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- PDB-7vph: Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 compl... -

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基本情報

登録情報
データベース: PDB / ID: 7vph
タイトルCrystal structure of the C-terminal tail of SARS-CoV-2 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 / Protein binding
機能・相同性
機能・相同性情報


Translation of Accessory Proteins / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body ...Translation of Accessory Proteins / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / : / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / mitotic spindle pole / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / serine-type peptidase activity / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / nuclear periphery / protein sequestering activity / SUMOylation of chromatin organization proteins / HCMV Late Events / ubiquitin binding / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / RHO GTPases Activate Formins / molecular condensate scaffold activity / ISG15 antiviral mechanism / fibrillar center / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / microtubule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / nuclear membrane / transcription coactivator activity / host cell endoplasmic reticulum membrane / nuclear body / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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
ORF6 protein / Nuclear pore complex protein Nup98-Nup96 / mRNA export factor RAE1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 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

ダウンロードとリンク

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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
I: ORF6 protein
J: ORF6 protein
K: ORF6 protein
X: ORF6 protein


分子量 (理論値)分子数
合計 (水以外)210,68412
ポリマ－210,68412
非ポリマー00
水1,00956
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)52,6713
ポリマ－52,6713
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-15 kcal/mol
Surface area17070 Å2
手法PISA
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)52,6713
ポリマ－52,6713
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-17 kcal/mol
Surface area16430 Å2
手法PISA
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)52,6713
ポリマ－52,6713
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-15 kcal/mol
Surface area17140 Å2
手法PISA
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)52,6713
ポリマ－52,6713
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-18 kcal/mol
Surface area16760 Å2
手法PISA
単位格子
Length a, b, c (Å)150.657, 103.319, 136.588
Angle α, β, γ (deg.)90.00, 97.45, 90.00
Int Tables number5
Space group name H-MC121

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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 / ORF6 / Accessory protein 6 / Non-structural protein 6 / ns6 / Protein X3


分子量: 2486.661 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
参照: UniProt: P0DTC6
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 56 / 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: 2.5 Å3/Da / 溶媒含有率: 50.83 %
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: 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: BL17U1 / 波長: 0.979 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2021年1月23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: 2.796→41.065 Å / Num. obs: 51228 / % possible obs: 99.32 % / 冗長度: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 1
反射 シェル解像度: 2.8→2.85 Å / Num. unique obs: 5087 / CC1/2: 0.58

