[日本語] English
万見
- PDB-6lbi: Crystal Structure of FOXO1-DBD homodimer bound to a palindromic D... -

+
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: 6lbi
タイトルCrystal Structure of FOXO1-DBD homodimer bound to a palindromic DNA sequence
要素
  • Forkhead box protein O1
  • IRE0
キーワードDNA BINDING PROTEIN / Transcription factor / FOXO1 / protein-DNA complex / DNA binding
機能・相同性
機能・相同性情報


cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / Regulation of FOXO transcriptional activity by acetylation ...cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / Regulation of FOXO transcriptional activity by acetylation / negative regulation of stress-activated MAPK cascade / negative regulation of cardiac muscle hypertrophy in response to stress / regulation of reactive oxygen species metabolic process / temperature homeostasis / protein acetylation / cellular response to cold / negative regulation of fat cell differentiation / blood vessel development / FOXO-mediated transcription of cell death genes / Constitutive Signaling by AKT1 E17K in Cancer / fat cell differentiation / intracellular glucose homeostasis / Regulation of gene expression in beta cells / energy homeostasis / Regulation of localization of FOXO transcription factors / canonical Wnt signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of autophagy / positive regulation of gluconeogenesis / cellular response to nitric oxide / protein phosphatase 2A binding / cellular response to starvation / MAPK6/MAPK4 signaling / promoter-specific chromatin binding / chromatin DNA binding / negative regulation of insulin secretion / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to insulin stimulus / positive regulation of protein catabolic process / insulin receptor signaling pathway / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / gene expression / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / apoptotic process / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
: / FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 ...: / FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Forkhead box protein O1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.067 Å
データ登録者Li, J. / Dai, S.Y. / Chen, Y.H.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China81570537 中国
引用ジャーナル: Nucleic Acids Res. / 年: 2021
タイトル: Mechanism of forkhead transcription factors binding to a novel palindromic DNA site.
著者: Li, J. / Dai, S. / Chen, X. / Liang, X. / Qu, L. / Jiang, L. / Guo, M. / Zhou, Z. / Wei, H. / Zhang, H. / Chen, Z. / Chen, L. / Chen, Y.
履歴
登録2019年11月14日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年2月10日Provider: repository / タイプ: Initial release
改定 1.12021年9月8日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023年11月22日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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: IRE0
B: IRE0
C: Forkhead box protein O1
D: Forkhead box protein O1
E: IRE0
F: IRE0
G: Forkhead box protein O1
H: Forkhead box protein O1
I: IRE0
J: IRE0
K: Forkhead box protein O1
L: Forkhead box protein O1


分子量 (理論値)分子数
合計 (水以外)116,12312
ポリマ－116,12312
非ポリマー00
水00
1
A: IRE0
B: IRE0
C: Forkhead box protein O1
D: Forkhead box protein O1


分子量 (理論値)分子数
合計 (水以外)38,7084
ポリマ－38,7084
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-43 kcal/mol
Surface area14130 Å2
手法PISA
2
E: IRE0
F: IRE0
G: Forkhead box protein O1
H: Forkhead box protein O1


分子量 (理論値)分子数
合計 (水以外)38,7084
ポリマ－38,7084
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-40 kcal/mol
Surface area14370 Å2
手法PISA
3
I: IRE0
J: IRE0
K: Forkhead box protein O1
L: Forkhead box protein O1


分子量 (理論値)分子数
合計 (水以外)38,7084
ポリマ－38,7084
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-39 kcal/mol
Surface area14180 Å2
手法PISA
単位格子
Length a, b, c (Å)67.732, 89.090, 194.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
要素

#1: DNA鎖
IRE0


分子量: 6132.991 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#2: タンパク質
Forkhead box protein O1 / Forkhead box protein O1A / Forkhead in rhabdomyosarcoma


分子量: 13220.834 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FOXO1, FKHR, FOXO1A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q12778

-
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: 2.52 Å3/Da / 溶媒含有率: 51.24 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 50 mM NaAc, pH 4.7, 12%-18% PEG4000 (w/v), 200 mM NaCl, 10 mM MgCl2 and 1 mM TCEP.

