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- PDB-8ym6: 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: 8ym6
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 subunit p10
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 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / 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 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / 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 / Microbial modulation of RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / 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 / positive regulation of glomerular mesangial cell proliferation / self proteolysis / response to cobalt ion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / : / skeletal muscle tissue regeneration / death-inducing signaling complex / negative regulation of hepatocyte apoptotic process / CLEC7A/inflammasome pathway / : / negative regulation of necroptotic process / : / regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / tumor necrosis factor 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 / execution phase of apoptosis / negative regulation of cardiac muscle cell apoptotic process / 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 / protein maturation / : / response to tumor necrosis factor / extrinsic apoptotic signaling pathway via death domain receptors / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of reactive oxygen species biosynthetic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of canonical NF-kappaB signal transduction / skeletal muscle tissue development / keratinocyte differentiation / cysteine-type peptidase activity / extrinsic apoptotic signaling pathway / cellular response to epidermal growth factor stimulus / enzyme activator activity / cellular response to nitric oxide / cellular response to dexamethasone stimulus / regulation of cytokine production / erythrocyte differentiation / positive regulation of interleukin-1 beta production / T cell activation / proteolysis involved in protein catabolic process / apoptotic signaling pathway / Regulation of NF-kappa B signaling / negative regulation of extrinsic apoptotic signaling pathway / Regulation of TNFR1 signaling / cellular response to estradiol stimulus / wound healing / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / neuron differentiation / positive regulation of neuron projection development / cellular response to mechanical stimulus / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / lamellipodium / response to estradiol / peptidase activity / heart development / positive regulation of NF-kappaB transcription factor activity / cell body / scaffold protein binding / protease binding / angiogenesis / cellular response to hypoxia / positive regulation of canonical NF-kappaB signal transduction
類似検索 - 分子機能
Caspase-8 / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / 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-8 / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / 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: 3.3 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 subunit p10
B: Caspase-8 subunit p10
A: Caspase-8 subunit p10
D: Caspase-8 subunit p10
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
M: CASP8 and FADD-like apoptosis regulator subunit p43
O: CASP8 and FADD-like apoptosis regulator subunit p43
N: CASP8 and FADD-like apoptosis regulator subunit p43


分子量 (理論値)分子数
合計 (水以外)278,49313
ポリマ－278,49313
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 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)150.311, 158.640, 353.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
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 3 through 4 or resid 6...
d_2ens_1(chain "B" and (resid 3 through 4 or resid 6...
d_3ens_1(chain "C" and (resid 3 through 4 or resid 6...
d_4ens_1(chain "D" and (resid 3 through 4 or resid 6...
d_1ens_2(chain "F" and (resid 2 through 3 or resid 5...
d_2ens_2(chain "G" and (resid 2 through 3 or resid 5...
d_3ens_2(chain "H" and (resid 2 through 3 or resid 5...
d_4ens_2(chain "I" and (resid 2 through 3 or resid 5...
d_5ens_2(chain "J" and (resid 2 through 3 or resid 5...
d_6ens_2(chain "K" and (resid 2 through 3 or resid 5...
d_7ens_2(chain "M" and (resid 2 through 3 or resid 5...
d_8ens_2(chain "N" and (resid 2 through 3 or resid 5...
d_9ens_2(chain "O" and (resid 2 through 3 or resid 5...

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_1PHEPHESERSERAC3 - 43 - 4
d_12ens_1ASNASNGLNGLNAC6 - 466 - 46
d_13ens_1LEULEUGLUGLUAC48 - 8748 - 87
d_14ens_1GLUGLUGLYGLYAC89 - 9489 - 94
d_15ens_1ALAALASERSERAC96 - 11396 - 113