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.19.2_4158: ???)精密化
HKL-2000データ削減
HKL-2000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: 2.8→41.06 Å / SU ML: 0.43 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 28.88 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2442 1992 3.89 %
Rwork0.1924 --
obs0.1945 51064 99.36 %
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
精密化ステップサイクル: LAST / 解像度: 2.8→41.06 Å
タンパク質核酸リガンド溶媒全体
原子数12503 0 0 56 12559
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0112839
X-RAY DIFFRACTIONf_angle_d1.3817416
X-RAY DIFFRACTIONf_dihedral_angle_d7.7661672
X-RAY DIFFRACTIONf_chiral_restr0.0711855
X-RAY DIFFRACTIONf_plane_restr0.0112278
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.41351390.34553441X-RAY DIFFRACTION97
2.87-2.940.37831420.32113505X-RAY DIFFRACTION100
2.94-3.030.32681410.28963490X-RAY DIFFRACTION100
3.03-3.130.32921440.26913543X-RAY DIFFRACTION100
3.13-3.240.31921390.26063462X-RAY DIFFRACTION99
3.24-3.370.29611440.2453528X-RAY DIFFRACTION100
3.37-3.520.29471430.22783527X-RAY DIFFRACTION100
3.52-3.710.25021410.20093474X-RAY DIFFRACTION100
3.71-3.940.26181420.18173527X-RAY DIFFRACTION100
3.94-4.240.23211440.16293528X-RAY DIFFRACTION100
4.24-4.670.18211430.13163535X-RAY DIFFRACTION100
4.67-5.350.15941450.13223557X-RAY DIFFRACTION100
5.35-6.730.28071430.16713547X-RAY DIFFRACTION100
6.73-41.060.18521420.17563520X-RAY DIFFRACTION97
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)
12.93151.831.8852.38381.34881.3058-0.38230.4791-0.0174-0.48740.2797-0.1191-0.25240.92130.03560.4542-0.05990.15530.7646-0.02190.7499-15.939626.3828-1.2791
22.88820.18150.13923.6622-1.20112.87350.02320.0134-0.1052-0.0983-0.017-0.5559-0.19960.4026-0.02310.27730.04730.06770.4675-0.04660.4262-22.239813.33346.5938
32.0341-1.264-1.11194.90691.34392.8492-0.07460.0651-0.24870.08540.02470.39920.3822-0.06430.10210.3421-0.0338-0.02210.3988-0.01760.3033-38.771912.33712.2218
41.8882-0.0613-0.73155.1342-1.30182.92620.1045-0.28190.03530.35270.05620.2151-0.1175-0.1429-0.14910.3056-0.0196-0.03310.3954-0.01320.2966-38.536930.014420.6294
53.14391.28820.16993.55042.14961.58430.09650.32270.3755-0.6301-0.1888-0.1554-0.3989-0.02660.01840.4471-0.03160.09910.34420.00340.4333-28.557937.94999.1268
63.1610.45080.51274.0344-0.31093.92110.0572-0.16480.45760.3554-0.1822-0.4549-0.52960.196-0.05310.4929-0.10680.0460.4019-0.03160.5256-24.830738.256113.9097
73.24110.8280.83963.38090.85862.76730.20320.3118-0.0469-0.65620.0618-0.8277-0.06390.5329-0.25590.48670.00480.15360.4878-0.02790.5528-22.281629.22543.3081
83.09210.4572-1.5885.51793.75883.75030.2919-0.3183-0.17270.22940.30690.5371-0.3372-0.6216-0.56150.78640.0708-0.0510.64850.17120.4956-41.781338.7644-5.5791
97.94993.02023.50897.37422.0112.26720.2348-0.57840.16920.23390.6872-2.0329-2.3681-1.2966-0.68381.35610.18840.0520.5728-0.03110.8737-38.409350.33554.5794
105.32961.74710.63018.4014-1.70621.65470.04450.27530.1317-0.25590.1920.11770.2472-0.1788-0.16030.57220.0691-0.10230.50460.01830.2314-41.0427.1914-6.1004
112.4664-0.82830.96721.59730.46561.8408-0.20110.2935-0.46830.2492-0.10290.78290.3982-0.79080.26060.5505-0.2920.04840.86420.04111.2859-2.625844.681925.1695
125.17290.6425-0.42940.13150.16290.9491-0.01120.4903-0.312-0.53850.06411.04310.2637-0.66240.11270.5435-0.1931-0.16860.67530.03481.12423.262349.173215.6113
133.86170.76871.31382.8980.89224.8938-0.08880.1219-0.1488-0.09240.13010.4511-0.06440.1029-0.00660.363-0.09130.00840.3675-0.0060.440419.340957.596923.6392
