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- PDB-7vpg: Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 compl... -

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基本情報

登録情報
データベース: PDB / ID: 7vpg
タイトルCrystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98
要素
  • Isoform 3 of Nuclear pore complex protein Nup98-Nup96
  • ORF6 protein
  • mRNA export factor
キーワードVIRAL PROTEIN / Complex / Coronavirus / RNA nuclear export
機能・相同性
機能・相同性情報


transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear inclusion body / Nuclear Pore Complex (NPC) Disassembly / nuclear pore nuclear basket ...transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear inclusion body / Nuclear Pore Complex (NPC) Disassembly / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / NS1 Mediated Effects on Host Pathways / Transport of the SLBP Dependant Mature mRNA / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / nuclear localization sequence binding / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / mitotic spindle pole / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / host cell Golgi membrane / SUMOylation of DNA replication proteins / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Mitotic Prometaphase / serine-type peptidase activity / EML4 and NUDC in mitotic spindle formation / nuclear periphery / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / ubiquitin binding / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / RHO GTPases Activate Formins / molecular condensate scaffold activity / SARS-CoV-1 activates/modulates innate immune responses / fibrillar center / Separation of Sister Chromatids / HCMV Early Events / protein import into nucleus / nuclear envelope / snRNP Assembly / nuclear membrane / microtubule binding / transcription coactivator activity / nuclear body / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / cell division / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Non-structural protein NS6, betacoronavirus / Betacoronavirus NS6 protein / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. ...Non-structural protein NS6, betacoronavirus / Betacoronavirus NS6 protein / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
類似検索 - ドメイン・相同性
Nuclear pore complex protein Nup98-Nup96 / ORF6 protein / mRNA export factor RAE1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome-related coronavirus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.49 Å
データ登録者Li, T. / Guo, H. / Yang, T. / Wen, Y. / Ji, X.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)81871639 中国
引用ジャーナル: Front Mol Biosci / 年: 2021
タイトル: Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export.
著者: Li, T. / Wen, Y. / Guo, H. / Yang, T. / Yang, H. / Ji, X.
履歴
登録2021年10月17日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年1月19日Provider: repository / タイプ: Initial release
改定 1.12022年2月16日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: mRNA export factor
B: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
C: mRNA export factor
D: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
E: mRNA export factor
F: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
G: mRNA export factor
H: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
X: ORF6 protein
I: ORF6 protein
J: ORF6 protein
K: ORF6 protein


分子量 (理論値)分子数
合計 (水以外)211,36912
ポリマ－211,36912
非ポリマー00
水7,332407
1
A: mRNA export factor
B: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
X: ORF6 protein


分子量 (理論値)分子数
合計 (水以外)52,8423
ポリマ－52,8423
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: mRNA export factor
D: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
I: ORF6 protein


分子量 (理論値)分子数
合計 (水以外)52,8423
ポリマ－52,8423
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: mRNA export factor
F: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
J: ORF6 protein


分子量 (理論値)分子数
合計 (水以外)52,8423
ポリマ－52,8423
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: mRNA export factor
H: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
K: ORF6 protein


