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- PDB-7oje: Crystal structure of the covalent complex between Tribolium casta... -

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基本情報

登録情報
データベース: PDB / ID: 7oje
タイトルCrystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA
要素
  • Lys-63-specific deubiquitinase ZUFSP
  • Polyubiquitin-B
キーワードHYDROLASE / ZUFSP / deubiquitinase / Tribolium castaneum / Red flour beetle / cysteine peptidase / Ubiquitin / Ubiquitin-Propargylamide
機能・相同性
機能・相同性情報


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / neuron projection morphogenesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling
類似検索 - 分子機能
Peptidase C78, ubiquitin fold modifier-specific peptidase 1/ 2 / Peptidase family C78 / : / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2-type / : ...Peptidase C78, ubiquitin fold modifier-specific peptidase 1/ 2 / Peptidase family C78 / : / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
CITRIC ACID / Zinc finger-containing ubiquitin peptidase 1 / Polyubiquitin-B
類似検索 - 構成要素
生物種Tribolium castaneum (コクヌストモドキ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.05 Å
データ登録者Pichlo, C. / Hermanns, T. / Hofmann, K. / Baumann, U.
引用ジャーナル: Nat Commun / 年: 2022
タイトル: A structural basis for the diverse linkage specificities within the ZUFSP deubiquitinase family.
著者: Hermanns, T. / Pichlo, C. / Baumann, U. / Hofmann, K.
履歴
登録2021年5月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年2月2日Provider: repository / タイプ: Initial release
改定 1.12024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年11月6日Group: Derived calculations / Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Lys-63-specific deubiquitinase ZUFSP
B: Polyubiquitin-B
C: Lys-63-specific deubiquitinase ZUFSP
D: Polyubiquitin-B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)101,86515
ポリマ－101,0324
非ポリマー83211
水7,080393
1
A: Lys-63-specific deubiquitinase ZUFSP
B: Polyubiquitin-B
ヘテロ分子


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: native gel electrophoresis, Complexes between A and B or C and D respectively are biochemically (SDS-PAGE) validated complexes. In addition, Zup is a validated deubiquitinase and thus has to ...根拠: native gel electrophoresis, Complexes between A and B or C and D respectively are biochemically (SDS-PAGE) validated complexes. In addition, Zup is a validated deubiquitinase and thus has to interact with ubiqutin
  • 51 kDa, 2 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)51,0069
ポリマ－50,5162
非ポリマー4907
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
C: Lys-63-specific deubiquitinase ZUFSP
D: Polyubiquitin-B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,8596
ポリマ－50,5162
非ポリマー3434
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)151.607, 151.607, 83.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
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 227 through 234 or (resid 235...
d_2ens_1(chain "C" and (resid 227 through 244 or resid 246...
d_1ens_2chain "B"
d_2ens_2chain "D"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1CYSALAA5 - 22
d_12ens_1HISPROA24 - 34
d_13ens_1ALAGLUA36 - 41
d_14ens_1ARGGLUA43 - 76
d_15ens_1SERTHRA78 - 124
d_16ens_1LEUGLUA126 - 164
d_17ens_1LEUSERA166 - 184
d_18ens_1LEUTRPA186 - 194
d_19ens_1GLNASNA196 - 261
d_110ens_1GLYGLYA264
d_111ens_1GLUALAA266 - 317
d_112ens_1ALAALAA319 - 332
d_113ens_1GLNGLUA334 - 347
d_114ens_1GLNARGA349 - 365
d_21ens_1CYSALAH2 - 19
d_22ens_1HISGLUH21 - 37
d_23ens_1ARGGLUH39 - 72
d_24ens_1SERTHRH74 - 120
d_25ens_1LEUGLUH122 - 160
d_26ens_1LEUSERH162 - 180
d_27ens_1LEUTRPH182 - 190
d_28ens_1GLNASNH192 - 257
d_29ens_1GLYALAH261 - 313
d_210ens_1ALAALAH315 - 328
d_211ens_1GLNGLUH330 - 343
d_212ens_1GLNARGH345 - 361
d_11ens_2METGLYE1 - 75
d_21ens_2METGLYJ1 - 75

