[日本語] English
万見
- PDB-3c0r: Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 3c0r
タイトルStructure of Ovarian Tumor (OTU) domain in complex with Ubiquitin
要素
  • Ubiquitin thioesterase OTU1
  • Ubiquitinユビキチン
キーワードCELL CYCLE (細胞周期) / HYDROLASE (加水分解酵素) / ubiquitin hydrolase / deubiquitinase (脱ユビキチン化酵素)
機能・相同性
機能・相同性情報


Ovarian tumor domain proteases / : / : / protein modification process => GO:0036211 / : / protein deubiquitination / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination ...Ovarian tumor domain proteases / : / : / protein modification process => GO:0036211 / : / protein deubiquitination / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / endoplasmic reticulum unfolded protein response / 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 / グリコーゲン合成 / 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) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import
類似検索 - 分子機能
: / OTU1, UBXL domain / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e ...: / OTU1, UBXL domain / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / ユビキチン様タンパク質 / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
類似検索 - ドメイン・相同性
3-AMINOPROPANE / Polyubiquitin-C / Ubiquitin thioesterase OTU1 / Ubiquitin-60S ribosomal protein L40
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 多波長異常分散 / 解像度: 2.315 Å
データ登録者Messick, T.E. / Marmorstein, R.
引用ジャーナル: J.Biol.Chem. / 年: 2008
タイトル: Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein
著者: Messick, T.E. / Russell, N.S. / Iwata, A.J. / Sarachan, K.L. / Shiekhattar, R. / Shanks, J.R. / Reyes-Turcu, F.E. / Wilkinson, K.D. / Marmorstein, R.
履歴
登録2008年1月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02008年2月19日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22011年11月16日Group: Atomic model
改定 1.32017年10月25日Group: Refinement description / カテゴリ: software

-
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

-
集合体

登録構造単位
A: Ubiquitin thioesterase OTU1
B: Ubiquitin
C: Ubiquitin thioesterase OTU1
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,4596
ポリマ－65,3404
非ポリマー1182
水5,873326
1
C: Ubiquitin thioesterase OTU1
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,7293
ポリマ－32,6702
非ポリマー591
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-14 kcal/mol
Surface area11660 Å2
手法PISA
2
A: Ubiquitin thioesterase OTU1
B: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,7293
ポリマ－32,6702
非ポリマー591
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-14 kcal/mol
Surface area11550 Å2
手法PISA
単位格子
Length a, b, c (Å)107.311, 107.311, 100.239
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDモデル要素
11A-313-

HOH

21B-100-

HOH

-
要素

#1: タンパク質 Ubiquitin thioesterase OTU1 / E.C.3.4.19.12 / Otu1 / OTU domain-containing protein 1


分子量: 24150.406 Da / 分子数: 2 / 断片: Otu domain / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: Otu1 / プラスミド: pTYB2 / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P43558, ubiquitinyl hydrolase 1
#2: タンパク質 Ubiquitin / ユビキチン / Ubiquitin B


分子量: 8519.778 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 解説: propylamine added by intein-mediated ligation / 遺伝子: ubiquitin B / プラスミド: pTYB2 / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62988, UniProt: P0CG48*PLUS
#3: 化合物 ChemComp-3CN / 3-AMINOPROPANE / プロピルアミン / プロピルアミン


分子量: 59.110 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H9N
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 326 / 由来タイプ: 天然 / 式: H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.55 Å3/Da / 溶媒含有率: 51.76 %
結晶化温度: 277 K / 手法: ハンギングドロップ法 / pH: 6.5
詳細: MES, ammonium acetate, PEG3350, pH 6.5, hanging drop, temperature 277K

