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- PDB-5zrf: Crystal structure of human topoisomerase II beta in complex with ... -

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基本情報

登録情報
データベース: PDB / ID: 5zrf
タイトルCrystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21
要素
  • DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
  • DNA topoisomerase 2-beta
  • DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
キーワードISOMERASE/DNA / Type II topoisomerase / Anti-cancer drug / TopoII cleavage complex / Isomerase-DNA complex / ISOMERASE-DNA-ISOMERASE INHIBITOR complex
機能・相同性
機能・相同性情報


positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / forebrain development / B cell differentiation / axonogenesis / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
類似検索 - 分子機能
DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta ...DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
類似検索 - ドメイン・相同性
Chem-EVP / DNA / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA topoisomerase 2-beta
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å
データ登録者Chen, S.F. / Wang, Y.R. / Wu, C.C. / Chan, N.L.
引用ジャーナル: Nat Commun / 年: 2018
タイトル: Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.
著者: Chen, S.F. / Huang, N.L. / Lin, J.H. / Wu, C.C. / Wang, Y.R. / Yu, Y.J. / Gilson, M.K. / Chan, N.L.
履歴
登録2018年4月24日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年8月8日Provider: repository / タイプ: Initial release
改定 1.12019年2月20日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
改定 1.22023年11月22日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: DNA topoisomerase 2-beta
B: DNA topoisomerase 2-beta
C: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
D: DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
E: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
F: DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)198,12914
ポリマ－196,8066
非ポリマー1,3238
水9,440524
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17030 Å2
ΔGint-99 kcal/mol
Surface area60200 Å2
手法PISA
単位格子
Length a, b, c (Å)80.147, 176.270, 94.331
Angle α, β, γ (deg.)90.00, 111.44, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 / DNA鎖 / DNA/RNAハイブリッド , 3種, 6分子 ABCEDF

#1: タンパク質 DNA topoisomerase 2-beta / DNA topoisomerase II / beta isozyme


分子量: 91928.367 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TOP2B / プラスミド: pET51b / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q02880, EC: 5.99.1.3
#2: DNA鎖 DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')


分子量: 2436.619 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: DNA/RNAハイブリッド DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')


分子量: 4037.988 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 3種, 532分子

#4: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Mg
#5: 化合物 ChemComp-EVP / (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside / Etoposide / VP-16 / エトポシド


分子量: 588.557 Da / 分子数: 2 / 由来タイプ: 天然 / 式: C29H32O13 / コメント: 薬剤, 化学療法薬*YM
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 524 / 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: 3.14 Å3/Da / 溶媒含有率: 60.86 %
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: Magnesium Acetate, 2-(N-morpholino)ethanesulfonic, 2-methyl-2,4-pentanediol

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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: NSRRC / ビームライン: BL15A1 / 波長: 1 Å
検出器タイプ: RAYONIX MX300HE / 検出器: CCD / 日付: 2016年5月17日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.3→20 Å / Num. obs: 99792 / % possible obs: 92.2 % / 冗長度: 2.9 % / CC1/2: 0.93 / Net I/σ(I): 18.4
反射 シェル解像度: 2.3→2.38 Å / CC1/2: 0.738 / Rsym value: 0.473

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)精密化
HKL-2000データ収集
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3QX3