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.970601935947, -0.222613915662, 0.0915146244552), (-0.227569284731, 0.724945702239, -0.650127640893), (0.0783843261282, -0.651841064493, -0.754293791608)-99.0533051907, -17.3004098805, -11.130941625
2given(-0.97474434322, -0.213023840529, 0.0670396056545), (-0.201246846128, 0.707735208729, -0.677207930586), (0.0968151449092, -0.673596108726, -0.732731267263)-99.8571294091, -16.1742420952, -9.40861880344

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要素

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タンパク質 , 2種, 4分子 ACBD

#1: タンパク質 Lys-63-specific deubiquitinase ZUFSP / Zinc finger with UFM1-specific peptidase domain protein / Zinc finger-containing ubiquitin peptidase 1


分子量: 41957.246 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Tribolium castaneum (コクヌストモドキ)
遺伝子: TcasGA2_TC005718 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: D6WWN1
#2: タンパク質 Polyubiquitin-B


分子量: 8558.857 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: Ubiquitin functionalized with propargylamine replacing Gly76
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG47

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非ポリマー , 5種, 404分子

#3: 化合物 ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H8O7
#4: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#6: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Na
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 393 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 2.75 Å3/Da / 溶媒含有率: 55.23 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 8 % (v/v) Tacsimate pH 7; 22 %PEG3350

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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: SLS / ビームライン: X06DA / 波長: 1.000021 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2018年3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: 1.000021 Å / 相対比: 1
反射解像度: 2.05→51.67 Å / Num. obs: 67359 / % possible obs: 97.94 % / 冗長度: 8.6 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.83
反射 シェル解像度: 2.05→2.123 Å / Num. unique obs: 6329 / CC1/2: 0.411

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.1_4122精密化
PHENIX1.19.1_4122精密化
XDS20180126データ削減
XDS20180126データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6EI1

