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- PDB-5tvp: SUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylat... -

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基本情報

登録情報
データベース: PDB / ID: 5tvp
タイトルSUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex
要素
  • DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
  • Small ubiquitin-related modifier 2
  • Tyrosyl-DNA phosphodiesterase 2
キーワードhydrolase/dna / hydrolase / dna repair / endonuclease/exonuclease/phosphatase (EEP) domain / hydrolase-dna complex
機能・相同性
機能・相同性情報


SUMO is proteolytically processed / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA damage response and repair proteins / tyrosyl-RNA phosphodiesterase activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins ...SUMO is proteolytically processed / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA damage response and repair proteins / tyrosyl-RNA phosphodiesterase activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / 5'-tyrosyl-DNA phosphodiesterase activity / SUMOylation of intracellular receptors / Nonhomologous End-Joining (NHEJ) / Formation of Incision Complex in GG-NER / Processing of DNA double-strand break ends / positive regulation of protein sumoylation / 加水分解酵素; エステル加水分解酵素; リン酸ジエステル加水分解酵素 / phosphoric diester hydrolase activity / SUMO transferase activity / aggresome / ubiquitin-like protein ligase binding / protein sumoylation / neuron development / nuclear retinoid X receptor binding / protein localization / PML body / protein tag activity / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / manganese ion binding / single-stranded DNA binding / endonuclease activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
類似検索 - 分子機能
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Ubiquitin homologues / Ubiquitin domain profile. ...Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHATE ION / DNA / Small ubiquitin-related modifier 2 / Tyrosyl-DNA phosphodiesterase 2
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.399 Å
データ登録者Schellenberg, M.J. / Williams, R.S.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 米国
引用ジャーナル: Science / 年: 2017
タイトル: ZATT (ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links.
著者: Schellenberg, M.J. / Lieberman, J.A. / Herrero-Ruiz, A. / Butler, L.R. / Williams, J.G. / Munoz-Cabello, A.M. / Mueller, G.A. / London, R.E. / Cortes-Ledesma, F. / Williams, R.S.
履歴
登録2016年11月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年10月11日Provider: repository / タイプ: Initial release
改定 1.12019年12月18日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
I: Tyrosyl-DNA phosphodiesterase 2
J: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
O: Tyrosyl-DNA phosphodiesterase 2
P: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
Q: Small ubiquitin-related modifier 2
E: Tyrosyl-DNA phosphodiesterase 2
F: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
G: Tyrosyl-DNA phosphodiesterase 2
H: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
A: Tyrosyl-DNA phosphodiesterase 2
D: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
K: Tyrosyl-DNA phosphodiesterase 2
L: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
M: Tyrosyl-DNA phosphodiesterase 2
N: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)264,10242
ポリマ－262,33417
非ポリマー1,76825
水12,430690
1
I: Tyrosyl-DNA phosphodiesterase 2
J: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
E: Tyrosyl-DNA phosphodiesterase 2
F: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,68710
ポリマ－63,2424
非ポリマー4456
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
O: Tyrosyl-DNA phosphodiesterase 2
P: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
G: Tyrosyl-DNA phosphodiesterase 2
H: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,86613
ポリマ－63,2424
非ポリマー6249
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
3
Q: Small ubiquitin-related modifier 2
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
A: Tyrosyl-DNA phosphodiesterase 2
D: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,95710
ポリマ－72,6085
非ポリマー3505
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
4
K: Tyrosyl-DNA phosphodiesterase 2
L: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
M: Tyrosyl-DNA phosphodiesterase 2
N: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,5929
ポリマ－63,2424
非ポリマー3505
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)106.547, 113.772, 125.434
Angle α, β, γ (deg.)90.000, 91.520, 90.000
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 2種, 9分子 IOEGBAKMQ

#1: タンパク質
Tyrosyl-DNA phosphodiesterase 2 / Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ...Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / TRAF and TNF receptor-associated protein