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.9793, 0.9795, 0.9566
検出器タイプ: MARRESEARCH / 検出器: CCD / 日付: 2005年3月25日
放射プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID波長 (Å)相対比
10.97931
20.97951
30.95661
Reflection冗長度: 18.1 % / Av σ(I) over netI: 15.8 / 数: 517121 / Rmerge(I) obs: 0.091 / Χ2: 1.07 / D res high: 2.31 Å / D res low: 50 Å / Num. obs: 28554 / % possible obs: 99.8
Diffraction reflection shell
最高解像度 (Å)最低解像度 (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.985099.810.0711.03217.9
3.954.9810010.071.00918.3
3.453.9510010.0711.08418.5
3.133.4510010.0871.08318.6
2.913.1310010.1131.03818.6
2.742.9110010.1611.08718.6
2.62.7410010.2021.08418.6
2.492.699.910.2721.08918.4
2.392.4910010.3531.07517.7
2.312.3998.210.4081.0715.6
反射解像度: 2.315→36.626 Å / Num. obs: 28554 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / 冗長度: 18.1 % / Biso Wilson estimate: 50.66 Å2 / Rsym value: 0.08 / Net I/σ(I): 30.2
反射 シェル解像度: 2.315→2.39 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.29 / Num. unique all: 2785 / Rsym value: 0.529

-
位相決定

位相決定手法: 多波長異常分散
Phasing MAD set
ID最高解像度 (Å)最低解像度 (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.3136.630027555972
ISO_22.3136.630.0590.05127159971
ANO_12.3136.632.220274720
ANO_22.3136.631.5470268490
Phasing MAD set shell
ID解像度 (Å)Power acentricPower centricReflection acentricReflection centric
ISO_19.98-36.630031849
ISO_17.19-9.980056847
ISO_15.91-7.190071553
ISO_15.14-5.910087546
ISO_14.6-5.140098449
ISO_14.21-4.600107549
ISO_13.9-4.2100119248
ISO_13.65-3.900126447
ISO_13.44-3.6500133850
ISO_13.27-3.4400143545
ISO_13.12-3.2700149554
ISO_12.98-3.1200157244
ISO_12.87-2.9800163750
ISO_12.76-2.8700170848
ISO_12.67-2.7600175252
ISO_12.59-2.6700184745
ISO_12.51-2.5900188449
ISO_12.44-2.5100194247
ISO_12.37-2.4400197952
ISO_12.31-2.3700197548
ANO_19.98-36.633.49703180
ANO_17.19-9.984.13205680
ANO_15.91-7.194.74407150
ANO_15.14-5.914.25108740
ANO_14.6-5.143.30409840
ANO_14.21-4.62.808010750
ANO_13.9-4.212.881011920
ANO_13.65-3.92.861012640
ANO_13.44-3.652.682013380
ANO_13.27-3.442.606014350
ANO_13.12-3.272.542014950
ANO_12.98-3.122.347015720
ANO_12.87-2.982.085016370
ANO_12.76-2.871.816017080
ANO_12.67-2.761.729017520
ANO_12.59-2.671.497018470
ANO_12.51-2.591.247018840
ANO_12.44-2.511.087019390
ANO_12.37-2.440.897019630
ANO_12.31-2.370.834019120
ISO_29.98-36.630.1070.08131349
ISO_27.19-9.980.0950.06156347
ISO_25.91-7.190.10.05771153
ISO_25.14-5.910.0890.05587146
ISO_24.6-5.140.0720.05198149
ISO_24.21-4.60.0570.048107349
ISO_23.9-4.210.0570.044118948
ISO_23.65-3.90.0550.052126147
ISO_23.44-3.650.0510.044133750
ISO_23.27-3.440.0540.043143445
ISO_23.12-3.270.0560.044149554
ISO_22.98-3.120.0570.037157144
ISO_22.87-2.980.0540.049163750
ISO_22.76-2.870.0530.035170648
ISO_22.67-2.760.0520.055175252
ISO_22.59-2.670.050.043184045
ISO_22.51-2.590.0450.036186549
ISO_22.44-2.510.0410.031189747
ISO_22.37-2.440.0370.024187052
ISO_22.31-2.370.0310.029179347
ANO_29.98-36.633.3503130
ANO_27.19-9.984.23605630
ANO_25.91-7.194.68907110
ANO_25.14-5.913.84208710
ANO_24.6-5.142.98809810
ANO_24.21-4.62.464010710
ANO_23.9-4.212.306011870
ANO_23.65-3.92.096012590
ANO_23.44-3.652.002013350
ANO_23.27-3.441.823014320
ANO_23.12-3.271.763014940
ANO_22.98-3.121.491015710
ANO_22.87-2.981.266016360
ANO_22.76-2.871.14017050
ANO_22.67-2.761017500
ANO_22.59-2.670.878018330
ANO_22.51-2.590.781018370
ANO_22.44-2.510.681018520
ANO_22.37-2.440.63018090
ANO_22.31-2.370.565016390

