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- PDB-8yd8: Structure of FADD/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: 8yd8
タイトルStructure of FADD/Caspase-8/cFLIP death effector domain assembly
要素
  • CASP8 and FADD-like apoptosis regulator subunit p43
  • Caspase-8
  • FAS-associated death domain protein
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


positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of myoblast fusion / negative regulation of activation-induced cell death of T cells / skeletal myofibril assembly / caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / skeletal muscle atrophy / tumor necrosis factor receptor superfamily binding ...positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of myoblast fusion / negative regulation of activation-induced cell death of T cells / skeletal myofibril assembly / caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / skeletal muscle atrophy / tumor necrosis factor receptor superfamily binding / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / TRAIL-activated apoptotic signaling pathway / death-inducing signaling complex assembly / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / regulation of necroptotic process / positive regulation of adaptive immune response / Caspase activation via Death Receptors in the presence of ligand / positive regulation of extracellular matrix organization / skeletal muscle tissue regeneration / positive regulation of glomerular mesangial cell proliferation / positive regulation of macrophage differentiation / necroptotic signaling pathway / caspase binding / self proteolysis / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / negative regulation of hepatocyte apoptotic process / CLEC7A/inflammasome pathway / receptor serine/threonine kinase binding / natural killer cell activation / negative regulation of necroptotic process / activation of cysteine-type endopeptidase activity / cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of innate immune response / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of hepatocyte proliferation / cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of cellular response to transforming growth factor beta stimulus / motor neuron apoptotic process / TNFR1-induced proapoptotic signaling / execution phase of apoptosis / RIPK1-mediated regulated necrosis / negative regulation of cardiac muscle cell apoptotic process / response to testosterone / B cell activation / regulation of innate immune response / positive regulation of activated T cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / positive regulation of execution phase of apoptosis / T cell homeostasis / positive regulation of proteolysis / behavioral response to cocaine / macrophage differentiation / protein maturation / cellular response to organic cyclic compound / extrinsic apoptotic signaling pathway via death domain receptors / cellular response to nitric oxide / Caspase-mediated cleavage of cytoskeletal proteins / response to tumor necrosis factor / lymph node development / signaling adaptor activity / negative regulation of reactive oxygen species biosynthetic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / skeletal muscle tissue development / extrinsic apoptotic signaling pathway in absence of ligand / cysteine-type peptidase activity / keratinocyte differentiation / spleen development / enzyme activator activity / cellular response to epidermal growth factor stimulus / regulation of cytokine production / T cell activation / cellular response to dexamethasone stimulus / erythrocyte differentiation / thymus development / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / kidney development / Regulation of NF-kappa B signaling / positive regulation of interleukin-8 production
類似検索 - 分子機能
: / FADD / Caspase-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain ...: / FADD / Caspase-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death 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 / FAS-associated death domain protein / 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: 3.11 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: Deciphering DED assembly mechanisms in FADD-procaspase-8-cFLIP complexes regulating apoptosis.
著者: Chao-Yu Yang / Chia-I Lien / Yi-Chun Tseng / Yi-Fan Tu / Arkadiusz W Kulczyk / Yen-Chen Lu / Yin-Ting Wang / Tsung-Wei Su / Li-Chung Hsu / Yu-Chih Lo / Su-Chang Lin /
要旨: Fas-associated protein with death domain (FADD), procaspase-8, and cellular FLICE-inhibitory proteins (cFLIP) assemble through death-effector domains (DEDs), directing death receptor signaling ...Fas-associated protein with death domain (FADD), procaspase-8, and cellular FLICE-inhibitory proteins (cFLIP) assemble through death-effector domains (DEDs), directing death receptor signaling towards cell survival or apoptosis. Understanding their three-dimensional regulatory mechanism has been limited by the absence of atomic coordinates for their ternary DED complex. By employing X-ray crystallography and cryogenic electron microscopy (cryo-EM), we present the atomic coordinates of human FADD-procaspase-8-cFLIP complexes, revealing structural insights into these critical interactions. These structures illustrate how FADD and cFLIP orchestrate the assembly of caspase-8-containing complexes and offer mechanistic explanations for their role in promoting or inhibiting apoptotic and necroptotic signaling. A helical procaspase-8-cFLIP hetero-double layer in the complex appears to promote limited caspase-8 activation for cell survival. Our structure-guided mutagenesis supports the role of the triple-FADD complex in caspase-8 activation and in regulating receptor-interacting protein kinase 1 (RIPK1). These results propose a unified mechanism for DED assembly and procaspase-8 activation in the regulation of apoptotic and necroptotic signaling across various cellular pathways involved in development, innate immunity, and disease.
履歴
登録2024年2月19日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年5月15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