分子量: 28905.230 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Tdp2, Ttrap / 細胞株 (発現宿主): Rosetta 2 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q9JJX7, 加水分解酵素; エステル加水分解酵素; リン酸ジエステル加水分解酵素
#3: タンパク質 Small ubiquitin-related modifier 2 / SUMO-2 / SMT3 homolog 2 / Ubiquitin-like protein SMT3B / Smt3B


分子量: 9365.512 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Sumo2, Smt3b, Smt3h2 / 細胞株 (発現宿主): Rosetta2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61957

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DNA鎖 , 1種, 8分子 JPFHCDLN

#2: DNA鎖
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')


分子量: 2715.799 Da / 分子数: 8 / 由来タイプ: 合成 / 詳細: synthetic DNA sequence / 由来: (合成) Homo sapiens (ヒト)

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非ポリマー , 4種, 715分子

#4: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 9 / 由来タイプ: 合成 / 式: PO4
#5: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 13 / 由来タイプ: 合成 / 式: C2H6O2
#6: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Cl
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 690 / 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: 2.9 Å3/Da / 溶媒含有率: 57.54 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4.2
詳細: 100 mM citrate-phosphate, 200mM NaCl, 12% (w/v) PEG3350

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2012年11月4日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.399→50 Å / Num. obs: 116619 / % possible obs: 99.7 % / 冗長度: 3.7 % / Biso Wilson estimate: 39.79 Å2 / Rmerge(I) obs: 0.147 / Net I/av σ(I): 5.896 / Net I/σ(I): 4.2
反射 シェル
解像度 (Å)冗長度 (%)Diffraction-ID% possible allRmerge(I) obs
2.4-2.493.4198.9
2.49-2.593.5199.3
2.59-2.73.7199.7
2.7-2.853.7199.6
2.85-3.023.8199.80.716
3.02-3.263.7199.80.391
3.26-3.583.711000.213
3.58-4.13.7199.90.122
4.1-5.173.7199.80.081
5.17-503.7199.70.07

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解析

ソフトウェア
名称バージョン分類
DENZOデータ削減
SCALEPACKデータスケーリング
PHENIX精密化
PDB_EXTRACT3.2データ抽出
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4GZ1