-
データ収集

回折平均測定温度: 100 K / Serial crystal experiment: Y
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: 0.97915 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年6月25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: 0.97915 Å / 相対比: 1
反射解像度: 3.06→46.793 Å / Num. obs: 17379 / % possible obs: 99 % / 冗長度: 10.1 % / Biso Wilson estimate: 26.62 Å2 / Rpim(I) all: 0.107 / Net I/σ(I): 8.8
反射 シェル解像度: 3.06→3.17 Å / Num. unique obs: 314 / Rpim(I) all: 1.208
Serial crystallography sample delivery手法: fixed target

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
HKL-20001.11.1_2575data processing
HKL-2000データ収集
PDB_EXTRACT1.11.1_2575データ抽出
HKL-20003.25データ削減
PHENIX位相決定
Cootモデル構築
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 3CO6

3co6


解像度: 3.067→46.793 Å / SU ML: 0.38 / 交差検証法: THROUGHOUT / σ(F): 1.97 / 位相誤差: 26.78 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2641 866 5.01 %
Rwork0.2267 16434 -
obs0.2286 17300 76.11 %
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: 103.73 Å2 / Biso mean: 43.6204 Å2 / Biso min: 8.31 Å2
精密化ステップサイクル: final / 解像度: 3.067→46.793 Å
タンパク質核酸リガンド溶媒全体
原子数3730 2442 0 0 6172
残基数----598
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0036564
X-RAY DIFFRACTIONf_angle_d0.4679409
X-RAY DIFFRACTIONf_chiral_restr0.031030
X-RAY DIFFRACTIONf_plane_restr0.002757
X-RAY DIFFRACTIONf_dihedral_angle_d19.9673363
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0675-3.25960.3265410.269378922
3.2596-3.51120.35651060.2426190654
3.5112-3.86440.29361600.2565281780
3.8644-4.42330.2361800.2207355299
4.4233-5.57140.25131830.21333637100
5.5714-46.7930.23861960.2132373399
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)
13.71831.64640.29792.8878-0.14341.1009-0.20730.53540.2645-0.61240.28090.3328-0.3056-0.38150.04630.4730.2491-0.08340.46130.0708-0.0041-0.387910.5085-31.1849
20.4071-0.1463-0.45820.09090.18040.51740.1394-0.09450.07520.1141-0.0343-0.0832-0.06930.0642-0.02920.3293-0.15060.15390.0978-0.10220.25913.032416.6474-14.9759
33.3971-2.1811.83443.5805-0.25434.0025-0.0428-0.2294-0.35640.330.05890.01890.32990.1659-0.07590.12260.0021-0.05680.18570.13120.1597-4.53638.863-0.0791
40.22220.19920.11540.28250.39620.9073-0.0448-0.3229-0.03880.21420.1086-0.0641-0.04050.0749-0.01930.6820.2125-0.17220.6560.10560.24834.244511.77717.0845
53.8554-0.8768-1.90841.4465-0.03912.22-0.2627-0.6244-0.38160.35560.27370.23630.594-0.12280.0890.5639-0.2281-0.00130.50620.14790.099-3.56813.573316.1562
60.85320.21320.29220.58211.26542.76740.0734-0.05440.1582-0.02490.1619-0.0858-0.2180.0357-0.05470.05430.0237-0.01570.141-0.07480.2026-0.464611.7446-7.5349
72.2349-0.6933-1.30850.47690.28992.13660.27110.23280.2297-0.4131-0.0299-0.1896-0.00580.274-0.10080.6961-0.09770.18940.76740.09490.16385.435816.2467-31.7308
81.93751.3468-2.82190.9361-1.96134.10990.6645-0.7860.97660.60550.408-0.4105-0.66590.9155-1.01860.79130.3908-0.05271.0929-0.41240.7071-8.787625.052315.3349
90.4591-0.158-0.5041.22950.23930.6929-0.042-0.04490.0056-0.0223-0.0269-0.044-0.0206-0.0153-0.01360.25910.3006-0.03330.3335-0.06960.1572-16.056220.95358.4172