ダウンロードとリンク

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集合体

登録構造単位
I: CASP8 and FADD-like apoptosis regulator subunit p43
D: Caspase-8
C: Caspase-8
B: Caspase-8
E: Caspase-8
H: CASP8 and FADD-like apoptosis regulator subunit p43
J: CASP8 and FADD-like apoptosis regulator subunit p43
K: CASP8 and FADD-like apoptosis regulator subunit p43
L: FAS-associated death domain protein
A: Caspase-8


分子量 (理論値)分子数
合計 (水以外)217,54710
ポリマ－217,54710
非ポリマー00
水00
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)113.170, 149.680, 175.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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_5ens_1(chain "E" and (resid 3 through 4 or resid 6...
d_1ens_2(chain "H" and (resid 3 or resid 5 through 10...
d_2ens_2(chain "I" and (resid 3 or resid 5 through 10...
d_3ens_2(chain "J" and (resid 3 or resid 5 through 10...
d_4ens_2(chain "K" and (resid 3 or resid 5 through 10...

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_1PHEPHESERSERAJ3 - 43 - 4
d_12ens_1ASNASNLEULEUAJ6 - 426 - 42
d_13ens_1LEULEUGLUGLUAJ44 - 5544 - 55
d_14ens_1SERSERTHRTHRAJ57 - 8157 - 81
d_15ens_1LYSLYSGLUGLUAJ83 - 8783 - 87
d_16ens_1GLUGLUGLYGLYAJ89 - 9489 - 94
d_17ens_1ALAALALEULEUAJ96 - 11796 - 117
d_18ens_1SERSERPHEPHEAJ119 - 120119 - 120
d_19ens_1GLYGLYGLNGLNAJ122 - 125122 - 125
d_110ens_1ILEILESERSERAJ128 - 129128 - 129
d_111ens_1CYSCYSASPASPAJ131 - 135131 - 135
d_112ens_1METMETGLYGLYAJ137 - 155137 - 155
d_113ens_1LEULEULYSLYSAJ157 - 161157 - 161
d_114ens_1VALVALALAALAAJ163 - 165163 - 165
d_115ens_1ILEILELEULEUAJ167 - 172167 - 172
d_116ens_1ILEILEGLUGLUAJ174 - 180174 - 180
d_21ens_1PHEPHESERSERBD3 - 43 - 4
d_22ens_1ASNASNLEULEUBD6 - 426 - 42
d_23ens_1LEULEUGLUGLUBD44 - 5544 - 55
d_24ens_1SERSERTHRTHRBD57 - 8157 - 81
d_25ens_1LYSLYSGLUGLUBD83 - 8783 - 87
d_26ens_1GLUGLUGLYGLYBD89 - 9489 - 94
d_27ens_1ALAALALEULEUBD96 - 11796 - 117
d_28ens_1SERSERPHEPHEBD119 - 120119 - 120
d_29ens_1GLYGLYGLNGLNBD122 - 125122 - 125
d_210ens_1ILEILESERSERBD128 - 129128 - 129
d_211ens_1CYSCYSASPASPBD131 - 135131 - 135
d_212ens_1METMETGLYGLYBD137 - 155137 - 155
d_213ens_1LEULEULYSLYSBD157 - 161157 - 161
d_214ens_1VALVALALAALABD163 - 165163 - 165
d_215ens_1ILEILELEULEUBD167 - 172167 - 172
d_216ens_1ILEILEGLUGLUBD174 - 180174 - 180
d_31ens_1PHEPHESERSERCC3 - 43 - 4
d_32ens_1ASNASNLEULEUCC6 - 426 - 42
d_33ens_1LEULEUGLUGLUCC44 - 5544 - 55
d_34ens_1SERSERTHRTHRCC57 - 8157 - 81
d_35ens_1LYSLYSGLUGLUCC83 - 8783 - 87
d_36ens_1GLUGLUGLYGLYCC89 - 9489 - 94
d_37ens_1ALAALALEULEUCC96 - 11796 - 117
d_38ens_1SERSERPHEPHECC119 - 120119 - 120
d_39ens_1GLYGLYGLNGLNCC122 - 125122 - 125
d_310ens_1ILEILESERSERCC128 - 129128 - 129
d_311ens_1CYSCYSASPASPCC131 - 135131 - 135
d_312ens_1METMETGLYGLYCC137 - 155137 - 155
d_313ens_1LEULEULYSLYSCC157 - 161157 - 161
d_314ens_1VALVALALAALACC163 - 165163 - 165
d_315ens_1ILEILELEULEUCC167 - 172167 - 172
d_316ens_1ILEILEGLUGLUCC174 - 180174 - 180
d_41ens_1PHEPHESERSERDB3 - 43 - 4