分子量 (理論値)分子数
合計 (水以外)52,8423
ポリマ－52,8423
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)149.614, 103.299, 134.936
Angle α, β, γ (deg.)90.000, 95.958, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 25 through 183 or resid 185...
d_2ens_1(chain "C" and (resid 25 through 183 or resid 185 through 205 or resid 207 through 365))
d_3ens_1(chain "E" and (resid 25 through 183 or resid 185 through 205 or resid 207 through 365))
d_4ens_1(chain "G" and (resid 25 through 183 or resid 185 through 205 or resid 207 through 365))
d_1ens_2(chain "B" and (resid 158 through 172 or resid 181 through 213))
d_2ens_2chain "D"
d_3ens_2(chain "F" and (resid 158 through 172 or resid 181 through 213))
d_4ens_2(chain "H" and (resid 158 through 172 or resid 181 through 213))
d_1ens_3chain "I"
d_2ens_3chain "J"
d_3ens_3chain "K"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNALAA1 - 159
d_12ens_1VALARGA161 - 181
d_13ens_1ILEASNA183 - 239
d_14ens_1SERARGA243 - 340
d_21ens_1ASNALAC1 - 159
d_22ens_1VALARGC161 - 181
d_23ens_1ILEARGC183 - 337
d_31ens_1ASNALAE2 - 160
d_32ens_1VALARGE162 - 182
d_33ens_1ILEARGE184 - 338
d_41ens_1ASNALAG2 - 160
d_42ens_1VALARGG162 - 182
d_43ens_1ILEARGG184 - 338
d_11ens_2THRTHRB1 - 15
d_12ens_2ASNLYSB20 - 52
d_21ens_2THRLYSD1 - 48
d_31ens_2THRTHRF1 - 15
d_32ens_2ASNLYSF22 - 54
d_41ens_2THRTHRH1 - 15
d_42ens_2ASNLYSH19 - 51
d_11ens_3ASPTYRJ1 - 10
d_21ens_3ASPTYRK1 - 10
d_31ens_3ASPTYRL1 - 10

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.999848051541, 0.00845764318596, 0.015242772087), (0.0134396523175, -0.182876651157, 0.983044000138), (0.0111017825029, 0.983099485674, 0.182735195548)-21.6664027973, 45.2902717295, 6.58008830063
2given(-0.984868600223, 0.0862822289477, -0.150297096654), (0.164150841714, 0.186341545041, -0.968675038264), (-0.0555728482216, -0.978689023929, -0.197685237135)-17.8201859947, 5.60411583934, 58.0787830831
3given(0.990456267532, -0.125930634688, 0.0560165810625), (-0.126045541194, -0.992023335343, -0.00149120088429), (0.055757543454, -0.00558367101385, -0.99842872503)0.675979474443, 36.8286945954, 69.1768832526
4given(-0.999978304543, 0.00410122807653, -0.00515464554073), (-0.00587621651607, -0.201784974615, 0.97941221868), (0.00297666287017, 0.979421259698, 0.201804696502)-21.6356221596, 45.1067653216, 6.58176732448
5given(-0.980531158201, 0.0762813652884, -0.180941430042), (0.19311970195, 0.207816274706, -0.958914582581), (-0.0355447396229, -0.975188981315, -0.218501767059)-17.5264384871, 6.10390557411, 58.6428322407
6given(0.990618149058, -0.118971953833, 0.0672410362665), (-0.118465416972, -0.992891753481, -0.0114852448886), (0.0681294924292, 0.00341175463405, -0.997670653167)0.466546540485, 37.0873922609, 69.3706949521
7given(0.969106832499, -0.242825495504, 0.0432171949157), (-0.245408934121, -0.966840792571, 0.070663546997), (0.0246252361714, -0.0790864119434, -0.996563564049)14.3944037119, 42.0912344446, 69.5648366901
8given(-0.981769219424, 0.165513178712, -0.0934590148872), (0.119169764076, 0.152927359093, -0.981025886596), (-0.148080272559, -0.974278507673, -0.169863540424)-28.3084177376, 39.2235038249, 112.219015277

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要素

#1: タンパク質
mRNA export factor / Rae1 protein homolog / mRNA-associated protein mrnp 41


分子量: 42398.527 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAE1, MRNP41
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P78406
#2: タンパク質
Isoform 3 of Nuclear pore complex protein Nup98-Nup96


分子量: 7785.728 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NUP98, ADAR2
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P52948, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ
#3: タンパク質・ペプチド
ORF6 protein / Accessory protein 6 / Non-structural protein 6 / ns6 / Protein X3


分子量: 2657.919 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Severe acute respiratory syndrome-related coronavirus (ウイルス)
参照: UniProt: P59634
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 407 / 由来タイプ: 天然 / 式: H2O

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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: 2.45 Å3/Da / 溶媒含有率: 49.86 %
解説: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
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 / pH: 5.5 / 詳細: 100 mM Sodium citrate pH 5.5, 20% PEG 3350