6ei1


解像度: 2.05→51.67 Å / SU ML: 0.2837 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.9919
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2186 1927 2.86 %
Rwork0.1852 65438 -
obs0.1862 67342 97.92 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 61.63 Å2
精密化ステップサイクル: LAST / 解像度: 2.05→51.67 Å
タンパク質核酸リガンド溶媒全体
原子数6898 0 55 393 7346
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00617126
X-RAY DIFFRACTIONf_angle_d0.78749630
X-RAY DIFFRACTIONf_chiral_restr0.05071059
X-RAY DIFFRACTIONf_plane_restr0.00681265
X-RAY DIFFRACTIONf_dihedral_angle_d13.36252699
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.82396691566
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.461582943211
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.34121320.30044350X-RAY DIFFRACTION91.81
2.1-2.160.29521340.2684506X-RAY DIFFRACTION95.43
2.16-2.220.2911340.2554658X-RAY DIFFRACTION97.76
2.22-2.290.28641390.24344635X-RAY DIFFRACTION97.91
2.29-2.370.26851390.22094684X-RAY DIFFRACTION97.95
2.37-2.470.25711310.21324642X-RAY DIFFRACTION98.13
2.47-2.580.2831360.21084708X-RAY DIFFRACTION98.7
2.58-2.720.22631380.19374681X-RAY DIFFRACTION98.29
2.72-2.890.21251390.21194716X-RAY DIFFRACTION98.52
2.89-3.110.24661410.18054692X-RAY DIFFRACTION98.94
3.11-3.430.26031420.18694746X-RAY DIFFRACTION99.21
3.43-3.920.18291390.15684750X-RAY DIFFRACTION99.23
3.92-4.940.16871380.14914800X-RAY DIFFRACTION99.38
4.94-56.20.18211450.16274870X-RAY DIFFRACTION99.66
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)
14.08768980301-0.4314095820170.8208590319073.587403700061.221456040246.83060627589-0.4307599057270.808645527592-0.024633132923-1.170456522130.343144479033-0.8443921256450.2931160885850.8304406989790.04720274534930.754190134107-0.1301856838420.1888525262770.609992870098-0.1428581239780.691094538073-58.3565382833-0.712295659959-42.5711952438
21.289196770520.07670046577420.6986046908221.03829978371-0.7969085785491.064966295880.290111110712-0.0449108289535-0.290294049610.41873589582-0.278223951825-0.629027709930.2316838546390.11801443869-0.1640008807540.478521284827-0.0236982124952-0.1893636524660.3705491193830.06451181610960.480400164107-58.443915437815.6690074553-5.7390834459
33.359412319320.04827657506441.52681099914.09206274771-1.703767775586.081449176440.1030079428920.2274559471520.240455965650.0162809961248-0.08299419875510.0985757587107-0.3594582682590.254094343693-0.01525602872310.2891004197890.003307151680310.008844003165050.22048613498-0.01477645208430.205525925515-72.902517861944.8733053014-18.2666691247
40.464683167833-0.100366260678-0.1298957553581.59901540202-0.3446410693551.000492147850.0449992744629-0.0769588550105-0.03537449055570.428400679898-0.0603463420585-0.00442607101870.272722728845-0.09045409250670.01875210343840.494136230786-0.0768775722661-0.03713014512490.2999285641360.003029043882480.219772709932-74.817165486420.4198929654-3.20301902713
51.293120335720.49119172712-0.6197980121282.39109600439-1.24616705224.277721851510.02725462753620.09863923100150.0428961720107-0.02848217650020.0536839718260.2757934325540.157497408276-0.424111215988-0.07722930270370.278535087645-0.0402003678006-0.04038194823310.2644414904020.001802518084980.228866892054-82.852450585825.5879249643-19.1731047966
61.045030851370.868269671778-0.2091853945190.928653631402-0.7491318752693.024249069780.116907533619-0.03286419094450.0296270409990.163065126621-0.06084282984020.0381488378782-0.0970452124705-0.12656652194-0.07914993068430.274448337729-0.00239309186302-0.02142642447030.217541207164-0.008100521587710.169561710013-75.859104463733.3330429145-19.5239708468
71.75789410412-0.007896944597071.186300817961.09311845290.9439098351863.22268609682-0.04851415367650.05899359381420.314689744144-0.02709036403270.0315638112976-0.304745470664-0.4144650634120.4564519305230.0346108352080.348606556336-0.0379346310506-0.02238879100730.290721269658-0.003550021769290.325305261892-63.081584311636.8559039009-18.0907582137