-
解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
SHARP位相決定
SOLOMON位相決定
PHENIX精密化
PDB_EXTRACT3.004データ抽出
HKL-2000データ収集
精密化構造決定の手法: 多波長異常分散 / 解像度: 2.315→36.626 Å / 交差検証法: THROUGHOUT / 立体化学のターゲット値: MLHL
Rfactor反射数%反射Selection details
Rfree0.243 1438 5.04 %random
Rwork0.196 ---
obs0.198 28527 99.64 %-
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 max: 16.46 Å2 / Biso mean: 54.26 Å2 / Biso min: 174.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.065 Å20 Å20 Å2
2--0.065 Å2-0 Å2
3----0.131 Å2
精密化ステップサイクル: LAST / 解像度: 2.315→36.626 Å
タンパク質核酸リガンド溶媒全体
原子数3962 0 8 326 4296
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.014036
X-RAY DIFFRACTIONf_angle_d1.235444
X-RAY DIFFRACTIONf_chiral_restr0.079628
X-RAY DIFFRACTIONf_plane_restr0.004700
X-RAY DIFFRACTIONf_dihedral_angle_d18.3341490
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.315-2.3970.3251350.2452613274897
2.397-2.4930.2691700.24426942864100
2.493-2.6070.2681480.2326732821100
2.607-2.7440.291260.22127422868100
2.744-2.9160.2831280.22927252853100
2.916-3.1410.2821500.20826972847100
3.141-3.4570.221420.19427352877100
3.457-3.9570.2181270.1727322859100
3.957-4.9830.2051710.14826932864100
4.983-36.6310.2061410.1727852926100
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)
1-0.0298-0.070.01040.08520.05390.14910.66850.3437-0.07280.04520.3191-1.53090.01220.95910.00030.26570.10670.02450.3722-0.18050.728840.415136.380241.0376
20.75610.81870.13490.8867-0.66121.6681-0.3387-0.0072-0.34920.04360.1168-0.06460.22740.2504-0.00110.2492-0.0018-0.05390.14910.03460.222125.332638.359442.695
30.06430.19750.02790.3957-0.62240.9850.22910.41230.865-0.32740.69660.9135-0.4895-0.58810.02980.30510.0294-0.09790.26920.00360.465310.473945.168642.6828
45.95854.8351.07399.98993.23871.35220.28172.1628-0.5233-2.24080.6322-1.2987-0.28180.46561.4255-0.16620.1446-0.44050.31110.23970.6330.060738.148648.8024
50.11330.07350.09360.1251-0.09610.2678-0.1972-0.02570.10470.04280.91441.7055-0.0967-0.7596-0.00130.19950.08830.09060.94730.24810.9090.148835.374158.5727
6-0.56632.52175.18439.24654.81915.1741-0.26790.40221.954-1.4782-0.3814-1.1919-1.24730.58730.43070.20530.3645-0.16590.5437-0.13040.7247.444346.331255.0128
70.50220.85750.30457.86470.63250.6783-0.5335-0.83790.1051-1.14410.2522.5681-0.4564-0.9397-0.0360.03830.13890.11330.38720.01180.210811.136638.454653.8085
80.8036-0.4522-0.53461.36040.07390.4850.0016-0.4902-0.1534-0.0550.18120.29540.1901-0.31030.00010.1533-0.0315-0.07620.20640.11760.265218.344630.653746.8019
91.09735.08311.53722.02960.6101-0.3675-0.23590.7507-0.4707-1.18320.2724-1.12870.31540.83770.03120.30790.0343-0.1250.32520.11130.227424.814433.924434.4479
10-0.04690.04090.0510.09990.11540.1537-0.533-0.4485-1.66040.0676-0.0895-0.38320.34250.4246-0.00110.48890.0594-0.05030.2664-0.01930.346524.056422.204135.4324