3qx3


解像度: 2.3→19.869 Å / SU ML: 0.22 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.34 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2265 1989 1.99 %
Rwork0.1886 --
obs0.1894 99750 92.02 %
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: 2.3→19.869 Å
タンパク質核酸リガンド溶媒全体
原子数10414 822 90 524 11850
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00611706
X-RAY DIFFRACTIONf_angle_d0.86316043
X-RAY DIFFRACTIONf_dihedral_angle_d14.016818
X-RAY DIFFRACTIONf_chiral_restr0.0511804
X-RAY DIFFRACTIONf_plane_restr0.0061916
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35170.2971310.23876322X-RAY DIFFRACTION83
2.3517-2.41520.26711230.22816447X-RAY DIFFRACTION85
2.4152-2.48610.28651490.22126464X-RAY DIFFRACTION86
2.4861-2.56620.251330.21186603X-RAY DIFFRACTION87
2.5662-2.65770.25441290.20536664X-RAY DIFFRACTION88
2.6577-2.76380.24921440.21126837X-RAY DIFFRACTION90
2.7638-2.88930.26611380.21737007X-RAY DIFFRACTION93
2.8893-3.04110.23311380.21527080X-RAY DIFFRACTION93
3.0411-3.23090.28451450.20457183X-RAY DIFFRACTION95
3.2309-3.47910.23121460.18797263X-RAY DIFFRACTION96
3.4791-3.8270.20021570.17127314X-RAY DIFFRACTION96
3.827-4.37560.18441470.1617427X-RAY DIFFRACTION98
4.3756-5.49340.21971560.16427564X-RAY DIFFRACTION99
5.4934-19.86960.20061530.18957586X-RAY DIFFRACTION99
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)
10.01110.0250.03520.01680.01150.03480.19560.15180.0913-0.64690.0115-0.041-0.25740.23430.04150.65850.19350.11170.8818-0.10240.433349.190386.343639.9346
20.02280.1074-0.20820.2154-0.17340.15850.13480.89470.1388-0.1069-0.1136-0.2031-0.0983-0.02620.00030.39790.12780.09290.7214-0.01550.481954.254489.196646.8487
30.11520.1530.0080.16070.0693-0.00160.12850.70030.0431-0.3708-0.17150.0839-0.07790.2951-0.02490.50970.15390.15390.78290.05910.460955.551189.893144.901
40.07730.0076-0.01690.0090.03190.05790.0839-0.0382-0.2722-0.0913-0.1316-0.46110.2011-0.1131-0.00010.43670.03630.05020.41580.01740.462937.501282.906658.1861
50.10150.1286-0.11590.0419-0.26380.1825-0.36630.2846-0.4307-0.4157-0.12230.17040.2789-0.0135-0.01020.53870.13150.08520.4856-0.13340.637543.789775.283351.2914
60.1899-0.08410.11660.0131-0.07930.19250.0915-0.01960.0943-0.27690.1903-0.17340.00340.26690.00060.32390.13560.06630.5401-0.03890.366253.247484.872352.9036
70.34680.0695-0.10940.029-0.11720.29060.0287-0.1118-0.1047-0.25780.04880.0959-0.010.29330.00020.31770.103-0.04680.456-0.00720.44244.81684.90261.6361
80.0150.05230.02490.08660.03570.0150.1186-0.3621-0.4161-0.4812-0.14170.23350.0445-0.05190.00240.50740.10280.01310.5998-0.0020.722353.692674.32159.8331
90.0170.0018-0.03270.02640.0148-0.00540.34170.29520.2460.0152-0.0241-0.17110.0331-0.055100.46090.19110.00840.5867-0.09480.633755.616589.281658.0865
100.0097-0.0185-0.00430.0109-0.00320.0040.2814-0.1321-0.04620.21-0.1146-0.3326-0.01370.18670.00010.6273-0.15950.12270.8489-0.09170.930259.4114101.596850.6498
110.2931-0.06040.23850.30660.33780.65220.52370.5322-0.23490.06670.4277-0.48140.09451.27310.4701-0.23630.49130.26120.7689-0.07810.576959.799488.543261.2956
120.01320.0026-0.06710.1767-0.10020.2226-0.0976-0.2081-0.3847-0.3662-0.20710.08360.38540.5253-0.14860.38510.25660.01940.58380.12430.520646.52479.504671.1218
130.978-0.21130.00810.0392-0.0660.2284-0.214-0.5064-0.61880.21050.4497-0.20620.26550.3533-0.07370.43330.1327-0.07470.62250.04640.335440.721989.700179.7869