81.327703450280.432798167452-0.8442608698662.09777369557-0.6643113523023.278912808790.01348420371830.196495322856-0.1175804021090.0603916465951-0.0353400670410.3188373290790.448277019629-0.5797830950670.04963338371760.337935882343-0.0863654100883-0.01743072767270.32232916196-0.02914883092470.251011879651-86.695151684319.3432988511-16.5044440465
90.10382251173-0.221391182390.236854947440.8050836743420.2167384894912.257364871690.0986531378330.00358021339955-0.1213772823950.314967620948-0.0853842981173-0.04403133530630.716294995699-0.458366670427-0.004810994918170.695703411242-0.0829646967798-0.01956435761020.259867731948-0.02636983286960.261357256624-75.7260195605-5.85941802878-26.9700408165
104.66151796605-0.517252976434-1.830070301682.635743294260.3075795707094.27015166717-0.00696985206743-0.0808788211147-0.1131045991680.104314513808-0.208984277980.358818612920.22890538129-0.490037108930.2467363878080.468016162834-0.0953846683128-0.009003039768380.275082532198-0.05856087819880.245842545241-81.24034227082.49580999598-26.3951611348
117.143630818530.3221668196192.843370341580.8550178466491.066742776193.56396624213-0.3093725748640.3696003706840.554546662818-0.3955423958910.045763976895-0.0738171974295-0.1549320130330.09619342390760.2289458807020.545187078217-0.02169156454490.004260854156240.2941899780270.02574264572770.302780215103-71.30898320633.51033221389-35.3071534121
120.957554479768-0.224279280113-0.1435717602141.73030389851.057235918412.05316233443-0.04627567781460.142430827897-0.1590101163270.1261912022850.0588055175357-0.2177371629010.468398885095-0.02018006593720.002952427209850.5219613645-0.0196269085838-0.05731583663280.251148602589-0.0147825426450.275603777305-71.74996532370.80166099317-25.578896366
132.320628059962.176111763820.1370436315454.263159726491.968329191541.524980905260.100362505041-0.7942101781960.06355205823671.162756269090.252269768036-0.05241975282140.47996706613-0.215471947455-0.3084954987530.948928471671-0.140889023261-0.4247472206611.099831992560.3126529373410.918635340085-44.700921890424.05321576815.52897013
142.840578098732.291651350450.7928292085962.632442141532.288635669264.91867561386-0.010110202368-0.460369938405-0.4717581830410.395367472413-0.596432474375-0.3199072662520.226179437391-0.007576676454230.1379541748360.597742484239-0.139271185813-0.3774614628270.5322627840580.3272799842461.63696826465-40.11674559849.69067805911-4.02132984389
153.760590677351.12009239943-0.04589131384950.33390842255-0.07910732954311.48895049135-0.1561194123280.391415549092-0.522180487281-0.5260565607430.209082352269-1.16689561101-0.1796128470540.4450920523120.005679679816290.550693950723-0.1477082557030.2265131165750.479898290646-0.145081090680.894449886706-49.7258788511.676400595-31.5350029724
160.534952708613-0.1385610200450.5380674497720.753057293799-0.9332159914261.72911946057-0.5139121945760.49831803084-0.313275887159-0.4430111268730.29288942062-0.734734368799-0.3322444422440.1427436756750.1638933380290.677780354599-0.1843839692950.1658577725870.5125898654480.0183013538271.18149220482-38.944923196530.4728796591-29.9263899851
170.9102740949190.0342772533651-0.03484929916990.131635064488-0.2743240957540.571452830336-0.1736884082820.537536426834-0.621057612733-0.1644698561890.0084534967068-0.4068329852650.1208612778970.2382936569960.251955901330.92846428465-0.3216885773860.6200316523391.03993143851-0.4779785584032.00579036035-27.036043759217.3418705932-38.8423172795
180.1067812590190.1768166468920.2391241085190.2996722124050.3980320426240.5352239377950.08179279248740.127692136856-0.857814484948-0.05368048326250.120253831273-0.9499559862570.06395563517420.325956106282-0.008273690359380.518296107583-0.07166554775110.01014687650380.514118082103-0.02764617467942.05987650958-26.728881079615.3542600135-21.0466474963