11-0.1357-0.1252-0.45920.2486-0.42850.12630.1608-0.29590.23110.1454-0.39810.00060.3331-0.0519-0.00230.23260.0045-0.04560.18080.06490.238332.566630.86649.149
120.02670.20290.1062-0.0048-0.0029-0.1941-0.35110.02790.12070.7617-0.16280.65460.4581-0.18070.00360.65630.05680.16110.618-0.1480.41225.276635.512462.1601
13-0.12120.00730.00160.0851-0.2495-0.0318-0.0325-0.0428-1.4024-0.3518-0.54330.45260.9019-0.3301-0.00490.7846-0.4095-0.11810.85890.70521.23426.913711.099760.39
14-0.0094-0.0148-0.0147-0.07230.1347-0.01580.57080.6227-0.696-1.11590.42170.37450.1477-1.01290.00420.4626-0.198-0.2350.57830.1650.66246.794121.513852.0347
150.02460.0372-0.01730.0485-0.02480.1916-0.43320.6627-0.9470.47450.02060.27960.35490.3836-0.00190.6714-0.1421-0.31960.68450.40661.411211.26210.28561.2599
160.0818-0.0270.07230.0793-0.0610.0203-0.2379-0.69050.21120.41220.411-0.33440.6492-0.56470.0020.5435-0.2039-0.10251.19290.53220.577713.81815.190870.4803
170.05690.00150.01780.0605-0.02140.0679-0.2861-0.4713-1.00190.0489-0.77840.27670.07140.1240.0010.2978-0.10360.03480.69660.37950.573516.43117.274663.6346
18-0.0294-0.0148-0.0596-0.07240.07790.03450.50450.1096-0.9039-0.3806-0.14720.33650.72450.5025-0.00050.34270.11410.07630.47170.20360.735819.315318.975156.5483
19-0.02170.01330.03980.0294-0.03390.08760.0969-0.5935-0.1132-0.29910.3227-0.0003-0.6210.01390.00040.18950.02660.06630.73070.29270.403715.133626.579762.1558
20-0.062-0.0651-0.08920.15750.11930.1301-1.0294-0.21750.09680.1195-0.33151.2196-0.0037-0.5551-0.0010.3320.10280.10181.04260.45360.68064.761224.42668.1383
210.01070.0593-0.07140.0350.00450.028-0.5341-0.6314-0.18421.02750.13710.4264-0.2745-0.3013-0.00210.5886-0.06580.06551.72630.81960.988910.53318.472873.2792
22-0.0050.07040.0726-0.02450.01810.00890.2655-0.3492-0.40310.19040.37840.93830.4098-0.89080.00631.04510.23210.3432.42871.60081.65293.89813.268469.1931
230.08890.12690.08321.23521.18462.41160.15670.6233-0.9711-0.647-0.25350.0426-1.0063-0.6918-0.00270.226-0.3292-0.12780.78380.42151.15043.058416.460160.7555
240.1075-0.2396-0.163-0.05330.00590.08180.2734-0.98510.09350.35990.03050.3539-0.3914-0.5009-0.00050.18380.0592-0.02380.56630.09360.305813.835632.242257.984
250.1032-0.3476-0.16460.3489-0.12060.58330.34150.444-0.10540.0165-0.42991.2062-0.1097-1.0338-0.0060.35310.0316-0.06640.289-0.00380.41740.487652.911825.3598
260.29780.23730.04070.2145-0.13460.0409-0.2565-0.06160.229-0.07120.2230.56420.2532-0.98480.00550.22520.0310.02470.39010.00240.1279-2.282245.790731.9137
270.03860.3820.5540.26970.2152-0.25320.04250.4532-0.30680.2808-0.15670.0822-0.05660.245-0.00020.21160.0475-0.03960.33890.02940.180318.006543.239821.0894
280.3355-1.5579-0.27482.02271.25880.9883-0.230.2642-0.45841.05420.4775-0.12361.129-0.0377-0.00510.25040.064-0.10610.54140.01460.400526.124937.177623.1365
291.16721.0152-0.29721.15160.56910.0851.57160.4362-1.20150.6468-0.9849-0.55130.72361.01350.01490.12070.6149-0.18050.5431-0.35070.440125.519823.476410.6843