106.2716-2.6749-4.82783.77443.23664.24240.12720.2758-0.13250.0178-0.21060.3826-0.1474-0.28560.03980.18290.03390.15560.08860.04370.2873-22.955820.5057-0.3249
113.16840.51992.83876.29310.754.4714-0.144-0.59980.38690.3273-0.26560.1889-0.4018-0.43150.36130.0762-0.0784-0.05820.326-0.04360.0565-12.495325.89381.0765
123.4283-2.3506-1.86694.10651.79441.1226-0.1019-0.58940.8554-0.58730.4159-0.4721-0.60290.5049-0.28930.7227-0.0832-0.32910.4413-0.19380.8961-3.538730.21093.9193
131.4813-0.702-0.00140.4699-0.03591.6762-0.0728-0.1009-0.08860.0584-0.0108-0.03620.0150.0029-0.03650.14550.18190.04740.1010.1030.0438-5.529316.96044.0497
144.0259-0.22712.34030.2863-0.24061.4028-0.0924-0.2657-0.0460.1940.12990.08390.06930.11480.00750.32510.15920.19440.27870.09250.2754-15.824410.36874.1192
153.66893.6568-0.48123.6795-0.07184.81350.70360.63170.2806-0.72130.17651.2213-0.6318-0.8989-0.85980.34990.12460.02930.76830.05710.6941-17.696114.5281-11.2465
167.6193-4.82782.75716.4897-0.54078.3989-0.2362-0.7537-0.60380.65980.50580.59660.1055-0.9738-0.19620.18760.05590.04930.4837-0.07730.256-20.229612.34492.3839
170.2734-0.1838-0.13280.12350.08930.06460.03640.0422-0.0245-0.0325-0.0093-0.04530.09080.03450.02120.9210.19340.36181.0121-0.30650.68241.0293-1.9916-30.8657
181.353-0.5123-0.81541.7863-0.2351.8191-0.12470.178-0.2964-0.0924-0.08230.4680.4263-0.15560.15880.33340.0624-0.0870.0986-0.11330.2598-7.9592-2.7228-24.8056
195.7847-0.88735.55844.3664-0.21925.86370.0941-0.6991-0.9565-0.09160.00481.6350.1096-0.8457-0.04040.21650.1463-0.04310.3963-0.0330.5577-14.5581-5.6455-15.5439
200.78141.12510.85832.09330.97761.3299-0.02920.1876-0.5293-0.12860.1104-0.39470.24480.0138-0.08260.1205-0.08390.01010.1642-0.09320.5253-2.8542-5.3613-17.024
210.044-0.3688-0.28273.38022.05252.1368-0.01930.2482-0.5692-0.158-0.1045-0.52550.55260.24320.01860.2730.0570.06370.2211-0.08030.59356.5015-4.5523-19.2611
220.0735-0.0969-0.09391.1022-0.04590.1448-0.0451-0.04410.1315-0.0404-0.07960.1459-0.0223-0.0073-0.00740.0612-0.184-0.10330.2392-0.03740.1762-1.65026.264-19.5061
230.9229-0.1019-0.29570.0170.06750.23810.01470.1210.0369-0.0467-0.00680.0449-0.0136-0.0640.0225-0.00680.0004-0.27470.07070.04120.3829-13.38756.3659-20.4696
241.8633-0.81851.13291.9996-0.36070.6904-0.3159-1.1305-1.10021.00990.54110.25380.42270.0914-0.27210.33730.1652-0.09930.46060.15130.6149-13.69161.1761-5.3915
255.38036.0120.49717.65732.13564.1449-0.06940.1650.2032-0.34160.10330.81480.1628-0.2664-0.03580.1427-0.0087-0.02550.1156-0.08190.5976-16.36832.4751-19.4801
261.44580.3362.78370.31580.46995.4885-0.1189-0.11170.0231-0.21320.13480.05130.1008-0.66840.01660.99560.14270.01460.84550.06330.2235-29.5595-13.4465-63.342
270.890.34940.4451.6182-0.40920.81660.0548-0.22990.18620.24810.13060.13470.1331-0.2049-0.03770.6190.08030.30250.7396-0.07340.2976-34.1226-6.9941-47.711
281.8589-1.98713.52974.8741-2.45558.2537-0.4831-0.0831-0.04450.2639-0.0899-0.37760.20660.21260.43430.25770.06360.06070.67690.0010.155-31.6393-16.7356-32.3514
290.1742-0.728-0.24723.0671.27566.5127-0.0974-0.36180.15760.68460.4536-0.1887-0.13650.7689-0.20950.7042-0.1337-0.01090.98180.00750.1961-30.1747-6.7117-15.5029