140.1677-0.0756-0.19010.31020.33740.5352-0.0404-0.06440.02130.11280.1668-0.0221-0.08230.18790.00260.26630.018-0.00680.3819-0.01020.30434.6243104.229167.5638
150.30570.4236-0.01890.40060.65420.0685-0.08920.1529-0.0417-0.16540.1040.0775-0.0413-0.00200.30310.0585-0.03540.32250.02280.265619.4118105.580759.3237
160.288-0.3775-0.41130.24280.22850.72930.0621-0.10490.0189-0.04270.0001-0.088-0.00810.056100.32630.00950.03770.3199-0.00750.322425.7889108.557175.5856
170.34780.75960.65311.51971.00330.77040.0595-0.09050.03720.1921-0.19180.26730.2029-0.1083-00.29670.03090.03320.3469-0.04030.38012.652888.139666.5597
18-0.15570.1-0.03980.96080.61861.09340.0288-0.0378-0.0480.30110.071-0.0294-0.0848-0.01150.06010.31330.00290.0070.32710.01060.223124.9957118.372485.598
190.62960.03520.0470.3456-0.37930.33530.0792-0.1897-0.23160.8447-0.2459-0.1235-0.60730.332-0.01360.6635-0.0741-0.01520.4180.02630.397937.177147.957983.7456
20-0.14520.206-0.21530.5264-0.22430.5110.1613-0.00060.07560.2648-0.03790.2806-0.2725-0.0685-0.00260.54840.0350.09350.36390.06090.322522.886143.708181.9663
210.2938-0.1412-0.17910.5647-0.1010.14730.0151-0.01240.04640.0237-0.03750.0977-0.3781-0.1583-0.00020.34570.06990.02950.3439-0.0340.34387.9196115.325776.4301
22-0.00240.0110.00770.0347-0.03870.02340.00840.4782-0.3220.19130.3428-0.26430.21510.35880.00040.4620.0696-0.00370.41470.04240.704713.966486.893834.5088
230.1917-0.08820.04670.029-0.03060.12960.0167-0.2673-0.119-0.0630.10790.4229-0.02270.07960.00480.3388-0.0894-0.07390.33130.07070.68215.026492.210430.6391
240.04380.01040.00490.04660.05050.0980.1394-0.2793-0.31460.51140.10970.08120.1993-0.02930.00490.4898-0.15150.0440.57190.10230.68446.836898.075341.2349
250.0051-0.0262-0.00980.04390.0139-0.02640.1294-0.3503-0.26820.049-0.01510.579-0.1239-0.02830.00010.3655-0.02530.07340.40520.03550.64257.257394.723333.8762
260.0779-0.0025-0.00260.05670.0246-0.00220.08530.04440.0331-0.391-0.1186-0.08190.17380.0131-0.00030.3135-0.0346-0.01670.307-0.02440.36623.392101.631421.7983
270.1129-0.05710.01210.1008-0.14140.14490.0809-0.5239-0.342-0.3322-0.00820.07860.0570.388800.46310.0326-0.05730.3482-0.0170.460922.033792.221723.518
280.24080.0076-0.07060.03550.17760.68220.1553-0.14330.0941-0.60920.17620.55661.04940.08320.01360.6174-0.1703-0.20920.2938-0.04120.49269.318588.948314.0523
290.6511-0.1926-0.05150.28710.07970.94950.0793-0.00440.0673-0.34230.05080.5129-0.012-0.11010.14140.3177-0.0376-0.11410.2674-0.00690.464511.8789101.630624.472
300.0114-0.01490.0110.02160.02590.00660.1920.25470.0424-0.19760.093-0.22020.2422-0.2192-00.4977-0.0003-0.27140.4105-0.03910.54237.422697.478714.4833
310.0295-0.10480.0730.519-0.63930.77890.3037-0.5841-0.2003-0.07860.55810.82040.01720.1050.15920.2530.0346-0.00410.4605-0.02380.72135.3118105.640528.5826
320.0734-0.00520.08050.4532-0.26710.268-0.0576-0.8681-0.08050.13830.27030.84170.1833-0.12730.03270.3744-0.01350.26820.6751-0.07540.87260.4443106.476239.844
330.10970.04630.16470.34560.02220.667-0.16710.20440.0908-0.30780.05710.5786-0.1714-0.0665-0.06140.3046-0.0267-0.21750.2978-0.01160.5369.1953108.638915.3595
340.29120.0839-0.07330.0921-0.0790.0592-0.08820.38410.2256-0.4890.12370.3478-0.30710.09240.01050.43250.0462-0.07960.36110.09010.486318.8914124.557916.0119
350.22440.47880.09121.10270.25250.5110.0115-0.03260.04240.0411-0.01710.2455-0.17810.03790.00410.2493-0.01450.0090.3072-0.00650.330625.644121.01534.5984