300.3363-0.0197-0.16411.2743-5.1123.09280.20210.10660.85760.285-0.5184-0.937-0.67661.11760.00820.23780.251-0.1040.8548-0.09170.398829.186835.483111.4413
312.28960.18980.33861.2282-0.16621.21630.37890.3833-0.13690.0883-0.12680.07890.27010.1024-00.21150.0556-0.12380.1879-0.06840.17811.510134.44718.8468
321.24966.1087-1.7372.0396-4.83293.36940.3374-0.03090.68871.5273-0.13342.5117-0.6154-1.46450.5150.3145-0.0639-0.1610.2479-0.07770.19087.526441.211632.4897
33-0.06270.0387-0.02640.1273-0.01090.0540.3769-0.1994-0.37730.5444-0.59461.1211-0.493-0.662-0.00080.4057-0.0824-0.12530.39080.0740.45110.006632.413231.7674
340.1242-0.10270.06870.12660.10910.05520.2704-0.05160.07390.0876-0.26960.1028-0.21190.18690.0010.2119-0.0376-0.05930.2472-0.02180.2047-1.070842.444421.0887
350.06760.0677-0.0695-0.01230.05560.0380.03890.09420.8716-0.6985-0.791-0.3655-0.7223-0.34190.00050.299-0.0029-0.07080.26590.11670.39861.428449.862611.2575
36-0.0401-0.0149-0.02660.00080.09190.03790.06270.19020.4663-0.40950.1438-0.1120.2115-0.0709-0.00190.44330.0457-0.12440.8225-0.03070.73488.534942.594.7683
370.08970.00920.01610.0199-0.01810.0821-0.12320.0431-0.42371.08710.1850.34880.8859-0.7087-0.00440.72150.09-0.31260.482-0.44421.21372.162412.35767.2764
380.04190.0493-0.0056-0.02870.0391-0.09250.9168-0.5734-0.42940.4427-0.43120.41070.00460.1663-00.73150.031-0.23760.4516-0.27050.625811.411520.400215.5093
390.07440.05160.02740.082-0.00710.15470.33660.2173-1.3985-0.2186-0.68570.85010.0979-0.88130.00250.75550.2232-0.55550.7605-0.40091.1093-0.383415.04555.3228
40-0.0232-0.07430.0542-0.0891-0.0256-0.01430.25360.393-0.01120.13340.1660.5872-0.05470.07880.00230.520.3658-0.29910.8028-0.47950.53181.013922.1572-2.0387
41-0.15820.14540.03791.79491.04550.28750.67190.0361-0.57040.105-0.23061.29811.3979-0.0916-0.00060.49270.2286-0.39580.4558-0.29940.62540.696724.59315.3644
42-0.1059-0.0143-0.02990.0085-0.04330.06430.13510.6370.0055-1.02470.40780.85460.2715-0.12040.00380.32250.113-0.14550.4491-0.20320.51620.566426.766911.0938
430.0760.084-0.09790.1158-0.08560.19980.61191.361-0.7429-0.3331-0.33040.5485-0.24020.43910.00090.55770.421-0.30630.5843-0.30660.46769.654325.52974.2466
440.07580.08790.10150.0349-0.09630.131-0.18140.58230.2146-0.7784-0.0608-0.31170.3740.80820.00090.63830.4165-0.34711.0032-0.50260.608311.968421.1339-2.4633
450.0146-0.18140.0574-0.00620.0813-0.0096-0.19510.95550.0978-0.9394-0.351-0.8733-0.33820.504-0.00120.9830.3268-0.45641.1584-0.62440.77656.540916.4691-5.8841
46-0.0074-0.07980.08140.06770.0496-0.0481-0.3278-0.4128-1.05160.85790.23630.39840.6488-0.76290.00061.2410.5918-0.87671.1687-0.77871.59844.76038.21541.6609
470.67270.4137-1.3602-0.0006-1.40570.92250.5911-0.0586-0.67610.7081-0.23030.1490.19970.74450.01230.56820.3296-0.3630.4431-0.28220.699910.39317.65797.3728