d_16ens_1SERSERLEULEUAC115 - 117115 - 117
d_17ens_1SERSERSERSERAC119 - 129119 - 129
d_18ens_1CYSCYSGLYGLYAC131 - 155131 - 155
d_19ens_1LEULEULEULEUAC157 - 160157 - 160
d_110ens_1ARGARGALAALAAC162 - 165162 - 165
d_111ens_1ILEILEASNASNAC167 - 168167 - 168
d_112ens_1SERSERGLUGLUAC170 - 180170 - 180
d_21ens_1PHEPHESERSERBB3 - 43 - 4
d_22ens_1ASNASNGLNGLNBB6 - 466 - 46
d_23ens_1LEULEUGLUGLUBB48 - 8748 - 87
d_24ens_1GLUGLUGLYGLYBB89 - 9489 - 94
d_25ens_1ALAALASERSERBB96 - 11396 - 113
d_26ens_1SERSERLEULEUBB115 - 117115 - 117
d_27ens_1SERSERSERSERBB119 - 129119 - 129
d_28ens_1CYSCYSGLYGLYBB131 - 155131 - 155
d_29ens_1LEULEULEULEUBB157 - 160157 - 160
d_210ens_1ARGARGALAALABB162 - 165162 - 165
d_211ens_1ILEILEASNASNBB167 - 168167 - 168
d_212ens_1SERSERGLUGLUBB170 - 180170 - 180
d_31ens_1PHEPHESERSERCA3 - 43 - 4
d_32ens_1ASNASNGLNGLNCA6 - 466 - 46
d_33ens_1LEULEUGLUGLUCA48 - 8748 - 87
d_34ens_1GLUGLUGLYGLYCA89 - 9489 - 94
d_35ens_1ALAALASERSERCA96 - 11396 - 113
d_36ens_1SERSERLEULEUCA115 - 117115 - 117
d_37ens_1SERSERSERSERCA119 - 129119 - 129
d_38ens_1CYSCYSGLYGLYCA131 - 155131 - 155
d_39ens_1LEULEULEULEUCA157 - 160157 - 160
d_310ens_1ARGARGALAALACA162 - 165162 - 165
d_311ens_1ILEILEASNASNCA167 - 168167 - 168
d_312ens_1SERSERGLUGLUCA170 - 180170 - 180
d_41ens_1PHEPHESERSERDD3 - 43 - 4
d_42ens_1ASNASNGLNGLNDD6 - 466 - 46
d_43ens_1LEULEUGLUGLUDD48 - 8748 - 87
d_44ens_1GLUGLUGLYGLYDD89 - 9489 - 94
d_45ens_1ALAALASERSERDD96 - 11396 - 113
d_46ens_1SERSERLEULEUDD115 - 117115 - 117
d_47ens_1SERSERSERSERDD119 - 129119 - 129
d_48ens_1CYSCYSGLYGLYDD131 - 155131 - 155
d_49ens_1LEULEULEULEUDD157 - 160157 - 160
d_410ens_1ARGARGALAALADD162 - 165162 - 165
d_411ens_1ILEILEASNASNDD167 - 168167 - 168
d_412ens_1SERSERGLUGLUDD170 - 180170 - 180
d_11ens_2SERSERALAALAFG2 - 35 - 6
d_12ens_2VALVALILEILEFG5 - 68 - 9
d_13ens_2GLNGLNVALVALFG8 - 2811 - 31
d_14ens_2PROPROVALVALFG34 - 3737 - 40
d_15ens_2ASPASPGLUGLUFG39 - 4642 - 49
d_16ens_2GLYGLYGLYGLYFG4851
d_17ens_2LEULEUVALVALFG50 - 6253 - 65
d_18ens_2ARGARGLEULEUFG64 - 6867 - 71
d_19ens_2ARGARGLEULEUFG70 - 7273 - 75
d_110ens_2METMETASPASPFG74 - 7577 - 78
d_111ens_2ALAALALEULEUFG78 - 8481 - 87
d_112ens_2ASNASNALAALAFG86 - 9889 - 101
d_113ens_2ILEILEGLYGLYFG100 - 101103 - 104
d_114ens_2ASPASPASPASPFG103 - 105106 - 108
d_115ens_2SERSERMETMETFG107 - 120110 - 123
d_116ens_2SERSERILEILEFG130 - 168133 - 171
d_117ens_2TYRTYRSERSERFG171 - 174174 - 177
d_21ens_2SERSERALAALAGF2 - 35 - 6
d_22ens_2VALVALILEILEGF5 - 68 - 9
d_23ens_2GLNGLNVALVALGF8 - 2811 - 31
d_24ens_2PROPROVALVALGF34 - 3737 - 40
d_25ens_2ASPASPGLUGLUGF39 - 4642 - 49
d_26ens_2GLYGLYGLYGLYGF4851
d_27ens_2LEULEUVALVALGF50 - 6253 - 65
d_28ens_2ARGARGLEULEUGF64 - 6867 - 71
d_29ens_2ARGARGLEULEUGF70 - 7273 - 75
d_210ens_2METMETASPASPGF74 - 7577 - 78
d_211ens_2ALAALALEULEUGF78 - 8481 - 87
d_212ens_2ASNASNALAALAGF86 - 9889 - 101
d_213ens_2ILEILEGLYGLYGF100 - 101103 - 104
d_214ens_2ASPASPASPASPGF103 - 105106 - 108
d_215ens_2SERSERMETMETGF107 - 120110 - 123
d_216ens_2SERSERILEILEGF130 - 168133 - 171
d_217ens_2TYRTYRSERSERGF171 - 174174 - 177
d_31ens_2SERSERALAALAHE2 - 35 - 6
d_32ens_2VALVALILEILEHE5 - 68 - 9
d_33ens_2GLNGLNVALVALHE8 - 2811 - 31
d_34ens_2PROPROVALVALHE34 - 3737 - 40
d_35ens_2ASPASPGLUGLUHE39 - 4642 - 49
d_36ens_2GLYGLYGLYGLYHE4851
d_37ens_2LEULEUVALVALHE50 - 6253 - 65
d_38ens_2ARGARGLEULEUHE64 - 6867 - 71
d_39ens_2ARGARGLEULEUHE70 - 7273 - 75
d_310ens_2METMETASPASPHE74 - 7577 - 78
d_311ens_2ALAALALEULEUHE78 - 8481 - 87
d_312ens_2ASNASNALAALAHE86 - 9889 - 101
d_313ens_2ILEILEGLYGLYHE100 - 101103 - 104
d_314ens_2ASPASPASPASPHE103 - 105106 - 108
d_315ens_2SERSERMETMETHE107 - 120110 - 123
d_316ens_2SERSERILEILEHE130 - 168133 - 171
d_317ens_2TYRTYRSERSERHE171 - 174174 - 177
d_41ens_2SERSERALAALAII2 - 35 - 6
d_42ens_2VALVALILEILEII5 - 68 - 9
d_43ens_2GLNGLNVALVALII8 - 2811 - 31
d_44ens_2PROPROVALVALII34 - 3737 - 40
d_45ens_2ASPASPGLUGLUII39 - 4642 - 49
d_46ens_2GLYGLYGLYGLYII4851
d_47ens_2LEULEUVALVALII50 - 6253 - 65
d_48ens_2ARGARGLEULEUII64 - 6867 - 71
d_49ens_2ARGARGLEULEUII70 - 7273 - 75
d_410ens_2METMETASPASPII74 - 7577 - 78
d_411ens_2ALAALALEULEUII78 - 8481 - 87
d_412ens_2ASNASNALAALAII86 - 9889 - 101
d_413ens_2ILEILEGLYGLYII100 - 101103 - 104
d_414ens_2ASPASPASPASPII103 - 105106 - 108
d_415ens_2SERSERMETMETII107 - 120110 - 123
d_416ens_2SERSERILEILEII130 - 168133 - 171
d_417ens_2TYRTYRSERSERII171 - 174174 - 177
d_51ens_2SERSERALAALAJJ2 - 35 - 6
d_52ens_2VALVALILEILEJJ5 - 68 - 9
d_53ens_2GLNGLNVALVALJJ8 - 2811 - 31
d_54ens_2PROPROVALVALJJ34 - 3737 - 40
d_55ens_2ASPASPGLUGLUJJ39 - 4642 - 49
d_56ens_2GLYGLYGLYGLYJJ4851
d_57ens_2LEULEUVALVALJJ50 - 6253 - 65
d_58ens_2ARGARGLEULEUJJ64 - 6867 - 71