360.52060.2999-0.4880.55240.1990.32770.0472-0.0614-0.11620.0448-0.02190.10050.02330.062200.3042-0.0633-0.02870.32160.01070.280540.6292119.039440.6918
370.1165-0.2253-0.10650.34690.17560.11420.09730.1326-0.14970.2678-0.13880.182-0.2108-0.09170.00120.3667-0.02830.0560.3441-0.01480.368527.5015133.298338.1473
380.0735-0.336-0.14110.4528-0.00150.58050.07360.0350.0828-0.2135-0.0027-0.1325-0.18960.080100.3053-0.04220.04090.3015-0.01420.27248.2974127.3922.9738
390.2316-0.28290.07670.2874-0.26650.71580.13110.0747-0.20890.1664-0.0472-0.27110.1078-0.0630.03640.235-0.0383-0.04460.3405-0.05850.538658.9534103.181624.4612
400.9076-0.23780.24770.42030.08850.56570.0957-0.5387-0.65250.13720.3722-0.2840.42510.13280.11630.5066-0.0958-0.03760.3871-0.1440.779762.476194.81323.9088
410.01060.01980.01780.0520.02340.0485-0.7911-0.1179-0.31180.65460.5097-0.2417-0.30220.36770.00060.47790.0858-0.07130.5136-0.00060.410260.4126106.887435.013
420.12130.11550.05690.2844-0.03080.0250.18270.4166-0.48260.0577-0.2978-0.2403-0.4046-0.194-0.0080.25540.03540.0710.4716-0.07980.525568.396799.229218.085
430.0023-0.01890.00950.0958-0.03250.0122-0.14430.32630.0895-0.4174-0.2531-0.0536-0.1421-0.1239-0.00320.449-0.0188-0.00680.5164-0.1060.466661.7455106.131514.0303
440.1210.0209-0.16390.0052-0.02620.16250.39750.2570.1212-0.5588-0.15520.036-0.17710.2814-0.00090.4485-0.0129-0.00810.4303-0.03270.348950.3428112.989516.5593
450.05030.02950.12640.04850.03960.13920.06880.38350.7252-0.0465-0.12330.028-0.2559-0.0725-00.4322-0.0017-0.07430.3870.02240.367932.5964130.384119.9688
46-0.0311-0.2011-0.03310.4317-0.00040.2978-0.00370.10090.0121-0.0364-0.06470.0369-0.2861-0.045-0.00260.3917-0.05160.02640.30060.0260.32636.0991150.365143.3043
470.04060.06670.12940.02480.09470.11370.1039-0.32690.42480.75860.13930.5397-0.908-0.6261-0.00020.9050.13190.11030.47280.05550.559121.2792162.95768.8056
480.06750.0678-0.05510.0369-0.03490.02480.56040.2409-0.05420.2349-0.3167-0.5157-0.40760.4358-0.00040.6001-0.02770.00490.38560.06280.482625.2413162.024658.6662
490.0078-0.0026-0.01120.0032-0.00020.0091-0.05740.3434-0.1551-0.3009-0.1877-0.1683-0.0022-0.157700.52650.0046-0.00330.4455-0.02050.442725.4255151.547747.4456
500.0444-0.0769-0.08670.0979-0.10170.11330.2170.3395-0.11220.3694-0.0628-0.0579-0.00240.1631-0.00010.5643-0.02350.08870.38210.04590.369829.0088154.043766.0136
51-0.09560.2701-0.1268-0.1270.2670.2050.02440.0012-0.22150.0679-0.0692-0.0522-0.62051.08-0.00060.5278-0.05580.00610.39830.06730.362542.9758156.599354.2196
520.37240.215-0.14090.23220.14780.2264-0.0306-0.2676-0.00440.25740.1666-0.0273-0.16650.117600.3588-0.0492-0.02070.3516-0.04140.36452.4074134.957739.0578
530.2354-0.1343-0.18080.0928-0.00220.1756-0.03380.1051-0.2912-0.19360.05440.05070.16260.0217-0.00010.39590.0162-0.03230.30430.01160.367126.31490.52861.8902
540.1686-0.268-0.1172-0.1233-0.1988-0.14960.2031-0.1020.0104-0.2484-0.11910.05280.19690.5518-0.00010.3930.0187-0.02020.43680.0070.296832.3993105.436827.3457
550.17920.02940.01420.2677-0.34050.2422-0.30180.0873-0.23040.21210.1231-0.07780.64930.28070.00010.40930.01620.01840.4405-0.02120.347634.5058108.751126.6758
560.42620.27820.0896-0.2544-0.2332-0.00260.0298-0.0003-0.068-0.29730.26570.1260.6635-0.0020.00120.48560.033-0.02890.40210.08880.422328.397789.159358.6743
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 452 through 461 )
2X-RAY DIFFRACTION2chain 'A' and (resid 462 through 489 )
3X-RAY DIFFRACTION3chain 'A' and (resid 490 through 502 )