142.8798-1.8286-1.43122.13981.64991.24770.30260.43780.0890.7651-0.5786-0.14810.0217-0.36580.29880.7425-0.10350.29140.47440.03590.743113.373957.661937.9935
152.43051.7046-0.12912.4633-0.21973.08040.1529-0.4558-0.1430.9257-0.12250.68940.4682-0.2021-0.07760.8959-0.14520.37560.55080.0151.00578.193252.045344.9032
161.3176-0.6899-0.99270.62060.72332.9781-0.00070.2342-0.19510.4762-0.20650.84380.9832-0.91030.1690.7317-0.30650.23170.8093-0.03091.413-0.036142.524234.7729
170.08610.0789-0.01750.2535-0.15030.10020.1753-0.35620.65971.0479-0.44061.70470.68630.2317-0.21591.1052-0.03140.08920.8460.03360.939421.964928.086331.2805
181.93521.3736-0.07021.6744-0.70560.49390.1597-0.4319-0.23670.71790.1508-0.05810.96910.2248-0.20321.38010.06930.22160.57580.08721.10819.834834.28942.2349
197.1389-0.5921-1.47754.4099-4.70175.6837-0.29790.936-1.04730.08490.12220.80961.8933-0.44730.13191.142-0.14320.10870.4708-0.10040.957216.122932.481125.4768
205.8036-0.23530.12640.97840.10412.68220.24650.47481.2756-0.02610.1550.4291-1.0913-0.201-0.60690.61560.23310.27780.70750.02350.9853-0.08589.744632.7782
210.87321.2164-0.1191.9257-0.97872.87690.2497-0.18550.22940.7336-0.09180.6821-0.1588-0.5424-0.12130.90750.06230.46460.6304-0.02770.9393.1465-1.56244.3045
221.9172-0.3606-0.02561.25510.87923.71970.1399-0.29260.08120.99340.00120.46090.1811-0.16210.00170.8533-0.00760.21750.4681-0.0130.45717.368-10.059946.7585
234.3722-0.572-0.97884.8414-0.96267.23720.1155-0.0595-0.0795-0.0186-0.24670.12440.2873-0.03840.04670.45220.01450.14070.4301-0.04640.396520.1572-14.867530.6501
243.2397-1.2878-0.4656.132-0.45264.13990.2460.42390.0997-0.7066-0.1290.1988-0.0251-0.3583-0.11020.43470.03830.02970.45150.04080.459712.9733-6.188320.0868
255.191-0.22580.37514.39981.21296.4670.35570.0142-0.36950.3169-0.34061.15450.0752-0.4988-0.05110.58050.11450.20720.5831-0.03830.80463.33461.060829.4228
264.041-0.62531.02323.31660.82123.72660.1065-0.30410.92740.2449-0.07540.6278-0.8612-0.8135-0.01350.64240.17770.17560.57340.09570.65817.28887.168929.6299
272.7712-0.56751.53333.24591.5095.70290.0733-0.14250.06630.7419-0.1710.041-0.4135-0.27830.00410.7478-0.15070.22130.50990.07690.484727.897114.138127.2851
285.67455.4613-0.44976.166-3.46129.9188-0.7656-0.06690.0727-0.77230.8879-0.47910.9656-0.6857-0.43020.69170.02-0.11940.8138-0.05190.95721.07732.07576.3896
293.4825-0.0957-0.58391.0125-1.99074.56650.1931-0.02120.05420.2773-0.1719-0.1758-0.2822-0.0193-0.11290.7655-0.07510.17310.4260.01630.587225.17169.558733.3267
304.181-0.90270.81251.5285-0.79670.4254-0.1639-0.89110.03880.63390.4205-0.17610.71150.576-0.06751.29390.0345-0.421.02980.16620.5389-21.350518.382863.9724
311.73490.33820.59071.52060.36012.7437-0.0090.00840.24251.11020.0205-0.4440.01130.63290.01921.1125-0.155-0.32671.00530.05220.4322-24.741226.968563.723
322.03030.02280.79792.3981.55061.6501-0.116-0.39240.1820.6891-0.02330.0613-0.29860.18220.12961.0012-0.0721-0.0630.66990.01830.3548-38.719130.33255.443
333.1405-1.00961.00483.8463-0.6573.83850.0885-0.1877-0.3620.89880.09530.58090.3161-0.1563-0.07260.7985-0.0308-0.00690.42750.10650.3482-41.810714.56947.7858
343.3233-0.08260.56761.3186-1.21741.06440.3831-0.4893-0.78670.8473-0.2050.26461.16410.53480.04511.44480.0563-0.08040.6160.17410.7503-39.94140.355152.922
351.82070.3058-0.14530.19220.55362.1777-0.2369-0.3652-0.61161.7681-0.248-0.98010.68040.87930.09761.42430.0847-0.40280.82540.28560.4168-27.1657.477156.7986
362.9519-0.1977-0.56390.1671-0.27952.28430.1123-0.596-1.05521.2662-0.2322-0.1770.62420.3337-0.07461.50120.0587-0.26731.14470.34920.656-27.89969.605767.4783