480.0306-1.1362-0.80197.9245.07643.24260.47160.7025-0.3915-0.75960.3029-0.3896-0.36050.37420.21190.27180.2375-0.19750.6502-0.1360.091914.626234.33239.0266
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 92:97A92 - 97
2X-RAY DIFFRACTION2chain A and resseq 98:129A98 - 129
3X-RAY DIFFRACTION3chain A and resseq 130:140A130 - 140
4X-RAY DIFFRACTION4chain A and resseq 141:148A141 - 148
5X-RAY DIFFRACTION5chain A and resseq 149:167A149 - 167
6X-RAY DIFFRACTION6chain A and resseq 168:172A168 - 172
7X-RAY DIFFRACTION7chain A and resseq 173:183A173 - 183
8X-RAY DIFFRACTION8chain A and resseq 184:226A184 - 226
9X-RAY DIFFRACTION9chain A and resseq 227:236A227 - 236
10X-RAY DIFFRACTION10chain A and resseq 237:244A237 - 244
11X-RAY DIFFRACTION11chain A and resseq 245:261A245 - 261
12X-RAY DIFFRACTION12chain A and resseq 262:266A262 - 266
13X-RAY DIFFRACTION13chain B and resseq 1:5B1 - 5
14X-RAY DIFFRACTION14chain B and resseq 6:12B6 - 12
15X-RAY DIFFRACTION15chain B and resseq 13:18B13 - 18
16X-RAY DIFFRACTION16chain B and resseq 19:24B19 - 24
17X-RAY DIFFRACTION17chain B and resseq 25:30B25 - 30
18X-RAY DIFFRACTION18chain B and resseq 31:37B31 - 37
19X-RAY DIFFRACTION19chain B and resseq 38:43B38 - 43
20X-RAY DIFFRACTION20chain B and resseq 44:51B44 - 51
21X-RAY DIFFRACTION21chain B and resseq 52:57B52 - 57
22X-RAY DIFFRACTION22chain B and resseq 58:63B58 - 63
23X-RAY DIFFRACTION23chain B and resseq 64:68B64 - 68
24X-RAY DIFFRACTION24chain B and resseq 69:76B69 - 76
25X-RAY DIFFRACTION25chain C and resseq 92:99C92 - 99
26X-RAY DIFFRACTION26chain C and resseq 100:109C100 - 109
27X-RAY DIFFRACTION27chain C and resseq 110:130C110 - 130
28X-RAY DIFFRACTION28chain C and resseq 131:141C131 - 141
29X-RAY DIFFRACTION29chain C and resseq 142:166C142 - 166
30X-RAY DIFFRACTION30chain C and resseq 167:172C167 - 172
31X-RAY DIFFRACTION31chain C and resseq 173:227C173 - 227
32X-RAY DIFFRACTION32chain C and resseq 228:236C228 - 236
33X-RAY DIFFRACTION33chain C and resseq 237:243C237 - 243
34X-RAY DIFFRACTION34chain C and resseq 244:256C244 - 256
35X-RAY DIFFRACTION35chain C and resseq 257:261C257 - 261
36X-RAY DIFFRACTION36chain C and resseq 262:266C262 - 266
37X-RAY DIFFRACTION37chain D and resseq 1:5D1 - 5
38X-RAY DIFFRACTION38chain D and resseq 6:11D6 - 11
39X-RAY DIFFRACTION39chain D and resseq 12:20D12 - 20
40X-RAY DIFFRACTION40chain D and resseq 21:25D21 - 25
41X-RAY DIFFRACTION41chain D and resseq 26:31D26 - 31
42X-RAY DIFFRACTION42chain D and resseq 32:37D32 - 37
43X-RAY DIFFRACTION43chain D and resseq 38:45D38 - 45
44X-RAY DIFFRACTION44chain D and resseq 46:53D46 - 53
45X-RAY DIFFRACTION45chain D and resseq 54:59D54 - 59
46X-RAY DIFFRACTION46chain D and resseq 60:64D60 - 64
47X-RAY DIFFRACTION47chain D and resseq 65:70D65 - 70
48X-RAY DIFFRACTION48chain D and resseq 71:76D71 - 76

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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