4X-RAY DIFFRACTION4chain 'A' and (resid 503 through 513 )
5X-RAY DIFFRACTION5chain 'A' and (resid 514 through 542 )
6X-RAY DIFFRACTION6chain 'A' and (resid 543 through 559 )
7X-RAY DIFFRACTION7chain 'A' and (resid 560 through 576 )
8X-RAY DIFFRACTION8chain 'A' and (resid 577 through 583 )
9X-RAY DIFFRACTION9chain 'A' and (resid 584 through 591 )
10X-RAY DIFFRACTION10chain 'A' and (resid 638 through 645 )
11X-RAY DIFFRACTION11chain 'A' and (resid 646 through 658 )
12X-RAY DIFFRACTION12chain 'A' and (resid 659 through 670 )
13X-RAY DIFFRACTION13chain 'A' and (resid 671 through 694 )
14X-RAY DIFFRACTION14chain 'A' and (resid 707 through 771 )
15X-RAY DIFFRACTION15chain 'A' and (resid 772 through 828 )
16X-RAY DIFFRACTION16chain 'A' and (resid 829 through 884 )
17X-RAY DIFFRACTION17chain 'A' and (resid 885 through 1012 )
18X-RAY DIFFRACTION18chain 'A' and (resid 1013 through 1075 )
19X-RAY DIFFRACTION19chain 'A' and (resid 1076 through 1111 )
20X-RAY DIFFRACTION20chain 'A' and (resid 1135 through 1175 )
21X-RAY DIFFRACTION21chain 'A' and (resid 1176 through 1201 )
22X-RAY DIFFRACTION22chain 'B' and (resid 449 through 458 )
23X-RAY DIFFRACTION23chain 'B' and (resid 459 through 478 )
24X-RAY DIFFRACTION24chain 'B' and (resid 479 through 494 )
25X-RAY DIFFRACTION25chain 'B' and (resid 495 through 502 )
26X-RAY DIFFRACTION26chain 'B' and (resid 503 through 513 )
27X-RAY DIFFRACTION27chain 'B' and (resid 514 through 530 )
28X-RAY DIFFRACTION28chain 'B' and (resid 531 through 542 )
29X-RAY DIFFRACTION29chain 'B' and (resid 543 through 576 )
30X-RAY DIFFRACTION30chain 'B' and (resid 577 through 583 )
31X-RAY DIFFRACTION31chain 'B' and (resid 584 through 592 )
32X-RAY DIFFRACTION32chain 'B' and (resid 637 through 650 )
33X-RAY DIFFRACTION33chain 'B' and (resid 651 through 670 )
34X-RAY DIFFRACTION34chain 'B' and (resid 671 through 695 )
35X-RAY DIFFRACTION35chain 'B' and (resid 706 through 771 )
36X-RAY DIFFRACTION36chain 'B' and (resid 772 through 841 )
37X-RAY DIFFRACTION37chain 'B' and (resid 842 through 861 )
38X-RAY DIFFRACTION38chain 'B' and (resid 862 through 926 )
39X-RAY DIFFRACTION39chain 'B' and (resid 927 through 962 )
40X-RAY DIFFRACTION40chain 'B' and (resid 967 through 975 )
41X-RAY DIFFRACTION41chain 'B' and (resid 976 through 983 )
42X-RAY DIFFRACTION42chain 'B' and (resid 984 through 998 )
43X-RAY DIFFRACTION43chain 'B' and (resid 999 through 1004 )
44X-RAY DIFFRACTION44chain 'B' and (resid 1005 through 1015 )
45X-RAY DIFFRACTION45chain 'B' and (resid 1016 through 1030 )
46X-RAY DIFFRACTION46chain 'B' and (resid 1031 through 1076 )
47X-RAY DIFFRACTION47chain 'B' and (resid 1077 through 1095 )
48X-RAY DIFFRACTION48chain 'B' and (resid 1096 through 1101 )
49X-RAY DIFFRACTION49chain 'B' and (resid 1102 through 1110 )
50X-RAY DIFFRACTION50chain 'B' and (resid 1135 through 1150 )
51X-RAY DIFFRACTION51chain 'B' and (resid 1151 through 1175 )
52X-RAY DIFFRACTION52chain 'B' and (resid 1176 through 1201 )
53X-RAY DIFFRACTION53chain 'C' and (resid 1 through 8 )
54X-RAY DIFFRACTION54chain 'D' and (resid 10 through 19 )
55X-RAY DIFFRACTION55chain 'E' and (resid 1 through 8 )
56X-RAY DIFFRACTION56chain 'F' and (resid 10 through 19 )

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万見について

-
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://pdbjlvh1.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