192.100642393120.9497748579880.1839610497362.672238313520.2018108041092.25597700482-0.3106758969550.1376410475060.144402532495-0.2425782170130.130041926116-0.482713454693-0.545745831540.07558755520.1560482161340.665161904944-0.108423339549-0.05234274724830.421938024530.06846803845141.02430956151-37.27166711436.9788125859-21.9812340747
202.641591550050.261211183142-0.1813448032550.145031839044-0.3274129557390.807388785301-0.2030807351660.331183786992-0.895549666603-0.2320280292140.314706744755-1.016626812070.0376235929220.512586917526-0.1003048028390.630346372973-0.1874935191220.02935822360290.714563410678-0.05089276014612.07003682354-17.859194211625.6104509424-19.7833319465
212.00486688762-0.9359497140480.8024768511540.450113971886-0.2274700403811.89575159791-0.278626249772-0.659476605-0.1371911790320.4155267563160.268186003444-0.2190577754660.009912961555420.102413668178-0.02250539540660.859091389845-0.0739034107417-0.6331782416590.8018020937570.3908269070491.74294283141-27.096196234110.28272396374.3639015097
220.573952924262-0.01042574460040.06496019619560.156734005050.2634700258420.4544009787080.0323851622539-0.373608174589-0.1439270620660.1036785321130.132698629417-0.04685367178260.2235702518830.047654809245-0.08875259672551.07550083707-0.203334941177-0.71166759231.314417308820.3079835358081.40454691778-24.791963966221.191996472714.039135341
234.24794893749-0.6250020437570.4717166860570.4237079332010.2456905104741.5157472195-0.0345241034834-0.0567658856049-0.2417557406720.03577547811990.0454028964825-0.06364126763520.002211630542780.50991882874-0.1005972775560.634577174341-0.108535849141-0.4866938734570.9400850461040.2350599057651.76870545148-20.739734739819.01881530673.38330380966
241.321881015561.4689514889-0.2515391028341.64072369361-0.1946780818610.8278682562340.00948137533084-0.04455558259320.1035941470150.160527280259-0.0165735665854-0.683797525668-0.049122360780.305552548250.08898646316560.704420658535-0.190868732915-0.5370909489230.7698509468180.3309545208041.66635254246-29.919557915422.68242787760.536747673954
252.36076603147-0.6060798268640.7607017121780.247936701160.07223445149651.007532786680.0587545194758-0.799017525951-0.1705971535080.2935925201810.0181517045311-0.3499715465880.176583813889-0.205991732902-0.02427053723030.732669059145-0.201563297335-0.5879164500920.7427789397060.3486100948411.45786363311-32.020712620118.19755611954.39499073438
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 223 through 263 )AA223 - 2631 - 36
22chain 'A' and (resid 264 through 333 )AA264 - 33337 - 106
33chain 'A' and (resid 334 through 353 )AA334 - 353107 - 126
44chain 'A' and (resid 354 through 445 )AA354 - 445127 - 218
55chain 'A' and (resid 446 through 489 )AA446 - 489219 - 262
66chain 'A' and (resid 490 through 525 )AA490 - 525263 - 298
77chain 'A' and (resid 526 through 556 )AA526 - 556299 - 329
88chain 'A' and (resid 557 through 592 )AA557 - 592330 - 365
99chain 'B' and (resid 1 through 22 )BE1 - 221 - 22
1010chain 'B' and (resid 23 through 44 )BE23 - 4423 - 44
1111chain 'B' and (resid 45 through 59 )BE45 - 5945 - 59
1212chain 'B' and (resid 60 through 75 )BE60 - 7560 - 75
1313chain 'C' and (resid 226 through 263 )CH226 - 2631 - 32
1414chain 'C' and (resid 264 through 286 )CH264 - 28633 - 55
1515chain 'C' and (resid 287 through 333 )CH287 - 33356 - 102
1616chain 'C' and (resid 334 through 385 )CH334 - 385103 - 154
1717chain 'C' and (resid 386 through 409 )CH386 - 409155 - 178
1818chain 'C' and (resid 410 through 465 )CH410 - 465179 - 234
1919chain 'C' and (resid 466 through 561 )CH466 - 561235 - 330
2020chain 'C' and (resid 562 through 592 )CH562 - 592331 - 361
2121chain 'D' and (resid 1 through 16 )DJ1 - 161 - 16
2222chain 'D' and (resid 17 through 22 )DJ17 - 2217 - 22
2323chain 'D' and (resid 23 through 34 )DJ23 - 3423 - 34
2424chain 'D' and (resid 35 through 54 )DJ35 - 5435 - 54
2525chain 'D' and (resid 55 through 75 )DJ55 - 7555 - 75

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る