d_59ens_2ARGARGLEULEUJJ70 - 7273 - 75
d_510ens_2METMETASPASPJJ74 - 7577 - 78
d_511ens_2ALAALALEULEUJJ78 - 8481 - 87
d_512ens_2ASNASNALAALAJJ86 - 9889 - 101
d_513ens_2ILEILEGLYGLYJJ100 - 101103 - 104
d_514ens_2ASPASPASPASPJJ103 - 105106 - 108
d_515ens_2SERSERMETMETJJ107 - 120110 - 123
d_516ens_2SERSERILEILEJJ130 - 168133 - 171
d_517ens_2TYRTYRSERSERJJ171 - 174174 - 177
d_61ens_2SERSERALAALAKH2 - 35 - 6
d_62ens_2VALVALILEILEKH5 - 68 - 9
d_63ens_2GLNGLNVALVALKH8 - 2811 - 31
d_64ens_2PROPROVALVALKH34 - 3737 - 40
d_65ens_2ASPASPGLUGLUKH39 - 4642 - 49
d_66ens_2GLYGLYGLYGLYKH4851
d_67ens_2LEULEUVALVALKH50 - 6253 - 65
d_68ens_2ARGARGLEULEUKH64 - 6867 - 71
d_69ens_2ARGARGLEULEUKH70 - 7273 - 75
d_610ens_2METMETASPASPKH74 - 7577 - 78
d_611ens_2ALAALALEULEUKH78 - 8481 - 87
d_612ens_2ASNASNALAALAKH86 - 9889 - 101
d_613ens_2ILEILEGLYGLYKH100 - 101103 - 104
d_614ens_2ASPASPASPASPKH103 - 105106 - 108
d_615ens_2SERSERMETMETKH107 - 120110 - 123
d_616ens_2SERSERILEILEKH130 - 168133 - 171
d_617ens_2TYRTYRSERSERKH171 - 174174 - 177
d_71ens_2SERSERALAALAMK2 - 35 - 6
d_72ens_2VALVALILEILEMK5 - 68 - 9
d_73ens_2GLNGLNVALVALMK8 - 2811 - 31
d_74ens_2PROPROVALVALMK34 - 3737 - 40
d_75ens_2ASPASPGLUGLUMK39 - 4642 - 49
d_76ens_2GLYGLYGLYGLYMK4851
d_77ens_2LEULEUVALVALMK50 - 6253 - 65
d_78ens_2ARGARGLEULEUMK64 - 6867 - 71
d_79ens_2ARGARGLEULEUMK70 - 7273 - 75
d_710ens_2METMETASPASPMK74 - 7577 - 78
d_711ens_2ALAALALEULEUMK78 - 8481 - 87
d_712ens_2ASNASNALAALAMK86 - 9889 - 101
d_713ens_2ILEILEGLYGLYMK100 - 101103 - 104
d_714ens_2ASPASPASPASPMK103 - 105106 - 108
d_715ens_2SERSERMETMETMK107 - 120110 - 123
d_716ens_2SERSERILEILEMK130 - 168133 - 171
d_717ens_2TYRTYRSERSERMK171 - 174174 - 177
d_81ens_2SERSERALAALANM2 - 35 - 6
d_82ens_2VALVALILEILENM5 - 68 - 9
d_83ens_2GLNGLNVALVALNM8 - 2811 - 31
d_84ens_2PROPROVALVALNM34 - 3737 - 40
d_85ens_2ASPASPGLUGLUNM39 - 4642 - 49
d_86ens_2GLYGLYGLYGLYNM4851
d_87ens_2LEULEUVALVALNM50 - 6253 - 65
d_88ens_2ARGARGLEULEUNM64 - 6867 - 71
d_89ens_2ARGARGLEULEUNM70 - 7273 - 75
d_810ens_2METMETASPASPNM74 - 7577 - 78
d_811ens_2ALAALALEULEUNM78 - 8481 - 87
d_812ens_2ASNASNALAALANM86 - 9889 - 101
d_813ens_2ILEILEGLYGLYNM100 - 101103 - 104
d_814ens_2ASPASPASPASPNM103 - 105106 - 108
d_815ens_2SERSERMETMETNM107 - 120110 - 123
d_816ens_2SERSERILEILENM130 - 168133 - 171
d_817ens_2TYRTYRSERSERNM171 - 174174 - 177
d_91ens_2SERSERALAALAOL2 - 35 - 6
d_92ens_2VALVALILEILEOL5 - 68 - 9
d_93ens_2GLNGLNVALVALOL8 - 2811 - 31
d_94ens_2PROPROVALVALOL34 - 3737 - 40
d_95ens_2ASPASPGLUGLUOL39 - 4642 - 49
d_96ens_2GLYGLYGLYGLYOL4851
d_97ens_2LEULEUVALVALOL50 - 6253 - 65
d_98ens_2ARGARGLEULEUOL64 - 6867 - 71
d_99ens_2ARGARGLEULEUOL70 - 7273 - 75
d_910ens_2METMETASPASPOL74 - 7577 - 78
d_911ens_2ALAALALEULEUOL78 - 8481 - 87
d_912ens_2ASNASNALAALAOL86 - 9889 - 101
d_913ens_2ILEILEGLYGLYOL100 - 101103 - 104
d_914ens_2ASPASPASPASPOL103 - 105106 - 108
d_915ens_2SERSERMETMETOL107 - 120110 - 123
d_916ens_2SERSERILEILEOL130 - 168133 - 171
d_917ens_2TYRTYRSERSEROL171 - 174174 - 177

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.317872888146, 0.849910250727, -0.420249203081), (-0.879311719028, 0.430047322377, 0.20462209386), (0.354637459613, 0.304486233228, 0.88403642799)-20.7474657644, 265.944995141, -105.056757699
2given(-0.795113589468, 0.503377686832, -0.338238502012), (-0.580041433063, -0.468393347498, 0.666453005057), (0.177048907857, 0.726098186486, 0.664405830654)243.941825953, 367.872907321, -131.568295482
3given(-0.811923682328, -0.544187335117, 0.21128198781), (0.486037492548, -0.429704330889, 0.761000488734), (-0.323338042786, 0.720565286642, 0.613382570484)421.465274757, 166.530243696, -25.8292777656
4given(0.339216139084, 0.820588801915, -0.459963508505), (-0.844033182631, 0.481395043069, 0.236361585557), (0.415379823298, 0.308046799497, 0.855901145996)-17.6654676251, 249.725918994, -115.16616819
5given(-0.793400734153, 0.513138318337, -0.327420740487), (-0.584083552163, -0.490371836278, 0.646824447805), (0.171352499658, 0.704432060912, 0.688777026635)240.54107309, 373.727957384, -126.972039847
6given(-0.103529086583, -0.924191153303, 0.367630847982), (0.879899403905, 0.0872323257269, 0.467084104157), (-0.463744290788, 0.371834954657, 0.804164161883)359.681729747, 5.86842770291, 47.3678910801
7given(0.907963680383, -0.393247228157, 0.144770758969), (0.388796689623, 0.919428905407, 0.0590560923239), (-0.156330065066, 0.0026656049059, 0.987701273314)82.8306505655, -40.4204117432, 66.666352481
8given(0.717104248772, 0.617932957861, -0.322366803475), (-0.619726785597, 0.776963758597, 0.110752106257), (0.318904699883, 0.120358536944, 0.940113618121)-56.574752347, 175.198519949, -28.7524848236