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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: SSRF / ビームライン: BL19U1 / 波長: 0.979 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年6月4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: 0.979 Å / 相対比: 1
反射解像度: 2.49→47.44 Å / Num. obs: 317454 / % possible obs: 99.74 % / 冗長度: 4.4 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 7.6
反射 シェル解像度: 2.49→2.57 Å / Num. unique obs: 7090 / CC1/2: 0.62

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3MMY

3mmy


解像度: 2.49→47.44 Å / SU ML: 0.3955 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 26.0609
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2305 3856 2.78 %
Rwork0.1855 134659 -
obs0.1867 138515 97.86 %
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: 45.21 Å2
精密化ステップサイクル: LAST / 解像度: 2.49→47.44 Å
タンパク質核酸リガンド溶媒全体
原子数12717 0 0 407 13124
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.008713059
X-RAY DIFFRACTIONf_angle_d1.094717722
X-RAY DIFFRACTIONf_chiral_restr0.06181887
X-RAY DIFFRACTIONf_plane_restr0.00842322
X-RAY DIFFRACTIONf_dihedral_angle_d7.47621705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.709941832532
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.750587761874
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.759771965431
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.990063141655
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.936683736954
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.705373716682
ens_3d_2JX-RAY DIFFRACTIONTorsion NCS1.74663103221
ens_3d_3JX-RAY DIFFRACTIONTorsion NCS1.90682059469
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.520.45271330.35854622X-RAY DIFFRACTION93.62
2.52-2.550.35891390.33884823X-RAY DIFFRACTION98.86
2.55-2.580.37531370.29954866X-RAY DIFFRACTION98.5
2.58-2.620.28471390.29594857X-RAY DIFFRACTION98.62
2.62-2.650.36361390.29224848X-RAY DIFFRACTION98.11
2.65-2.690.32061390.27664788X-RAY DIFFRACTION97.93
2.69-2.740.32511410.28314786X-RAY DIFFRACTION97.72
2.74-2.780.34141390.28154812X-RAY DIFFRACTION97.46
2.78-2.830.32691400.26854795X-RAY DIFFRACTION97.76
2.83-2.880.33551370.25434809X-RAY DIFFRACTION98.8
2.88-2.930.30991410.25894943X-RAY DIFFRACTION98.76
2.93-2.990.3151340.22754770X-RAY DIFFRACTION98.83
2.99-3.060.29481380.22814877X-RAY DIFFRACTION98.47
3.06-3.130.28291430.20364884X-RAY DIFFRACTION98.67
3.13-3.210.24051370.20944780X-RAY DIFFRACTION98.79
3.21-3.30.23751390.19264839X-RAY DIFFRACTION98.5
3.3-3.390.25941410.19464899X-RAY DIFFRACTION98.5
3.39-3.50.24631380.18764740X-RAY DIFFRACTION97.27
3.5-3.630.19961340.174769X-RAY DIFFRACTION96.74
3.63-3.770.21831410.15914781X-RAY DIFFRACTION97.52
3.77-3.940.23791410.15814854X-RAY DIFFRACTION98.27
3.94-4.150.15861350.15024780X-RAY DIFFRACTION98.34
4.15-4.410.15591370.13564847X-RAY DIFFRACTION98.54
4.41-4.750.15131390.12094821X-RAY DIFFRACTION98.08
4.75-5.230.2011350.12534760X-RAY DIFFRACTION96.7
5.23-5.990.20991330.15044781X-RAY DIFFRACTION97.19
5.99-7.540.19991350.15354809X-RAY DIFFRACTION97.55
7.54-47.440.13761320.15174719X-RAY DIFFRACTION95.95
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)
12.2137191530.4612237210821.057563139892.191703065121.18723395260.927265165325-0.06548940422410.0183820555934-0.144947165655-0.75290985070.00905034831666-0.674349409792-0.2458850179480.6985034751270.1086494541990.366207568984-0.09705333231620.1653340538110.567572661225-0.05572578651010.472177986878-15.650051309526.431432236-1.74673978392
22.3187088975-0.5182891557280.5195993567112.648218634820.2078275720152.12569776717-0.07992177389390.0746389949862-0.2950054414180.03368902811070.0375121905361-0.2230095678020.2080131130630.2148227879980.04191507958190.3202211898610.02353387648390.04629083172450.251018487646-0.02291745704560.294166880297-26.59397798711.28873708457.88555648873