377.5706-1.62830.39852.613-2.69373.1919-0.6078-0.8224-2.04780.05250.11990.11240.1779-0.7090.23822.0694-0.30440.3340.85310.31981.006-47.70061.209471.6874
381.2355-1.26640.89155.6059-4.46083.7733-0.2995-1.0412-0.73420.2866-0.30620.43190.75570.62770.80081.6836-0.02340.11051.02140.15380.7089-48.27346.619368.9911
396.794-0.9124-0.62093.5579-2.98226.6322-0.5952-1.27630.27392.26850.57670.23770.1770.72380.231.59580.0450.05521.05890.1410.5599-42.669819.534275.4788
400.2137-0.97510.20594.6143-1.45842.7817-0.1097-0.3727-0.52340.12160.60751.23680.3222-0.15620.2621.7174-0.16580.86740.65930.35780.93443.783552.136253.0377
417.0673-2.48846.762.4335-1.36877.1328-0.06551.82781.5273-0.29850.19170.3412-0.6903-0.9548-0.27260.54640.0841-0.22190.83320.26080.796110.1644-6.16411.0032
425.7562-1.69522.30798.06822.47533.11340.79-0.5353-0.75620.21720.29781.2162-0.71120.4331-1.26261.21080.07820.07640.74720.1760.9512-31.094-5.247351.7349
430.042-0.2586-0.42113.57432.52094.37580.00170.9951.6901-0.52970.01060.0048-1.16140.3697-0.18440.9448-0.21590.04640.66770.04930.7444-26.217745.235515.9534
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 196 )
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 258 )
5X-RAY DIFFRACTION5chain 'A' and (resid 259 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 310 )
7X-RAY DIFFRACTION7chain 'A' and (resid 311 through 365 )
8X-RAY DIFFRACTION8chain 'B' and (resid 158 through 172 )
9X-RAY DIFFRACTION9chain 'B' and (resid 173 through 186 )
10X-RAY DIFFRACTION10chain 'B' and (resid 187 through 213 )
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 69 )
12X-RAY DIFFRACTION12chain 'C' and (resid 70 through 125 )
13X-RAY DIFFRACTION13chain 'C' and (resid 126 through 208 )
14X-RAY DIFFRACTION14chain 'C' and (resid 209 through 235 )
15X-RAY DIFFRACTION15chain 'C' and (resid 236 through 310 )
16X-RAY DIFFRACTION16chain 'C' and (resid 311 through 365 )
17X-RAY DIFFRACTION17chain 'D' and (resid 158 through 162 )
18X-RAY DIFFRACTION18chain 'D' and (resid 163 through 199 )
19X-RAY DIFFRACTION19chain 'D' and (resid 200 through 213 )
20X-RAY DIFFRACTION20chain 'E' and (resid 25 through 41 )
21X-RAY DIFFRACTION21chain 'E' and (resid 42 through 105 )
22X-RAY DIFFRACTION22chain 'E' and (resid 106 through 187 )
23X-RAY DIFFRACTION23chain 'E' and (resid 188 through 235 )
24X-RAY DIFFRACTION24chain 'E' and (resid 236 through 310 )
25X-RAY DIFFRACTION25chain 'E' and (resid 311 through 334 )
26X-RAY DIFFRACTION26chain 'E' and (resid 335 through 365 )
27X-RAY DIFFRACTION27chain 'F' and (resid 158 through 169 )
28X-RAY DIFFRACTION28chain 'F' and (resid 170 through 183 )
29X-RAY DIFFRACTION29chain 'F' and (resid 184 through 213 )
30X-RAY DIFFRACTION30chain 'G' and (resid 26 through 61 )
31X-RAY DIFFRACTION31chain 'G' and (resid 62 through 105 )
32X-RAY DIFFRACTION32chain 'G' and (resid 106 through 187 )
33X-RAY DIFFRACTION33chain 'G' and (resid 188 through 244 )
34X-RAY DIFFRACTION34chain 'G' and (resid 245 through 275 )
35X-RAY DIFFRACTION35chain 'G' and (resid 276 through 334 )
36X-RAY DIFFRACTION36chain 'G' and (resid 335 through 366 )
37X-RAY DIFFRACTION37chain 'H' and (resid 158 through 183 )
38X-RAY DIFFRACTION38chain 'H' and (resid 184 through 199 )
39X-RAY DIFFRACTION39chain 'H' and (resid 200 through 213 )
40X-RAY DIFFRACTION40chain 'I' and (resid 53 through 61 )
41X-RAY DIFFRACTION41chain 'J' and (resid 54 through 61 )
42X-RAY DIFFRACTION42chain 'K' and (resid 53 through 61 )
43X-RAY DIFFRACTION43chain 'X' and (resid 53 through 61 )

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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