9given(-0.106916440442, 0.838677803378, -0.534030352026), (-0.898411944834, 0.14860438128, 0.413246555031), (0.425939963074, 0.523962097853, 0.737589904941)65.2721120638, 297.785370032, -190.274930424
10given(-0.967879510966, 0.150139130858, -0.201661829898), (-0.251053396508, -0.620140761585, 0.743234571264), (-0.0134701282225, 0.76998940071, 0.637914475804)339.464404595, 316.625445483, -140.720070364
11given(-0.495355602333, -0.852237651217, 0.168267088537), (0.73544466678, -0.308341890792, 0.603362594537), (-0.462324528163, 0.422630174302, 0.779512518455)424.465709972, 87.1071102813, 10.9894204255

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要素

#1: タンパク質
Caspase-8 subunit p10


分子量: 22011.449 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
#2: タンパク質
CASP8 and FADD-like apoptosis regulator subunit p43 / cFLIP


分子量: 21160.756 Da / 分子数: 9 / 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
研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 3.78 Å3/Da / 溶媒含有率: 67.47 %
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 HEPES pH 7.5, 0.2 M Lithium chloride, 20 % PEG 400, 0.1 M TBG pH 9.0

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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: 2017年2月19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: 3.3→30 Å / Num. obs: 61626 / % possible obs: 96.8 % / 冗長度: 3.3 % / Biso Wilson estimate: 98.21 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.757
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
3.3-3.422.80.73959620.7750.9340.510.9030.89894.8
3.42-3.552.90.58260320.8690.9640.3940.7060.96695.9
3.55-3.723.10.48461040.910.9760.3160.5811.06896.8
3.72-3.913.30.34561800.9560.9890.2190.4111.07797.5
3.91-4.163.40.21661490.9840.9960.1350.2561.08697.4
4.16-4.483.40.16762260.9890.9970.1040.1971.06798.5
4.48-4.923.50.11262800.9940.9990.0690.1321.06298.6
4.92-5.633.60.163530.9940.9990.0610.1171.07899.2
5.63-7.083.50.08263360.9950.9990.050.0961.0998.6
7.08-303.40.03460040.99810.0220.0411.02690.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_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: 3.3→29.64 Å / SU ML: 0.4178 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 35.0467
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2643 3117 5.08 %
Rwork0.2183 58219 -
obs0.2207 61336 96.01 %
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: 137.82 Å2
精密化ステップサイクル: LAST / 解像度: 3.3→29.64 Å
タンパク質核酸リガンド溶媒全体
原子数18608 0 0 0 18608
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002418800
X-RAY DIFFRACTIONf_angle_d0.562325192
X-RAY DIFFRACTIONf_chiral_restr0.03772946
X-RAY DIFFRACTIONf_plane_restr0.00363194
X-RAY DIFFRACTIONf_dihedral_angle_d11.66897530
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.729462887967
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS0.81169785429
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS0.752069889676
ens_2d_2GFX-RAY DIFFRACTIONTorsion NCS0.958577111081
ens_2d_3GFX-RAY DIFFRACTIONTorsion NCS1.07614055803
ens_2d_4GFX-RAY DIFFRACTIONTorsion NCS1.0011619494
ens_2d_5GFX-RAY DIFFRACTIONTorsion NCS1.10809694932
ens_2d_6GFX-RAY DIFFRACTIONTorsion NCS1.44946139952
ens_2d_7GFX-RAY DIFFRACTIONTorsion NCS0.831849563191
ens_2d_8GFX-RAY DIFFRACTIONTorsion NCS0.787501223944
ens_2d_9GFX-RAY DIFFRACTIONTorsion NCS0.972134155649
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.350.38991310.36372366X-RAY DIFFRACTION87.71
3.35-3.40.40971210.35052605X-RAY DIFFRACTION94.95
3.4-3.460.38551360.34232605X-RAY DIFFRACTION94.65
3.46-3.520.33951500.3222600X-RAY DIFFRACTION95.72
3.52-3.590.33311410.31512618X-RAY DIFFRACTION96.3
3.59-3.660.37341370.30962616X-RAY DIFFRACTION96.53
3.66-3.740.33331340.29062650X-RAY DIFFRACTION96.87
3.74-3.830.34821460.27492686X-RAY DIFFRACTION97.22
3.83-3.930.27291460.25382626X-RAY DIFFRACTION96.65
3.93-4.030.34341240.24582640X-RAY DIFFRACTION96.64
4.03-4.150.25941600.2322651X-RAY DIFFRACTION96.66
4.15-4.280.3021460.20912666X-RAY DIFFRACTION97.4
4.28-4.440.28831520.20922691X-RAY DIFFRACTION98.03
4.44-4.610.27721340.19882695X-RAY DIFFRACTION97.79
4.61-4.820.24831460.18932686X-RAY DIFFRACTION97.93
4.82-5.080.25931290.19382742X-RAY DIFFRACTION98.8
5.08-5.390.27591310.20522755X-RAY DIFFRACTION99.07
5.39-5.810.291500.22662738X-RAY DIFFRACTION98.87
5.81-6.390.30471720.24022719X-RAY DIFFRACTION98.64
6.39-7.30.25911280.23132752X-RAY DIFFRACTION97.83
7.3-9.150.19081750.17242619X-RAY DIFFRACTION94.01
9.15-29.640.17381280.14572493X-RAY DIFFRACTION84.68