d_42ens_1ASNASNLEULEUDB6 - 426 - 42
d_43ens_1LEULEUGLUGLUDB44 - 5544 - 55
d_44ens_1SERSERTHRTHRDB57 - 8157 - 81
d_45ens_1LYSLYSGLUGLUDB83 - 8783 - 87
d_46ens_1GLUGLUGLYGLYDB89 - 9489 - 94
d_47ens_1ALAALALEULEUDB96 - 11796 - 117
d_48ens_1SERSERPHEPHEDB119 - 120119 - 120
d_49ens_1GLYGLYGLNGLNDB122 - 125122 - 125
d_410ens_1ILEILESERSERDB128 - 129128 - 129
d_411ens_1CYSCYSASPASPDB131 - 135131 - 135
d_412ens_1METMETGLYGLYDB137 - 155137 - 155
d_413ens_1LEULEULYSLYSDB157 - 161157 - 161
d_414ens_1VALVALALAALADB163 - 165163 - 165
d_415ens_1ILEILELEULEUDB167 - 172167 - 172
d_416ens_1ILEILEGLUGLUDB174 - 180174 - 180
d_51ens_1PHEPHESERSEREE3 - 43 - 4
d_52ens_1ASNASNLEULEUEE6 - 426 - 42
d_53ens_1LEULEUGLUGLUEE44 - 5544 - 55
d_54ens_1SERSERTHRTHREE57 - 8157 - 81
d_55ens_1LYSLYSGLUGLUEE83 - 8783 - 87
d_56ens_1GLUGLUGLYGLYEE89 - 9489 - 94
d_57ens_1ALAALALEULEUEE96 - 11796 - 117
d_58ens_1SERSERPHEPHEEE119 - 120119 - 120
d_59ens_1GLYGLYGLNGLNEE122 - 125122 - 125
d_510ens_1ILEILESERSEREE128 - 129128 - 129
d_511ens_1CYSCYSASPASPEE131 - 135131 - 135
d_512ens_1METMETGLYGLYEE137 - 155137 - 155
d_513ens_1LEULEULYSLYSEE157 - 161157 - 161
d_514ens_1VALVALALAALAEE163 - 165163 - 165
d_515ens_1ILEILELEULEUEE167 - 172167 - 172
d_516ens_1ILEILEGLUGLUEE174 - 180174 - 180
d_11ens_2ALAALAALAALAHF33
d_12ens_2VALVALGLUGLUHF5 - 105 - 10
d_13ens_2ALAALALEULEUHF12 - 4412 - 44
d_14ens_2GLUGLUVALVALHF46 - 6246 - 62
d_15ens_2ARGARGLEULEUHF64 - 8464 - 84
d_16ens_2ASNASNASPASPHF86 - 10586 - 105
d_17ens_2SERSERMETMETHF107 - 120107 - 120
d_18ens_2LYSLYSGLUGLUHF129 - 153129 - 153
d_19ens_2CYSCYSLYSLYSHF155 - 172155 - 172
d_110ens_2SERSERVALVALHF174 - 175174 - 175
d_21ens_2ALAALAALAALAIA33
d_22ens_2VALVALGLUGLUIA5 - 105 - 10
d_23ens_2ALAALAVALVALIA12 - 2812 - 28
d_24ens_2ASPASPLEULEUIA31 - 4431 - 44
d_25ens_2GLUGLUVALVALIA46 - 6246 - 62
d_26ens_2ARGARGLEULEUIA64 - 8464 - 84
d_27ens_2ASNASNASPASPIA86 - 10586 - 105
d_28ens_2SERSERMETMETIA107 - 120107 - 120
d_29ens_2LYSLYSGLUGLUIA129 - 153129 - 153
d_210ens_2CYSCYSLYSLYSIA155 - 172155 - 172
d_211ens_2SERSERVALVALIA174 - 175174 - 175
d_31ens_2ALAALAALAALAJG33
d_32ens_2VALVALGLUGLUJG5 - 105 - 10
d_33ens_2ALAALAVALVALJG12 - 2812 - 28
d_34ens_2ASPASPLEULEUJG31 - 4431 - 44
d_35ens_2GLUGLUVALVALJG46 - 6246 - 62
d_36ens_2ARGARGLEULEUJG64 - 8464 - 84
d_37ens_2ASNASNASPASPJG86 - 10586 - 105
d_38ens_2SERSERMETMETJG107 - 120107 - 120
d_39ens_2LYSLYSGLUGLUJG129 - 153129 - 153
d_310ens_2CYSCYSLYSLYSJG155 - 172155 - 172
d_311ens_2SERSERVALVALJG174 - 175174 - 175
d_41ens_2ALAALAALAALAKH33
d_42ens_2VALVALGLUGLUKH5 - 105 - 10
d_43ens_2ALAALAVALVALKH12 - 2812 - 28
d_44ens_2ASPASPLEULEUKH31 - 4431 - 44
d_45ens_2GLUGLUVALVALKH46 - 6246 - 62
d_46ens_2ARGARGLEULEUKH64 - 8464 - 84
d_47ens_2ASNASNASPASPKH86 - 10586 - 105
d_48ens_2SERSERMETMETKH107 - 120107 - 120
d_49ens_2LYSLYSGLUGLUKH129 - 153129 - 153
d_410ens_2CYSCYSLYSLYSKH155 - 172155 - 172
d_411ens_2SERSERVALVALKH174 - 175174 - 175