302.67360.10441.20413.7408-1.84285.42060.363-0.2717-0.25840.7901-0.1039-0.37721.34280.7818-0.24470.6140.0017-0.1650.586-0.15080.2547-35.3899-12.9788-16.5572
310.9736-0.0549-0.58810.01350.03620.34960.26280.41020.119-0.4438-0.1422-0.0599-0.52650.0644-0.03130.7412-0.15490.1350.60660.03450.1687-31.7353-9.9461-48.1519
321.1088-1.3165-1.21382.58780.62662.43030.13610.24460.0581-0.43460.0778-0.4875-0.3799-0.0614-0.18020.9283-0.08060.21850.6799-0.33580.6001-47.871-11.0028-17.0909
331.7540.2975-1.81432.48830.28762.65310.01360.02210.06320.2025-0.13290.3250.1478-0.4640.14280.2036-0.0370.12970.5427-0.12530.2219-48.2785-20.6997-24.0042
345.57572.799-2.71024.349-2.08961.5137-0.0268-0.0871-0.41750.01440.07640.21750.2288-0.244-0.02180.2061-0.17230.10370.1732-0.01350.238-50.5648-27.0179-32.9094
351.3621-0.1218-0.38590.19630.01320.27170.0129-0.03630.020.00920.05010.19330.0083-0.1199-0.0137-0.0713-0.15580.10630.3972-0.050.3239-50.2215-15.3051-31.9502
361.44050.3771-1.26130.2358-0.32042.83590.0480.02920.7446-0.3152-0.10980.3519-1.49290.28770.0431.0369-0.13650.05320.4967-0.12040.6627-49.6285-4.5695-29.4431
373.44481.21790.81042.65660.30023.1402-0.05090.0676-0.34-0.0064-0.0844-0.3996-0.12370.26760.1160.106-0.07360.01370.24440.03740.0904-39.2272-13.4968-28.602
382.3803-0.190.64224.79580.49063.6507-0.08010.454-0.8731-0.46080.1164-0.26960.63520.1945-0.07660.47490.00540.09360.2306-0.14520.5806-40.3885-25.9656-35.351
390.48050.95020.60691.95570.90141.91260.0940.0361-0.15030.15090.0193-0.24170.2636-0.0049-0.12920.2846-0.14340.13920.342-0.32080.5473-43.144-27.4713-31.2697
403.3998-1.2783-1.57941.29951.40242.6068-0.1742-0.1936-0.29980.13120.04650.00450.3750.1830.19540.57610.3410.31020.54270.05830.5309-20.4036-23.163-57.8161
411.1799-0.5926-0.28680.81010.54750.3882-0.0718-0.0023-0.2922-0.16360.0431-0.20480.63520.13590.03770.63290.1149-0.0380.20730.10950.7171-19.4929-26.3563-47.8742
424.4327-0.99252.29084.5377-0.9821.235-0.0676-0.25110.3649-0.24970.0957-1.11550.12740.727-0.04960.3871-0.04680.18630.75490.06090.8403-13.5147-13.9467-51.1548
433.09350.14120.07468.1063-2.38668.6119-0.164-0.0179-0.4464-0.3663-0.08750.34160.0412-0.17540.25590.35190.09680.07670.489-0.01370.2775-29.5921-21.7156-50.2191
441.2156-1.30240.31961.730.59348.41570.2561-0.4356-0.5868-0.1311-0.19330.03871.8315-0.4487-0.04640.7003-0.03640.00070.50310.25450.8206-28.9716-29.1086-45.861
452.19240.05820.73760.67790.36221.3773-0.0548-0.7069-0.33990.56970.0572-0.0290.3767-0.0450.01690.78490.0244-0.07310.76680.16270.1412-1.4233-30.9809-0.8674
462.3621.08350.75461.57820.09380.30.15120.49010.0795-0.02380.18030.0629-0.0777-0.1411-0.14170.4703-0.05760.15560.6990.03930.07625.9586-29.9972-17.0016
470.4508-1.0181-0.90032.40951.56283.91820.13390.6309-0.118-0.52430.0340.1587-0.5645-0.633-0.10070.5499-0.2475-0.13670.9011-0.04370.2447-0.5687-29.1209-40.8864
480.759-0.44030.18791.4696-0.99471.42440.20610.3025-0.1339-0.35860.01020.08730.1626-0.20110.12570.4722-0.14960.00780.7271-0.2346-0.11481.001-29.3729-40.2873
492.6429-2.94673.15824.0876-2.31225.59210.0024-0.3989-0.34150.2925-0.4167-0.23950.16070.3520.2820.5266-0.06580.01880.40670.20170.3505-0.8682-35.3199-17.0374