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.42250697470.3728979466361.925522168631.93464508983-1.97109630924.19112472115-0.156995028216-0.7668094287830.9459556949360.5460607081040.4121720946240.416262135414-0.322907880545-0.566727798101-0.2099054070091.014519319630.05284616353540.1294750367213.00386575145-0.5947164144180.721012983625165.922781095194.82920471493.0868106021
21.54214804797-0.747979843017-2.278706223184.217079841322.661419324334.006944407790.2624307185740.08104176275530.5090268869770.738068298507-0.396330029665-0.318792045543-0.03088103318410.3833426664550.07098751497070.878037023769-0.02118624991230.1215285229013.59539060786-0.684014199595-0.792061207913179.343464376191.21553144788.4110280079
32.02205662982-0.888188136271.067876059713.39431726239-0.4516053222091.80018305830.499546489032-0.81759250052-0.7929874647660.3207519154240.2950839591151.146988070240.9516086763690.0132123627694-0.2242214644931.10683309948-0.02120191966470.3166875250163.65287695334-0.449621225840.308610386693168.570434506186.218302799.6587108436
44.394303131010.50681885217-2.39167086062.471441089130.1091537729251.39798024648-0.456494933847-0.1607103112780.9305978443910.02901425639730.4489249952720.140372982701-1.204270477110.2592792260620.01418155717811.23157507418-0.08951425811130.07643637009814.17591360546-0.9722191503531.04995708291189.918360798204.282778882103.735514611
50.546719828892-0.09469540752811.682680605582.264976489980.7909521208929.696814763970.487127536692-1.79483991837-0.8831857711570.139862642103-0.0002463820813640.281110788984-0.1582830008180.044778789592-0.328348707241.082521070070.1415407177610.0634057867824.1354455144-0.7003540376820.533185346158188.862896895191.913469922108.461119865
62.214156446971.217706368540.1053101159883.5828528496-2.328782259741.85541805285-0.0829370080429-1.1667999584-0.1153185790530.760777694450.3916224193210.08419645903860.04845490205650.279471968545-0.2406027567371.002145877580.0573704201553-0.01640780120672.88952813981-0.4931637321880.657278072699192.212503562188.86307796882.2164420228
77.644705078750.2860072290383.432990371424.062439583021.719354198597.57073260488-0.652828352863-0.08777823862380.752829847995-0.4106037245940.1062260078750.457535054239-1.081429343630.1559330181460.5431076269880.909419506863-0.0794092034395-0.2590601270213.13283089439-0.685603846370.709460341683197.898571259197.06188809771.6239942285
82.810999204341.139070062680.9277736136624.344451076020.8984386409675.20937845092-0.114436565069-0.518318496749-1.212930570970.3757349930960.5194514789350.1049866665620.3355806647290.00537128389169-0.1115254561740.9392722427990.00652584297096-0.1915172575333.5821610521-0.627732441253-0.353818091275201.121730162185.83200971284.5343966096
92.35980375614-0.9567648386170.07183092189075.72302300079-0.01229414069380.4665173609420.132955235021-0.2559737787830.239844588727-0.0929352655103-0.07218781421810.477624323401-0.4283904977730.822546894915-0.02994602191641.26900983374-0.25111028313-0.03478708331732.70812442101-0.4883678247260.90761861483201.346566288208.5840473383.2492545826
103.94840925331-0.1004092381681.670885983795.743957864090.8527909669288.23281298527-0.219521033794-1.127358679520.8872613261190.9639043725370.803185941542-1.31221899426-0.7188423365431.32434535374-0.5353668568211.22542324819-0.542177352539-0.05268100496872.80439430662-0.7740825569671.29780449279209.311422839214.28279020585.1617880478
111.799884931963.285805813172.763128157927.300064384212.948567737957.486134452180.0300608777185-2.114792981190.04265720701472.405135745950.201284562965-1.9503402520.1821377779641.75320190092-0.194647861071.40252781255-0.252949212268-0.3647654003692.63268761596-0.02814964833621.12011009194213.499585134206.99992347792.2949936571
125.97183006583-5.17469720541.027975319026.73468517709-2.198303049714.13774028212-0.599287707408-0.4573235213710.1471336599290.5797009045510.7551589014680.03148017532550.07147412302170.674958374833-0.1287542591770.902575130202-0.363106202535-0.05881245300312.56295681845-0.3284367660860.795757836552202.000910458204.9647134760.3509035458
139.062769796121.616725813660.06463356702116.0249704429-4.125631443687.716019350010.244383257311.78641114592-0.74565671086-0.6220859896520.337111348852-0.0449688748565-0.1930549593650.377290784848-0.5759299680410.903086759165-0.176537021279-0.04578487056422.13531417536-0.3711400943160.815912067776192.82983618210.08938040950.4524721832
147.976856594221.51424160174-5.008813508046.70429769069-6.256264124317.515759744290.6785787313881.12753490637-0.493080680048-1.01845301419-0.2219492156240.6312927057621.17965625973-0.685493844876-0.2404866101130.915514328217-0.296127114717-0.05381396642792.41371564219-0.5821594881641.02316526266200.713543996204.71404092850.5278310178