31.7385748439-0.2152361327680.07601338171583.48826549071-0.03754493990192.60086441317-0.00610707123224-0.00046514480082-0.03131186923390.135035538403-0.1067976517310.155099524934-0.0206964010129-0.01757095921810.1028352792690.231207426555-0.0139564778780.02769799278970.2436968383550.002271788424710.209878123859-39.837296598823.92175461617.7693407373
42.6841097653-3.288391260111.734305279254.07330481912-2.559517140424.34323829651-0.1304004166910.02627647045690.397684258217-0.135808174314-0.213633718302-0.637878904562-0.7906098332780.07859931602760.3246871446710.560925905363-0.0568610757036-0.02317973458040.2475487122270.04878885151450.325684494455-30.475036731241.99865631184.85104310755
51.709496158730.120813681778-0.09824125422382.758362687660.5239146458271.801200044430.0979178555301-0.0519468628010.0459795022308-0.0374283894331-0.0319166072668-0.538149438678-0.2870060764160.379587996045-0.1104579270370.239057466342-0.05296423051940.01644255254270.265463987265-0.02033950509190.302324249702-22.157027786532.518216815211.1598465015
62.497235515770.04902828778750.1119336413662.990393912690.04603882420452.431022174880.003973241738940.2681290936180.0555292982562-0.4434589645870.0820664862943-0.379338218898-0.1889596681320.364884232219-0.1226954696430.367547789983-0.0138663670220.09950081559820.3004463982990.008639393831170.382617869963-22.80794948530.15183658061.12730959184
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122.133784895080.853767881236-0.1886886239012.126994812030.7138179522732.22874706584-0.1042741428990.327982519503-0.142837338994-0.3849869488360.1201020619210.1646588196380.093010810133-0.250237845038-0.007262481144470.339217208523-0.0837863274123-0.02551524262520.316181892619-0.03184955275220.35201256965515.952515946654.529654724519.0968327769
133.05326827641-0.06666803211050.4137508307485.59864517848-1.916267842543.715806956570.210073352947-0.2779049591840.316126763666-0.432857270759-0.149286581719-0.294116061921-0.0117036937960.228294949629-0.0601317300330.262714149577-0.002390754367840.01598051379230.249585100696-0.03843837109690.34233981797423.14790189961.860793050529.8762410814
143.71569383437-0.1549458071020.7125815195234.30866198888-0.27109951282.568322979570.0272478089559-0.3153345806910.01285839668260.03157476790170.04041748951450.5521626960540.167870344041-0.152717710826-0.05107150705920.366370909354-0.09931153075260.04048470198560.314863493301-0.02151474858510.31239941779515.016582508457.8228229738.6719610362
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186.69020976361.30370612483-0.1288829825141.830606259432.244101412735.471047039250.601696622333-0.553817333650.03076136932650.620687346596-0.241551465788-0.5583826315060.314539787314-0.235710621718-0.3972769405110.677792809893-0.06809742145270.02872875971040.3639539858690.06963804428150.48113338772719.291338065633.694826244946.5763473209
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215.48164797508-0.7875265616193.487587641351.458490056161.721449645135.835905302020.06379789991480.03439800646050.582373275769-0.170235588211-0.149681867730.0944771769836-1.08676840039-0.8829784701120.06387530049170.5072257058830.2178848101210.03506615897330.5074900412340.03455514868510.6452732953130.21780085187810.19539239732.9921843866
223.37030048271.345570285510.2841971787823.689502030260.5426129442793.05226416942-0.002786563132-0.4055484832770.169090420885-0.0219752118768-0.06075277248780.429772356766-0.173570940652-0.6352933932910.09332413202450.340960937990.02607811564350.05797659162010.418695375408-0.03898992881410.4181092727733.01173573706-1.056364013743.0781300949