502.467-0.3721-2.79470.64141.84846.64460.396-0.60230.03910.09110.0114-0.0111-0.01150.1598-0.26870.9330.08490.08330.77850.10410.13816.4453-28.8033-0.1253
510.6186-0.0875-0.08440.61760.12960.2620.08170.07560.08-0.02740.042-0.2882-0.0931-0.0456-0.1261.19430.10580.17490.8322-0.4640.80128.9178-43.2155-47.9487
527.69963.90482.2443.57540.30963.57910.7879-0.3278-0.8642-0.2089-0.8780.13430.598-0.4550.06021.011-0.01130.01720.4382-0.27830.9481-0.6005-50.8755-37.4895
533.0177-2.7027-0.33864.92712.32691.921-0.12340.131-1.0435-0.23720.0053-0.50230.6732-0.17110.13640.9293-0.2146-0.0940.3247-0.03810.87336.7101-47.9034-33.226
541.75481.5661-0.5241.6583-0.81520.61930.87970.5221-0.23980.1651-0.6149-0.7134-0.0812-0.01-0.2580.84680.23980.28090.64360.01680.834213.658-41.4504-34.8126
551.42780.6251.93514.07931.09024.0542-0.15670.05630.09110.1304-0.11140.002-0.2037-0.08370.14630.1967-0.1232-0.01190.3211-0.20540.32062.0601-37.2519-36.5788
560.31730.5196-0.83920.8469-1.36792.20760.073-0.0269-0.03950.07-0.0123-0.02560.2964-0.1683-0.0350.5645-0.2651-0.13660.4472-0.15850.9925-7.3736-44.1045-31.9329
571.40251.41971.12141.57881.5742.25370.0729-0.0593-0.1743-0.06640.1318-0.22320.2945-0.0326-0.18650.8839-0.3368-0.22520.6662-0.32821.0214-7.6653-47.8743-34.5128
582.6941-0.3619-2.29412.61560.86443.4587-0.0352-0.35510.04320.40540.07750.4285-0.0287-0.2042-0.05860.47780.08210.35450.93120.07330.6103-13.94-26.3674-4.1911
594.6452-3.9759-1.84863.40261.59454.21880.08110.4948-0.16030.03820.10270.65180.0553-0.5787-0.13060.2220.00630.09820.90040.30070.5746-17.8872-27.1524-15.8027
604.72912.2767-1.54824.3471-5.43047.2576-0.3057-1.26320.09891.09970.05260.588-0.0162-0.3880.22180.41550.05520.16950.4636-0.14710.3014-10.2921-15.7777-10.8483
610.68170.450.03420.5479-0.14131.56740.0951-0.3308-0.15280.4034-0.0698-0.016-0.2716-0.03970.01910.28350.05230.00790.60060.18740.117-5.3386-28.7792-12.7517
621.91680.84691.25031.54990.04692.5078-0.2340.3376-0.2460.09130.13420.47290.318-0.51880.05670.5155-0.28170.22690.80190.13880.7845-13.8637-38.5342-16.4887
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )A1 - 5
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 10 )A6 - 10
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 15 )A11 - 15
4X-RAY DIFFRACTION4chain 'A' and (resid 16 through 20 )A16 - 20
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 5 )B1 - 5
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 15 )B6 - 15
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 20 )B16 - 20
8X-RAY DIFFRACTION8chain 'C' and (resid 159 through 164 )C159 - 164
9X-RAY DIFFRACTION9chain 'C' and (resid 165 through 175 )C165 - 175
10X-RAY DIFFRACTION10chain 'C' and (resid 176 through 182 )C176 - 182
11X-RAY DIFFRACTION11chain 'C' and (resid 183 through 193 )C183 - 193
12X-RAY DIFFRACTION12chain 'C' and (resid 194 through 206 )C194 - 206
13X-RAY DIFFRACTION13chain 'C' and (resid 207 through 219 )C207 - 219
14X-RAY DIFFRACTION14chain 'C' and (resid 220 through 226 )C220 - 226
15X-RAY DIFFRACTION15chain 'C' and (resid 227 through 235 )C227 - 235
16X-RAY DIFFRACTION16chain 'C' and (resid 236 through 242 )C236 - 242
17X-RAY DIFFRACTION17chain 'D' and (resid 160 through 164 )D160 - 164