157.8533920579-2.061145744342.287618234874.06303458172-3.109577394915.87630099883-0.2389399725590.6082345407141.25505516211-0.11386047863-0.612340666553-0.732495892072-0.0670223742936-0.07855068712220.8409639625271.03100076499-0.451219025264-0.07785184121911.94960093632-0.3273885665861.00759477191208.120351224212.49338666553.376316568
162.03001905321-1.473058266550.6564319485696.19058042013-1.700533720841.62418718813-0.450874122893-1.014811425641.099194959580.5642948951080.0632276432208-1.23824996021-1.256682992611.302686990550.4498816111051.38009983173-0.543581953349-0.1530388431252.79143424157-0.4404281585551.24635016621206.418489299218.70416746562.1523793514
172.01203894362-3.206266369985.694573843249.334605436472.687855155275.52553816235-0.943460843578-2.4099469330.3542854851682.158022412481.14184636017-0.0828224629484-2.393277496050.791630065112-0.1219938750242.07106871917-0.1911201396220.09395082365472.53956909473-0.5078935127861.11859786861182.542057046221.53570801170.7155610783
186.42629968348-2.67921134612.327104504751.34071656408-1.396054714872.304248804540.312038938549-1.16206261676-0.8103941908061.166867796850.827446792361.84639915801-0.734706241957-0.456066695607-1.124096377871.591382468380.04007954038190.5423337287192.57662441062-0.3084414082151.95457911092176.476489635218.9756837361.0465884108
199.36759277332-0.6814469786995.139735463759.75699833449-3.201014154843.64589056145-1.19976256562-1.262265274051.509057641831.80602176530.822976605728-1.05634997944-1.314843745190.07196394167240.3087357713571.343014744030.0128583626976-0.2076051688511.67317554223-0.4094976783931.13424705566185.428266515227.08048314159.1900325732
205.92772451986-3.033378648310.5527183296922.53651832896-0.1103644360070.0811960205831-0.576445390475-2.730660384611.835685388080.346452031030.740892718915-0.668803646739-0.133188148185-0.963841527823-0.07427090335851.24833411355-0.00438589972192-0.3355720892592.20752073129-0.2015511999741.51525284203195.394242717233.67720523265.2496026894
216.215225759451.849913371782.171516432172.921735312132.281667609692.8472888314-0.8556900805550.1590246105482.075238884290.2023429368890.936024396844-0.735529831711-1.292863102971.42627306241-0.04647161245591.60437442495-0.3544217426720.007931352095151.98558807357-0.3833755587711.55438380255156.687962858226.57428224887.0451937275
227.17376697106-2.263545534662.930602410424.63366222605-7.482888324522.00892941333-1.34845834562-0.4016550303430.5648798593111.62537273704-0.209154047159-0.136409434674-0.983976203760.5768780907881.259024925581.1346533469-0.09085913678970.1118862985323.04595956215-0.8255687290481.22494565702161.018517279217.699163443100.34476279
234.52964471726-1.800966442131.456565947447.95435468831-3.92833811163.82673841752-0.257579360980.3402351058860.1370856973-0.667880537341-0.251199450389-0.5341094479980.3104055070170.1149142668750.6040938840371.01585071146-0.07084972910710.1881574120572.98756125487-0.6382295700611.19785157169159.834209567210.97409099191.5556323612
242.60939611815-0.5394576099480.230700148444.42438116897-1.47660605744.20632454304-0.243571545828-0.3185442755890.4545644859490.4122874793390.1887402532350.300446415129-0.484496337922-0.1440834729190.02957081948460.9007419815840.009682060819690.08582370923462.67051941737-0.589669021731.15354727876147.996473311219.346617598100.017664941
256.88396980389-3.296529818056.288546020227.88153186978-6.827843008728.03961763814-0.770804380842-0.9987951075111.474171446331.02011638401-0.127942143998-0.596916936166-1.7755974141.15254250420.7714685731981.38306172560.254964647805-0.241721764624.38953067742-0.9394697105631.32196850193167.76246246213.241954506118.226849345
265.44994347921-1.487733539151.343619593477.4175053056-0.7048758272190.373270707138-0.10979074877-0.4794041596160.4211469530051.09695220381-0.472874981221-0.482857231433-0.150533022003-0.05055889101950.4277257588451.183127274920.07475119266410.1596842536833.06137627466-0.5543735108910.91488237287168.1433587204.717513599110.793860968
273.679297557292.565782280063.591814891282.096055706583.14397577783.6740893953-0.217226895979-1.403912065030.9059907501261.89034309598-0.104593711661.165449234281.06400800212-0.2903988808130.198901346441.59705972747-0.04154554908050.1739230774522.99251781829-0.4658576371491.18850050422157.537993191203.511520297117.896223886
289.16174856711-1.48933106907-1.21228817157.63945000698-4.099975219052.66392685586-1.2819628204-0.609324406683-0.340313355611.736080629390.7982673423730.91406053035-1.04510499545-1.857171284060.3344875681831.263883688670.3030085346440.2741679328783.17523594606-0.64861542771.24490169074148.499529672210.552339086118.381930216