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.306588114495, 0.3953341365, -0.865860640385), (-0.315222245977, 0.900506683202, 0.299537391906), (0.898130649567, 0.181103931561, 0.400702760512)34.7063549643, 33.0468144142, -51.0381087319
2given(-0.806289671266, 0.312747084656, -0.502081892771), (-0.139741910565, 0.724062830556, 0.675429652768), (0.574777491244, 0.61475383565, -0.540100506492)102.891520985, 39.3154015892, -35.9317655367
3given(-0.808235900289, -0.143056873576, 0.571217524597), (0.332987381951, 0.689020931215, 0.643715433875), (-0.485668748167, 0.710482151268, -0.509255318856)113.168515699, 24.6749964766, 28.4239090047
4given(0.365316842106, -0.410042710444, 0.835708430306), (0.488990636668, 0.848449146553, 0.202539386204), (-0.792105903352, 0.334662548434, 0.510459808947)52.2735550411, 24.0596626313, 57.0061318969
5given(-0.567725306933, 0.355685152986, -0.742412316582), (-0.264193274682, 0.775415642663, 0.573526367944), (0.779672937507, 0.521745774357, -0.346253458408)87.8618693118, 21.247928038, -55.8793151479
6given(-0.963745414241, -0.00388513340765, 0.266795206606), (0.191545824479, 0.686024781481, 0.701911815201), (-0.185755144354, 0.727567800918, -0.660409056126)118.563144121, 8.53524237681, 0.372829629122
7given(-0.076549268222, -0.326345057711, 0.942146014608), (0.475161956585, 0.818777217827, 0.322218842686), (-0.87656221944, 0.472337560305, 0.0923899592822)73.6525455187, 1.61372436107, 51.5893820045

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要素

#1: タンパク質
CASP8 and FADD-like apoptosis regulator subunit p43 / cFLIP


分子量: 20797.385 Da / 分子数: 4 / 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 BL21 (大腸菌) / 参照: UniProt: O15519
#2: 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: 22011.449 Da / 分子数: 5 / 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 BL21 (大腸菌) / 参照: UniProt: Q14790, caspase-8
#3: タンパク質 FAS-associated death domain protein / FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of ...FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of receptor induced toxicity