4gz1


解像度: 2.399→49.273 Å / SU ML: 0.38 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 27.58
Rfactor反射数%反射Selection details
Rfree0.2332 5881 5.07 %RANDOM
Rwork0.1908 ---
obs0.193 115887 98.91 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 159.92 Å2 / Biso mean: 55.168 Å2 / Biso min: 7.92 Å2
精密化ステップサイクル: final / 解像度: 2.399→49.273 Å
タンパク質核酸リガンド溶媒全体
原子数16473 1472 100 690 18735
Biso mean--53.52 41.73 -
残基数----2147
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00618561
X-RAY DIFFRACTIONf_angle_d0.73725398
X-RAY DIFFRACTIONf_chiral_restr0.0482812
X-RAY DIFFRACTIONf_plane_restr0.0053016
X-RAY DIFFRACTIONf_dihedral_angle_d13.6910830
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3986-2.42580.40151630.36943299346289
2.4258-2.45440.36371860.3433527371395
2.4544-2.48430.36851900.33153523371396
2.4843-2.51580.36222020.32553582378497
2.5158-2.54890.31141950.31223627382298
2.5489-2.58380.33621750.30913606378199
2.5838-2.62070.36011880.301637253913100
2.6207-2.65980.3542140.29993653386799
2.6598-2.70140.33462010.291636403841100
2.7014-2.74560.32161980.274736973895100
2.7456-2.7930.31521970.265236973894100
2.793-2.84380.33192070.258836693876100
2.8438-2.89850.29611950.248936633858100
2.8985-2.95760.32891880.241637263914100
2.9576-3.02190.26312040.23236813885100
3.0219-3.09220.26042010.216836873888100
3.0922-3.16950.29792140.222936503864100
3.1695-3.25520.25892010.197937323933100
3.2552-3.3510.23061780.186236843862100
3.351-3.45910.22341760.175837503926100
3.4591-3.58270.22211820.175137053887100
3.5827-3.72610.21932010.163336913892100
3.7261-3.89560.22631910.153337243915100
3.8956-4.10090.17552020.142337333935100
4.1009-4.35770.16012010.127336933894100
4.3577-4.69390.15742140.115736883902100
4.6939-5.16580.13861870.115537403927100
5.1658-5.91230.20692010.141337323933100
5.9123-7.44470.18742200.174637473967100
7.4447-49.28330.19532090.16533735394498
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)
10.0297-0.0291-0.05360.14470.21340.3089-0.0761-0.00510.1744-0.39660.1177-0.4653-0.1278-0.03180.00110.422-0.01250.06940.43780.01530.521862.3647-14.318717.1278
20.0775-0.0415-0.00480.06030.08020.1336-0.0970.3097-0.1679-0.02730.07440.02870.49020.2435-00.5277-0.03380.07680.5131-0.0070.546167.683-19.362811.3388
30.3073-0.0427-0.02150.01840.00450.2219-0.08540.32540.1849-0.26860.1350.0309-0.2076-0.041-00.4978-0.0120.06790.4370.05130.472563.5089-8.124110.1031
40.4766-0.2944-0.26140.38950.11610.15360.29660.21260.4351-0.4864-0.1158-0.0139-0.1971-0.32360.02730.54940.0138-0.06960.47740.07810.417152.037-5.45079.6963
50.89040.17970.12031.18720.05170.93270.1866-0.12210.32630.4295-0.02450.2479-0.2635-0.014500.49410.00040.1320.37460.00330.498957.5591-7.381327.8921
60.0879-0.0420.05210.06650.04970.13060.11240.11120.40040.05670.10870.12290.0339-0.099300.4368-0.02480.05160.41060.05740.495147.7334-15.032924.8566
70.06720.03770.00520.0772-0.13030.3048-0.33170.0431-0.13130.11570.2133-0.16380.0771-0.044800.3756-0.0330.03240.3188-0.02070.334663.8399-20.292319.7874
80.3365-0.0659-0.42290.02360.10230.50210.22940.4831-0.30040.72920.0371-0.4642-0.1944-0.14110.06710.6446-0.0312-0.22060.4662-0.05980.595581.2796-1.200233.7731