299.28560667584-4.1294946039-6.8427973486.647848980070.38839184412.00800240792-0.351430910965-0.07101243345510.306297919380.420381519930.0473417825711-0.3261624356950.3234162064871.077605808160.3275994117340.964884310967-0.133821296692-0.1393696840132.22718641326-0.318443168890.819589573706204.07329061197.29468670429.0635083635
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786.005544373610.601017404093-2.195797269484.36301417923-1.323023295481.256243734660.2786501248010.5321971465710.472353826053-0.7765973041460.30174280181-0.24841207755-0.3799093360690.97968760383-0.6260560249871.35268483168-0.2652386241580.09155890629562.976832664510.0110663986150.757203417159184.844394463191.492087235-25.4043989568
793.932790289110.973550805699-1.406600226557.510102111770.689150716760.958864737004-0.100204029468-0.1451574306210.151490509391-0.1779830876510.255436032576-0.170373364792-0.2418677777961.02478184882-0.1807554131550.875273240327-0.116243527826-0.04084495660722.269663105820.003317364077820.588773692941165.925026597183.408270398-11.1604787228
803.205191909752.810908270331.734167513546.408502526752.31471218371.09617535893-0.9214997585771.91653505237-0.759759662877-0.7328257319111.12417412964-0.1814235884990.0860939344616-0.301137050827-0.02785062882911.26300031077-0.1964151054450.2170638843322.51418510443-0.3026908980031.0002717674200.070104098161.36183914216.1409724415
817.048338213070.241738508286-2.007111346989.796764936441.388362899580.761726207367-1.02961140168-0.760545854457-0.4414886076570.8054537756190.521044823120.03176981384360.777063470880.5245846246410.5498381091771.388968674030.272470079990.1131239123952.90635495426-0.009363056849040.91007612044202.693724076154.99115067721.0266703865
823.889751698554.763025750630.5477403526255.93447348745-0.110988046455.358122630960.13526361742.05221215836-1.33666486520.542725476770.45303024901-1.777316078060.435707468004-0.709004443396-0.6684921271981.531254738750.2906898674470.1042871524872.21606868312-0.4625054490381.29938866288212.222680245155.22440721628.5760899109
833.33639638321-2.93525939396-0.7082749186129.701863583723.318714113391.20568755985-0.304010291958-0.3520886193990.0513567699319-0.2874723696920.752867573096-0.1893541444860.350991230172-0.37412165546-0.4504837278391.144321301830.030253256245-0.03407240234692.61599066932-0.107808629150.694327712694204.989906895180.50474835225.6208895421
842.4973285574-0.777448955727-0.02295476567352.663442824621.29837946913.2960725221-0.07406216780760.4731980176320.00248949530326-0.7384140158870.069302479227-0.1113514456490.1406425090220.114627552922-0.04021430088861.07381097012-0.1525359239930.002079749939652.56917336732-0.3208693553340.85719552434209.730635876180.40904591224.5352083972
857.20182627626-5.773611851596.847304666756.53985960598-6.531365559637.022016368850.413751269841.03427953199-0.440735388393-1.04821739297-0.168648273912-0.05861102789211.39603113476-0.403242424671-0.2637734844021.1679537951-0.2631869459770.2080609405932.58352392254-0.2923723819980.875777640815205.745774304176.740791109-1.84245112088
864.6585275605-3.121998065510.07629985031687.89245913325-1.69017568882.886908271920.3031739640211.592757180720.324350596755-1.35074399486-0.477247195209-0.6633927227820.2143300840381.040456755690.1024777790781.23264305557-0.2444907309510.214593754152.74688730896-0.1239135175190.826154881233212.391442544182.652607996-3.95361498995
876.18934367911-3.450485024-3.694543882877.94216454590.7397292012395.055609908870.1183169460270.1143412702220.105128322476-0.319248618267-0.328576858261-0.308103938699-0.04321238658670.9345820289660.06279706141480.921852931131-0.3165781185930.03463665087072.39373543495-0.1268649222860.742564275279192.2229516193.541591219-0.490952454295
888.23010066888-1.65673869119-1.249057164846.70129272586-1.97686979625.42571945358-0.123178428512-1.692174968691.402229247320.329937018570.117952566496-0.31039737434-0.366442866845-0.7845882491060.01614834115850.856281060492-0.3088032910560.01816955665211.97441117115-0.168948585990.871506527574198.040359529203.8508140263.61680409557
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 'C' and (resid 2 through 25 )CA2 - 251 - 24
22chain 'C' and (resid 26 through 40 )CA26 - 4025 - 39
33chain 'C' and (resid 41 through 110 )CA41 - 11040 - 109
44chain 'C' and (resid 111 through 138 )CA111 - 138110 - 137
55chain 'C' and (resid 139 through 180 )CA139 - 180138 - 179
66chain 'B' and (resid 2 through 25 )BB2 - 251 - 24
77chain 'B' and (resid 26 through 40 )BB26 - 4025 - 39
88chain 'B' and (resid 41 through 90 )BB41 - 9040 - 89
99chain 'B' and (resid 91 through 149 )BB91 - 14990 - 148
1010chain 'B' and (resid 150 through 168 )BB150 - 168149 - 167
1111chain 'B' and (resid 169 through 182 )BB169 - 182168 - 181