233.485168694311.140465611360.08762013855693.544616486610.3237856840372.982117339020.104673104198-0.189785087260.1372191602150.264901620726-0.2583245762060.563616542491-0.0905017959545-0.5533140869440.09670059056530.3434168571440.03479957134510.103200087760.385217016929-0.05000226439330.4320824492884.47932873268-1.9058673836746.5761693524
242.34211076166-0.347671893547-0.5376633174593.267244322831.139601509413.52504376846-0.11885244469-0.372977788724-0.1698068214370.5589878576030.02219839431080.07856247886470.1821986438850.01104533070040.06543642408560.370548793250.03466157717330.0136688575110.2566302866920.01952329738260.25571278056618.8881220238-10.233196174745.6904214669
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271.81994376551-0.466372141980.6702499896413.265082511550.7538635017843.19048617789-0.0277999016201-0.01491380788780.214641486512-0.324079275469-0.07999679882260.573922912873-0.405328886883-0.5943207004230.131970841060.3226314754790.07475451476730.02480820558820.3869073327570.01650684406990.3218889468946.25385023232.4319915062327.4047777187
281.396654961110.470952068397-0.0629094950252.176724656962.253817394579.020200547030.244616101857-0.0359376163248-0.00635059886821-0.39747854991-0.032504679037-0.223085461313-0.927223394422-0.181371054732-0.2711741226320.440715793223-0.03436349426430.1434691333640.3674918003310.0647447959390.43809689132326.506735096510.805744923622.2596624586
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302.01098084691-1.94598623735-0.7137014084494.13674210845-3.257086997397.76690469593-0.597817710418-0.1766988607760.0310020516938-1.026976034090.0158729136857-1.08660587253-0.4476204041510.9114627939660.7884600927240.481966049007-0.1278114457490.07643162354140.433554727140.01830883737480.58142408780831.06568284297.2860168604630.2553557875
318.641668164721.73124676983-0.09791829621851.00778790267-1.424819583822.025742571360.452105717082-0.158168372990.800887902449-0.398442960379-0.01191149969480.0212913708588-0.8932885381240.326251052412-0.3885714229620.4807559103740.007775047208540.01232321674250.322754626573-0.03930431302320.51627661024223.080598529611.593312913840.4518047016
321.51063401745-1.06925235754-0.3369002421521.604441276440.4375620914780.119425615749-0.248009039266-0.790012372197-0.393696407281.30678440180.352531470681-0.4012257417890.5080826117790.889333119552-0.05317431117520.8067382697440.175017867122-0.2638703411270.8527409662360.1256440661520.571939101223-18.012534091412.478489319770.3212080967
331.43982265394-0.6520455422730.08188972042171.597257378450.3115220446812.40252675347-0.0891572368801-0.04594638698210.1330409050670.3479117803750.00384435182489-0.394601561913-0.2545685589930.3142226256440.07661149218040.420868360931-0.0959129528943-0.1311300864650.5071525750730.05902416988980.350080368294-23.958976892828.790690159761.8437048229
344.817061594720.862896061844-1.93702641812.408822285071.841967868634.17623182186-0.256163846760.2705982385840.33472417385-0.3018094422040.1673594235320.107457457832-0.4266725078470.1794301155810.07901901372590.465813742463-0.0344565603269-0.1315553718130.329918439670.03578957801410.236326744159-36.129985407130.163506323452.623521018
353.004925143670.5247419800590.09515893459781.913832938851.772489041182.28930434335-0.00540305795311-0.1347917637180.164167270431-0.000613333682413-0.199837924688-0.019441854074-0.63429346681-0.06607679021030.1946555614250.444731020439-0.0022947289089-0.08979396603280.3580064443790.02715621537730.28365673938-41.257766656828.04689161653.0198380838