90.3453-0.14460.07410.22120.07590.1511-0.3402-0.0682-0.36760.04160.31260.01010.001-0.3472-0.0010.5485-0.0950.10990.49180.05670.46932.203764.49850.1126
100.13990.07930.01260.15680.0470.0795-0.3209-0.2369-0.2892-0.17360.07170.15070.2158-0.3357-0.00010.5769-0.12960.12060.54240.06780.624728.048358.566349.8613
110.8192-0.47460.37770.69030.26810.8198-0.3019-0.0897-0.2758-0.20850.13130.12970.7752-0.4465-0.31960.7287-0.3915-0.00290.5470.06140.670827.798452.322742.8106
120.7657-0.1484-0.98640.1593-0.09831.9047-0.55510.0062-0.53280.123-0.00620.07770.80090.359-0.02541.0712-0.22770.25910.42350.05240.709637.849746.579943.8999
131.17950.5378-0.7480.2715-0.34130.49-0.5321-0.0051-0.675-0.6458-0.1012-0.68330.7510.2707-0.87860.952-0.0430.3360.2811-0.01370.800844.277649.655641.489
141.2181-0.19780.56861.4815-0.69950.8955-0.37320.0592-0.2882-0.53710.1385-0.45630.38950.0558-0.24420.5658-0.08380.18350.3517-0.00220.501844.743862.484842.4231
151.66010.4396-0.79461.04590.74611.39370.04130.4831-0.69670.851-0.2914-0.05240.2090.2764-0.87090.73150.2326-0.26140.58410.14831.252451.804150.499966.7144
160.0628-0.0292-0.00220.01290.00640.0206-0.26050.28710.0587-0.21780.2762-0.38540.3021-0.2508-00.66020.09240.10930.75110.04270.558348.868417.519619.584
170.05580.01740.03880.00790.0070.0343-0.1190.0596-0.03690.0055-0.2906-0.04540.0119-0.04680.00021.11870.5010.17711.60350.05990.926943.237116.795640.1998
180.2545-0.0368-0.09870.3334-0.11450.1393-0.4695-0.56920.39860.25870.19830.01390.0173-0.0002-00.65350.1135-0.12380.8061-0.13050.797150.433423.624630.0059
190.0119-0.0060.00520.0046-0.00580.0052-0.0989-0.0174-0.0044-0.0766-0.08030.1467-0.23670.174200.4510.0891-0.15480.68320.09410.863958.130619.286222.1288
200.0168-0.0062-0.00320.01720.00910.00620.0025-0.058-0.0267-0.35750.18350.2310.1010.1919-0.00010.9801-0.00980.01980.74220.00850.828751.622612.488821.9115
210.00940.01860.00920.02490.01470.0235-0.4417-0.48640.0793-0.10480.0273-0.24310.0815-0.0384-00.91030.316-0.08180.9721-0.04270.52650.390517.029335.2939
220.25990.1371-0.20340.0925-0.09570.1451-0.0691-0.1980.033-0.0758-0.10390.08960.09050.14850.00010.42120.04480.00210.4557-0.01580.2493101.17518.165147.9703
230.2610.0369-0.12060.1407-0.01920.3421-0.06440.12160.0962-0.12090.260.0997-0.07730.3837-00.3963-0.02030.02090.4702-0.03550.3416106.441218.178743.3037
240.0633-0.0480.04020.0372-0.01170.14120.1351-0.1081-0.07230.1273-0.2357-0.16910.09080.110800.31620.05590.01950.4803-0.0080.446108.53968.873546.9071
250.64570.92330.54091.60241.2261.4023-0.0409-0.1129-0.2725-0.0570.4203-0.03260.08140.4760.38640.22940.1494-0.07430.55410.0210.4156111.519910.893357.0357
261.27230.4321-0.29850.8575-0.18810.7911-0.0493-0.158-0.20930.1595-0.00790.20950.3235-0.0138-0.00090.43230.06260.0080.3920.01570.325694.3359.080659.2702
270.2672-0.0170.02390.37490.13390.05820.081-0.1143-0.14460.12170.0852-0.02090.2186-0.13290.21020.1122-0.0048-0.14770.398-0.04690.154285.497519.029843.7106
280.312-0.0414-0.09860.083-0.0370.08310.0671-0.1095-0.19930.05620.0015-0.0529-0.15760.3163-00.35330.0522-0.04910.4492-0.0040.311697.610920.036763.905