1212chain 'A' and (resid 2 through 25 )AC2 - 251 - 24
1313chain 'A' and (resid 26 through 40 )AC26 - 4025 - 39
1414chain 'A' and (resid 41 through 50 )AC41 - 5040 - 49
1515chain 'A' and (resid 51 through 68 )AC51 - 6850 - 67
1616chain 'A' and (resid 69 through 111 )AC69 - 11168 - 110
1717chain 'A' and (resid 112 through 123 )AC112 - 123111 - 122
1818chain 'A' and (resid 124 through 138 )AC124 - 138123 - 137
1919chain 'A' and (resid 139 through 168 )AC139 - 168138 - 167
2020chain 'A' and (resid 169 through 180 )AC169 - 180168 - 179
2121chain 'D' and (resid 2 through 13 )DD2 - 131 - 12
2222chain 'D' and (resid 14 through 25 )DD14 - 2513 - 24
2323chain 'D' and (resid 26 through 50 )DD26 - 5025 - 49
2424chain 'D' and (resid 51 through 111 )DD51 - 11150 - 110
2525chain 'D' and (resid 112 through 123 )DD112 - 123111 - 122
2626chain 'D' and (resid 124 through 149 )DD124 - 149123 - 148
2727chain 'D' and (resid 150 through 168 )DD150 - 168149 - 167
2828chain 'D' and (resid 169 through 182 )DD169 - 182168 - 181
2929chain 'H' and (resid 1 through 12 )HE1 - 121 - 12
3030chain 'H' and (resid 13 through 26 )HE13 - 2613 - 26
3131chain 'H' and (resid 27 through 36 )HE27 - 3627 - 36
3232chain 'H' and (resid 37 through 61 )HE37 - 6137 - 61
3333chain 'H' and (resid 62 through 75 )HE62 - 7562 - 75
3434chain 'H' and (resid 76 through 91 )HE76 - 9176 - 91
3535chain 'H' and (resid 92 through 117 )HE92 - 11792 - 117
3636chain 'H' and (resid 118 through 130 )HE118 - 130118 - 130
3737chain 'H' and (resid 131 through 149 )HE131 - 149131 - 149
3838chain 'H' and (resid 150 through 175 )HE150 - 175150 - 175
3939chain 'G' and (resid 0 through 75 )GF0 - 751 - 76
4040chain 'G' and (resid 76 through 91 )GF76 - 9177 - 92
4141chain 'G' and (resid 92 through 161 )GF92 - 16193 - 162
4242chain 'G' and (resid 162 through 175 )GF162 - 175163 - 176
4343chain 'F' and (resid 0 through 14 )FG0 - 141 - 15
4444chain 'F' and (resid 15 through 26 )FG15 - 2616 - 27
4545chain 'F' and (resid 27 through 46 )FG27 - 4628 - 44
4646chain 'F' and (resid 47 through 61 )FG47 - 6145 - 59
4747chain 'F' and (resid 62 through 75 )FG62 - 7560 - 73
4848chain 'F' and (resid 76 through 91 )FG76 - 9174 - 89
4949chain 'F' and (resid 92 through 105 )FG92 - 10590 - 103
5050chain 'F' and (resid 106 through 119 )FG106 - 119104 - 117
5151chain 'F' and (resid 120 through 130 )FG120 - 130118 - 124
5252chain 'F' and (resid 131 through 140 )FG131 - 140125 - 134
5353chain 'F' and (resid 141 through 149 )FG141 - 149135 - 143
5454chain 'F' and (resid 150 through 161 )FG150 - 161144 - 155
5555chain 'F' and (resid 162 through 175 )FG162 - 175156 - 169
5656chain 'K' and (resid 1 through 61 )KH1 - 611 - 61
5757chain 'K' and (resid 62 through 91 )KH62 - 9162 - 91
5858chain 'K' and (resid 92 through 174 )KH92 - 17492 - 169
5959chain 'I' and (resid 1 through 12 )II1 - 121 - 12
6060chain 'I' and (resid 13 through 26 )II13 - 2613 - 26
6161chain 'I' and (resid 27 through 46 )II27 - 4627 - 43
6262chain 'I' and (resid 47 through 61 )II47 - 6144 - 58
6363chain 'I' and (resid 62 through 91 )II62 - 9159 - 88
6464chain 'I' and (resid 92 through 120 )II92 - 12089 - 117
6565chain 'I' and (resid 121 through 130 )II121 - 130118 - 127
6666chain 'I' and (resid 131 through 141 )II131 - 141128 - 138
6767chain 'I' and (resid 142 through 149 )II142 - 149139 - 146
6868chain 'I' and (resid 150 through 161 )II150 - 161147 - 158
6969chain 'I' and (resid 162 through 175 )II162 - 175159 - 172
7070chain 'J' and (resid 1 through 12 )JJ1 - 121 - 12
7171chain 'J' and (resid 13 through 26 )JJ13 - 2613 - 26
7272chain 'J' and (resid 27 through 91 )JJ27 - 9127 - 91
7373chain 'J' and (resid 92 through 120 )JJ92 - 12092 - 120
7474chain 'J' and (resid 121 through 161 )JJ121 - 161121 - 159
7575chain 'J' and (resid 162 through 175 )JJ162 - 175160 - 173
7676chain 'M' and (resid 1 through 26 )MK1 - 261 - 26
7777chain 'M' and (resid 27 through 36 )MK27 - 3627 - 36
7878chain 'M' and (resid 37 through 91 )MK37 - 9137 - 91
7979chain 'M' and (resid 92 through 175 )MK92 - 17592 - 169
8080chain 'O' and (resid 1 through 36 )OL1 - 361 - 36
8181chain 'O' and (resid 37 through 75 )OL37 - 7537 - 75
8282chain 'O' and (resid 76 through 91 )OL76 - 9176 - 91
8383chain 'O' and (resid 92 through 120 )OL92 - 12092 - 120
8484chain 'O' and (resid 121 through 175 )OL121 - 175121 - 175
8585chain 'N' and (resid 1 through 26 )NM1 - 261 - 26
8686chain 'N' and (resid 27 through 91 )NM27 - 9127 - 91
8787chain 'N' and (resid 92 through 149 )NM92 - 14992 - 146
8888chain 'N' and (resid 150 through 175 )NM150 - 175147 - 172

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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