分子量: 24300.438 Da / 分子数: 1 / 変異: H9G / 由来タイプ: 組換発現 / 詳細: FADD / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FADD, MORT1, GIG3 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q13158

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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: 3.44 Å3/Da / 溶媒含有率: 65 %
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: HEPES, PEG 8000, TBG, TCEP, sodium chloride / PH範囲: 7-9

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: NSRRC / ビームライン: TPS 05A / 波長: 0.99984 Å
検出器タイプ: RAYONIX MX300-HS / 検出器: CCD / 日付: 2018年4月26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: 0.99984 Å / 相対比: 1
反射解像度: 3.1→30.09 Å / Num. obs: 53985 / % possible obs: 99.7 % / 冗長度: 6.1 % / Biso Wilson estimate: 102.95 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 9
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
3.1-3.215.60.91751850.790.940.4231.0120.81897.5
3.21-3.346.20.753540.8750.9660.3060.7660.85899.9
3.34-3.496.30.45953360.9490.9870.1990.5010.934100
3.49-3.676.30.28553540.9760.9940.1240.3120.991100
3.67-3.96.30.18353820.9890.9970.080.21.06799.9
3.9-4.216.20.10853680.9950.9990.0470.1181.0699.9
4.21-4.636.20.08153960.9960.9990.0360.0891.07699.9
4.63-5.296.20.06854380.9970.9990.030.0741.08699.9
5.29-6.666.20.06354910.9970.9990.0270.0691.059100
6.66-30.095.80.04256810.99810.0190.0461.01899.6

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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: 3.11→30.09 Å / SU ML: 0.4226 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.9751
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2413 2623 4.89 %5
Rwork0.1995 51054 --
obs0.2015 53677 98.88 %-
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: 116.02 Å2
精密化ステップサイクル: LAST / 解像度: 3.11→30.09 Å
タンパク質核酸リガンド溶媒全体
原子数13754 0 0 0 13754
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001713893
X-RAY DIFFRACTIONf_angle_d0.434818597
X-RAY DIFFRACTIONf_chiral_restr0.03632143
X-RAY DIFFRACTIONf_plane_restr0.00342376
X-RAY DIFFRACTIONf_dihedral_angle_d3.37051836
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2JAX-RAY DIFFRACTIONTorsion NCS0.737379054013
ens_1d_3JAX-RAY DIFFRACTIONTorsion NCS0.800085098377
ens_1d_4JAX-RAY DIFFRACTIONTorsion NCS0.825031643248
ens_1d_5JAX-RAY DIFFRACTIONTorsion NCS0.963509025342
ens_2d_2FHX-RAY DIFFRACTIONTorsion NCS1.06345820494
ens_2d_3FHX-RAY DIFFRACTIONTorsion NCS0.92496759055
ens_2d_4FHX-RAY DIFFRACTIONTorsion NCS0.99539910409
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.170.44071210.35112361X-RAY DIFFRACTION87.86
3.17-3.230.36561420.31842620X-RAY DIFFRACTION98.68
3.23-3.290.31241470.28282661X-RAY DIFFRACTION98.94
3.29-3.360.3731430.28782640X-RAY DIFFRACTION98.97
3.36-3.440.32331370.2782688X-RAY DIFFRACTION99.19
3.44-3.530.3811600.26232634X-RAY DIFFRACTION99.25
3.53-3.620.29641180.24612688X-RAY DIFFRACTION99.4
3.62-3.730.26761550.23372675X-RAY DIFFRACTION99.4
3.73-3.850.30731230.22082665X-RAY DIFFRACTION99.43
3.85-3.990.23961480.20822689X-RAY DIFFRACTION99.72
3.99-4.150.23791300.19482712X-RAY DIFFRACTION99.54
4.15-4.340.27381280.19312693X-RAY DIFFRACTION99.89
4.34-4.560.23111340.17912723X-RAY DIFFRACTION99.9
4.56-4.850.22411360.18452716X-RAY DIFFRACTION99.76
4.85-5.220.23611270.18962743X-RAY DIFFRACTION99.86
5.22-5.740.27331300.20932719X-RAY DIFFRACTION99.75
5.74-6.570.29341380.22042769X-RAY DIFFRACTION99.97
6.57-8.240.22241460.19292791X-RAY DIFFRACTION100
8.24-30.090.15021600.14372867X-RAY DIFFRACTION99.18

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る