290.4053-0.01650.09040.68630.14090.09530.1086-0.20950.0339-0.22240.14130.123-0.36320.06160.02080.277-0.03160.00710.4069-0.02310.2798.149223.671447.9891
300.03790.1451-0.17680.5063-0.63720.7856-0.17260.0007-0.145-0.2661-0.31580.11490.12820.0035-0.31280.3428-0.0353-0.07820.501-0.12940.591981.75012.417134.2886
310.12880.3371-0.13691.2531-0.43580.1726-0.10940.12860.08580.28020.170.1888-0.07810.26210.36940.22680.0819-0.04570.488-0.03710.274869.627630.103581.431
320.07430.06680.09590.10260.0680.14630.4116-0.6235-0.22580.10440.14210.19070.6552-0.28060.00970.62710.04390.07840.46490.03430.525963.975624.880186.5606
330.2617-0.03920.01110.06960.14650.37320.1701-0.25470.20570.05310.13860.1978-0.34730.058400.35540.04890.040.4235-0.07750.400769.71635.089589.2108
341.23020.5406-1.00921.4834-0.92911.03690.0346-0.35680.36610.23660.4725-0.1353-0.35460.4940.32740.36920.0137-0.08090.541-0.14850.335181.432936.149389.3252
350.84720.5386-1.07461.0901-0.66151.63610.28210.07810.450.0320.26740.2121-0.53550.09111.42320.3318-0.1003-0.02080.4094-0.23540.456576.06344.935580.7463
360.93950.4062-0.61280.7184-0.49940.70250.4992-0.027-0.0581-0.02480.268-0.00220.1340.20922.43110.15080.0082-0.16190.5866-0.16480.335379.557138.004179.3163
371.3841-0.3020.04151.86970.64720.29920.15830.27130.5729-0.87180.2339-0.4564-0.61470.41341.01530.4733-0.16220.14310.5407-0.08450.344879.581240.56869.1242
381.02830.30510.40281.9202-0.10190.869-0.04710.0616-0.2093-0.50060.07460.05490.0496-0.04810.44980.1377-0.0039-0.13340.45310.01240.2464.070729.000667.1542
390.41840.41870.361.28990.61250.3878-0.05950.0021-0.1369-0.35150.3216-0.5826-0.10970.33670.46080.2039-0.0165-0.07240.5656-0.2220.403783.659528.654272.8163
400.07230.0370.04450.20690.30030.3727-0.25110.1524-0.00130.11430.15110.0060.31060.127100.30570.03740.00860.4077-0.01930.381567.233224.956577.8244
410.4486-0.1381-0.10380.03710.00020.34760.0794-0.0313-0.0711-0.54830.13790.6193-0.0589-0.06540.60860.91290.0186-0.40540.51580.33420.884951.51147.468566.7762
420.5825-0.34010.23360.38990.00910.6549-0.1102-0.2920.041-0.07560.1512-0.03540.0497-0.054100.44070.00440.04330.4089-0.02560.381417.136530.968823.4887
430.16940.08280.12950.04550.09370.22510.1318-0.36020.3312-0.01460.0997-0.2114-0.1409-0.056800.3903-0.0436-0.03640.3985-0.10020.452728.670636.983126.5661
440.9687-0.4504-0.16661.1142-0.08680.76730.24360.12250.3327-0.369-0.1099-0.28-0.12060.07560.00310.3980.03220.070.33140.04090.387224.007133.35969.6266
450.48020.17630.08780.17220.11450.11710.06490.2838-0.01460.3993-0.22610.4067-0.43080.2207-0.0220.91520.1535-0.08890.46570.09260.5396-0.155344.54071.8241
460.2444-0.1429-0.61692.85740.00221.786-0.16810.23710.0880.5171-0.13380.18930.1691-0.1425-1.01570.177-0.056-0.07320.3808-0.01680.1973-17.415561.0016-16.8334
470.2260.06070.04530.02180.01290.0107-0.1796-0.1310.53750.2474-0.71410.10630.2945-0.4668-0.0240.5947-0.0440.0810.5052-0.06970.514-23.424665.6604-11.611
480.09050.0891-0.05480.12970.03680.16570.0274-0.1922-0.0305-0.0837-0.24540.20370.3009-0.4542-00.4496-0.06930.050.4881-0.06960.4405-24.303557.2166-15.5243