366.006533926591.54902333844-0.4999041139647.1815812146-3.943229382047.415091956560.2216957034110.2096125368060.09151511011770.4855568098650.005170528833650.139008871382-0.864814705135-0.49755093757-0.240481921980.3283055441920.0125314957964-0.02174078811950.2700471800030.001923891820240.202698654086-44.611390884522.37175325245.4053081001
374.25620683207-0.2367504505580.5912781345133.60294258987-0.8132794877945.430485104740.161275568546-0.277659134365-0.411769548172-0.019451387439-0.2694613649370.07144227782480.0132019734810.3054656231060.1702996474630.308056024081-0.0021030437938-0.06042337545550.2149359263680.01511722227440.233396092875-37.75401161312.043775300548.4575071258
383.6248854524-0.3580830203191.04550170793.478417958370.02848339534966.57871496580.0301611832209-0.243746205886-0.587398028639-0.0426189811098-0.161533672949-0.1086843727050.607196269167-0.01704130968140.09423062177390.3588509965520.00808986391712-0.03601658762020.272418274830.03804406108770.37839218121-39.93077570714.6823977491646.0999207466
394.337184301611.13570007495-2.210701797281.63932284339-0.5863461159085.45931292093-0.147447307127-0.405564889573-0.7631102089080.369230462424-0.410117332094-0.444403155930.4886848117130.261678700270.4978435241470.4854049340260.0305391811453-0.03846981839240.3951321427640.1209656178750.470389047217-31.46716297353.9797993511558.0838745093
401.944596265430.2545573842730.20313899332.168397455921.181718793171.86509482277-0.0754444110267-0.233164045234-0.2976576889870.58126575275-0.0596337075796-0.3253711691350.2145513387810.7029398829570.1063370111650.4840253454520.0498406515261-0.09471541413190.5436911138430.1477900203080.453743116097-24.75894932367.0110293916357.9194299317
413.88375626299-0.788063070625-0.7521628164692.895291746040.04459882773781.965114647610.230508578911-0.552981044362-0.5583336968270.472037329868-0.149553445686-0.3018606159520.02555058960980.447754896466-0.134976721540.424230388216-0.0489293397584-0.1546014547910.6224113215090.2054136217020.516159868362-25.74941895869.7427710814966.6373249424
422.035444029921.325184078892.105941304134.705524684612.313473902312.44371529023-0.0749633140805-0.266946138998-0.402847188143-0.235722522870.119791803505-0.1775136035230.0259250283167-0.390445074462-0.06125720820820.61912879766-0.07826937031820.07875623560760.6567971994490.2261272027110.481552617972-45.8879343973.5555735111772.2904647414
435.34968957902-0.305037071872-0.8605259836534.802287288650.3752239238883.253816975260.469193133311-0.0626202602909-1.05889252574-0.15906411405-0.758192181562-0.2199529123150.043592730886-0.4110765682690.2694395443741.10118498594-0.219443699646-0.1165675697620.6135048037670.08952419263440.766380223386-42.6547709019-8.3146338627162.6199822386
443.681154237530.1920338329-0.8341885629375.28751032142-0.7857326354444.05478726522-0.0378905905065-0.680242695692-0.3178132113510.725339088221-0.01539031862620.03916333600780.0487036297725-0.4067499917150.1236149797410.551937958007-0.0522033233202-0.005114548348190.506123600060.1056479473990.293036689504-43.524927690415.274033952372.8360384535
452.003991126411.77644081474-3.466076670356.08885556464-1.543092843849.512130183540.896607625935-0.06408483672870.7646510018140.574558586357-0.376304532662-0.259975548751-0.7533979799430.342363485744-0.5141235697390.6620159282830.0297912090115-0.09813063372120.318227975460.0121646299380.550058204899-23.707700105244.550323240315.8454676818
463.65935741838-2.938488653281.077284082536.535730554560.2793852797399.236463096820.526938230959-0.663115360881-0.179136541996-0.244969776747-0.1116588318890.2572932826131.08372911127-0.023403878048-0.3668508116880.792489350934-0.2090976693390.1946015141130.43064692146-0.05677544237880.4327585244436.9783741349152.368933274354.0428634416