18X-RAY DIFFRACTION18chain 'D' and (resid 165 through 175 )D165 - 175
19X-RAY DIFFRACTION19chain 'D' and (resid 176 through 182 )D176 - 182
20X-RAY DIFFRACTION20chain 'D' and (resid 183 through 193 )D183 - 193
21X-RAY DIFFRACTION21chain 'D' and (resid 194 through 207 )D194 - 207
22X-RAY DIFFRACTION22chain 'D' and (resid 208 through 219 )D208 - 219
23X-RAY DIFFRACTION23chain 'D' and (resid 220 through 226 )D220 - 226
24X-RAY DIFFRACTION24chain 'D' and (resid 227 through 235 )D227 - 235
25X-RAY DIFFRACTION25chain 'D' and (resid 236 through 243 )D236 - 243
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 5 )E1 - 5
27X-RAY DIFFRACTION27chain 'E' and (resid 6 through 10 )E6 - 10
28X-RAY DIFFRACTION28chain 'E' and (resid 11 through 15 )E11 - 15
29X-RAY DIFFRACTION29chain 'E' and (resid 16 through 20 )E16 - 20
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 5 )F1 - 5
31X-RAY DIFFRACTION31chain 'F' and (resid 6 through 20 )F6 - 20
32X-RAY DIFFRACTION32chain 'G' and (resid 158 through 164 )G158 - 164
33X-RAY DIFFRACTION33chain 'G' and (resid 165 through 175 )G165 - 175
34X-RAY DIFFRACTION34chain 'G' and (resid 176 through 182 )G176 - 182
35X-RAY DIFFRACTION35chain 'G' and (resid 183 through 193 )G183 - 193
36X-RAY DIFFRACTION36chain 'G' and (resid 194 through 206 )G194 - 206
37X-RAY DIFFRACTION37chain 'G' and (resid 207 through 219 )G207 - 219
38X-RAY DIFFRACTION38chain 'G' and (resid 220 through 235 )G220 - 235
39X-RAY DIFFRACTION39chain 'G' and (resid 236 through 240 )G236 - 240
40X-RAY DIFFRACTION40chain 'H' and (resid 158 through 175 )H158 - 175
41X-RAY DIFFRACTION41chain 'H' and (resid 176 through 193 )H176 - 193
42X-RAY DIFFRACTION42chain 'H' and (resid 194 through 208 )H194 - 208
43X-RAY DIFFRACTION43chain 'H' and (resid 209 through 229 )H209 - 229
44X-RAY DIFFRACTION44chain 'H' and (resid 233 through 240 )H233 - 240
45X-RAY DIFFRACTION45chain 'I' and (resid 1 through 5 )I1 - 5
46X-RAY DIFFRACTION46chain 'I' and (resid 6 through 10 )I6 - 10
47X-RAY DIFFRACTION47chain 'I' and (resid 11 through 20 )I11 - 20
48X-RAY DIFFRACTION48chain 'J' and (resid 1 through 10 )J1 - 10
49X-RAY DIFFRACTION49chain 'J' and (resid 11 through 15 )J11 - 15
50X-RAY DIFFRACTION50chain 'J' and (resid 16 through 20 )J16 - 20
51X-RAY DIFFRACTION51chain 'K' and (resid 158 through 164 )K158 - 164
52X-RAY DIFFRACTION52chain 'K' and (resid 165 through 182 )K165 - 182
53X-RAY DIFFRACTION53chain 'K' and (resid 183 through 193 )K183 - 193
54X-RAY DIFFRACTION54chain 'K' and (resid 194 through 207 )K194 - 207
55X-RAY DIFFRACTION55chain 'K' and (resid 208 through 219 )K208 - 219
56X-RAY DIFFRACTION56chain 'K' and (resid 220 through 235 )K220 - 235
57X-RAY DIFFRACTION57chain 'K' and (resid 236 through 241 )K236 - 241
58X-RAY DIFFRACTION58chain 'L' and (resid 156 through 175 )L156 - 175
59X-RAY DIFFRACTION59chain 'L' and (resid 176 through 193 )L176 - 193
60X-RAY DIFFRACTION60chain 'L' and (resid 194 through 206 )L194 - 206
61X-RAY DIFFRACTION61chain 'L' and (resid 207 through 219 )L207 - 219
62X-RAY DIFFRACTION62chain 'L' and (resid 220 through 240 )L220 - 240

+
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