION44chain 'G' and (resid 106 through 118 )
45X-RAY DIFFRACTION45chain 'G' and (resid 119 through 140 )
46X-RAY DIFFRACTION46chain 'G' and (resid 141 through 149 )
47X-RAY DIFFRACTION47chain 'G' and (resid 150 through 161 )
48X-RAY DIFFRACTION48chain 'G' and (resid 162 through 175 )
49X-RAY DIFFRACTION49chain 'F' and (resid 2 through 36 )
50X-RAY DIFFRACTION50chain 'F' and (resid 37 through 72 )
51X-RAY DIFFRACTION51chain 'F' and (resid 73 through 91 )
52X-RAY DIFFRACTION52chain 'F' and (resid 92 through 140 )
53X-RAY DIFFRACTION53chain 'F' and (resid 141 through 175 )
54X-RAY DIFFRACTION54chain 'K' and (resid 0 through 36 )
55X-RAY DIFFRACTION55chain 'K' and (resid 37 through 91 )
56X-RAY DIFFRACTION56chain 'K' and (resid 92 through 175 )
57X-RAY DIFFRACTION57chain 'I' and (resid -1 through 12 )
58X-RAY DIFFRACTION58chain 'I' and (resid 13 through 36 )
59X-RAY DIFFRACTION59chain 'I' and (resid 37 through 72 )
60X-RAY DIFFRACTION60chain 'I' and (resid 73 through 91 )
61X-RAY DIFFRACTION61chain 'I' and (resid 92 through 119 )
62X-RAY DIFFRACTION62chain 'I' and (resid 120 through 140 )
63X-RAY DIFFRACTION63chain 'I' and (resid 141 through 175 )
64X-RAY DIFFRACTION64chain 'J' and (resid 1 through 91 )
65X-RAY DIFFRACTION65chain 'J' and (resid 92 through 175 )
66X-RAY DIFFRACTION66chain 'A' and (resid 2 through 25 )
67X-RAY DIFFRACTION67chain 'A' and (resid 26 through 40 )
68X-RAY DIFFRACTION68chain 'A' and (resid 41 through 68 )
69X-RAY DIFFRACTION69chain 'A' and (resid 69 through 99 )
70X-RAY DIFFRACTION70chain 'A' and (resid 100 through 127 )
71X-RAY DIFFRACTION71chain 'A' and (resid 128 through 138 )
72X-RAY DIFFRACTION72chain 'A' and (resid 139 through 157 )
73X-RAY DIFFRACTION73chain 'A' and (resid 158 through 180 )

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万見について

-
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