476.461270835593.034707198570.8406712964116.2861608675-0.249935850315.731364254820.4457626055351.381155488290.147546171058-0.43367027773-0.269284123494-0.135004766369-0.0565371671898-0.53570821384-0.172300980250.5430865860540.1053785002130.07185453873410.592107695695-0.008390596220840.3748861134210.7718044797-6.2775985399711.7608336521
482.003716823571.60391298278-0.6061975405176.123669229520.09978257091324.40580909039-0.242530711492-0.0482316742517-0.78556117280.3847268138740.261985287450.1660894908060.1861374636590.0770216012347-0.03485818941980.6058249990060.03316093539020.0315325639790.4687314892090.1046380794510.565469729922-31.5300563842-4.893234702551.0407543381
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 25 through 41 )AA25 - 411 - 17
22chain 'A' and (resid 42 through 148 )AA42 - 14818 - 124
33chain 'A' and (resid 149 through 258 )AA149 - 258125 - 234
44chain 'A' and (resid 259 through 281 )AA259 - 281235 - 256
55chain 'A' and (resid 282 through 334 )AA282 - 334257 - 309
66chain 'A' and (resid 335 through 366 )AA335 - 366310 - 341
77chain 'B' and (resid 158 through 173 )BB158 - 1731 - 16
88chain 'B' and (resid 174 through 186 )BB174 - 18617 - 25
99chain 'B' and (resid 187 through 199 )BB187 - 19926 - 38
1010chain 'B' and (resid 200 through 213 )BB200 - 21339 - 52
1111chain 'C' and (resid 25 through 105 )CC25 - 1051 - 81
1212chain 'C' and (resid 106 through 187 )CC106 - 18782 - 163
1313chain 'C' and (resid 188 through 206 )CC188 - 206164 - 182
1414chain 'C' and (resid 207 through 235 )CC207 - 235183 - 211
1515chain 'C' and (resid 236 through 292 )CC236 - 292212 - 264
1616chain 'C' and (resid 293 through 334 )CC293 - 334265 - 306
1717chain 'C' and (resid 335 through 366 )CC335 - 366307 - 338
1818chain 'D' and (resid 158 through 186 )DD158 - 1861 - 21
1919chain 'D' and (resid 187 through 199 )DD187 - 19922 - 34
2020chain 'D' and (resid 200 through 213 )DD200 - 21335 - 48
2121chain 'E' and (resid 24 through 41 )EE24 - 411 - 18
2222chain 'E' and (resid 42 through 71 )EE42 - 7119 - 48
2323chain 'E' and (resid 72 through 105 )EE72 - 10549 - 82
2424chain 'E' and (resid 106 through 196 )EE106 - 19683 - 173
2525chain 'E' and (resid 197 through 258 )EE197 - 258174 - 235
2626chain 'E' and (resid 259 through 292 )EE259 - 292236 - 265
2727chain 'E' and (resid 293 through 365 )EE293 - 365266 - 338
2828chain 'F' and (resid 158 through 173 )FF158 - 1731 - 16
2929chain 'F' and (resid 174 through 191 )FF174 - 19117 - 32
3030chain 'F' and (resid 192 through 199 )FF192 - 19933 - 40
3131chain 'F' and (resid 200 through 213 )FF200 - 21341 - 54
3232chain 'G' and (resid 24 through 41 )GG24 - 411 - 18
3333chain 'G' and (resid 42 through 125 )GG42 - 12519 - 102
3434chain 'G' and (resid 126 through 148 )GG126 - 148103 - 125
3535chain 'G' and (resid 149 through 187 )GG149 - 187126 - 164
3636chain 'G' and (resid 188 through 206 )GG188 - 206165 - 183
3737chain 'G' and (resid 207 through 235 )GG207 - 235184 - 212
3838chain 'G' and (resid 236 through 258 )GG236 - 258213 - 235
3939chain 'G' and (resid 259 through 292 )GG259 - 292236 - 265
4040chain 'G' and (resid 293 through 334 )GG293 - 334266 - 307
4141chain 'G' and (resid 335 through 366 )GG335 - 366308 - 339
4242chain 'H' and (resid 158 through 172 )HH158 - 1721 - 15
4343chain 'H' and (resid 173 through 186 )HH173 - 18616 - 24
4444chain 'H' and (resid 187 through 213 )HH187 - 21325 - 51
4545chain 'X' and (resid 50 through 62 )XI50 - 621 - 13
4646chain 'I' and (resid 53 through 62 )IJ53 - 621 - 10
4747chain 'J' and (resid 53 through 62 )JK53 - 621 - 10
4848chain 'K' and (resid 53 through 62 )KL53 - 621 - 10

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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