490.1286-0.19-0.19930.5220.68311.8228-0.06820.0638-0.22380.3851-0.31640.22490.6385-0.2247-0.37250.373-0.0985-0.00040.3412-0.04730.3675-19.225850.3856-23.3808
500.4655-0.018-0.1629-0.0003-0.00490.1656-0.12840.163-0.66710.13690.0609-0.41850.33980.2868-0.03740.65890.08680.00270.39760.02130.5747-3.109546.4352-22.5059
510.5524-0.3579-0.18280.59510.07970.3993-0.05430.1552-0.03550.1209-0.0098-0.09960.24510.0864-00.4267-0.0348-0.02050.392-0.01190.3749-4.978160.5218-23.015
520.6371-0.0731-0.0932.32090.16870.0261-0.11980.05340.14760.75410.08560.17820.07870.133-0.36510.1523-0.0037-0.1360.4220.07630.2099-14.922767.0124-15.1254
530.7503-0.2707-0.58140.11220.21470.456-0.29-0.0002-0.44840.4872-0.004-0.15480.13090.3216-0.33990.75060.1938-0.20540.50420.07510.565-0.493447.84021.9791
540.09810.1391-0.03591.329-0.5630.2774-0.0892-0.28450.090.47090.29720.3342-0.02210.1780.10240.40410.00630.03410.3756-0.05660.305997.036941.987550.3779
550.09160.0626-0.00880.09110.07840.1190.3144-0.39940.19530.1597-0.11340.1816-0.31140.0119-00.5445-0.01380.14110.5036-0.11190.460798.59648.216353.7913
560.3790.2242-0.14450.24680.0960.32640.3864-0.22470.5540.1511-0.11180.08-0.41540.29340.00910.6253-0.07110.06320.5198-0.09460.4578105.485154.215151.5099
570.52680.2753-0.25520.606-0.43270.89460.20360.04290.4587-0.13990.04510.016-0.3510.099400.5492-0.02270.11670.3783-0.0130.4409103.855153.897634.7056
580.17250.1693-0.05570.42760.08770.1113-0.33940.02870.021-0.32320.38260.02240.214-0.14150.00280.40340.0261-0.04520.41140.04310.399791.047238.682134.9243
590.17720.03280.22220.55210.26880.4236-0.0181-0.06880.17620.01180.20810.06140.12210.1578-00.35260.0088-0.00360.4346-0.04910.3015103.480140.038441.1075
600.66790.4172-0.47340.37850.11061.92520.4550.36190.2928-0.1047-0.11490.7642-0.50110.16990.49510.69430.062-0.22060.48650.22440.890275.536655.614135.4948
611.115-0.11580.46580.0530.11891.0606-0.40730.3787-0.36170.3858-0.1563-0.06730.15130.2313-0.10840.6332-0.12010.11240.3617-0.0620.410459.931374.033217.3609
620.2990.0661-0.21890.0328-0.07380.1893-0.2462-0.12950.0330.1689-0.0112-0.12030.3294-0.3333-00.665-0.06780.1490.5247-0.00140.51853.455474.513120.4339
630.09080.0532-0.02430.0397-0.04010.0921-0.09980.2392-0.1922-0.1959-0.16680.01680.8132-0.088-0.00230.8333-0.21710.20960.5388-0.07410.464451.812764.925216.7815
640.1319-0.1848-0.10640.27930.07520.312-0.29690.2018-0.42960.2373-0.03570.31310.5667-0.6191-0.02080.5651-0.27030.10760.6485-0.11080.503751.970466.49756.3241
650.94420.1434-0.41940.3715-0.59921.2475-0.40010.3663-0.6273-0.301-0.0526-0.34981.3083-0.1166-0.53980.8276-0.05740.29810.3953-0.10580.637767.376661.68399.6292
661.3748-1.41181.35971.4998-1.23062.1489-0.39990.4593-0.53260.0295-0.1643-0.2710.18370.3002-1.43650.6449-0.06730.35830.5747-0.13160.614474.529569.88712.4173
670.29560.08-0.03890.2526-0.19760.2279-0.27540.1425-0.2157-0.18670.1177-0.27090.28760.2163-0.00670.5821-0.0440.08330.45270.0250.488271.559675.664614.5393
680.43960.28050.14690.4556-0.0450.1158-0.19940.10580.11070.3120.12650.14080.2668-0.10840.00450.55280.0020.13710.41560.03520.436663.164479.310617.9823
69-0.0019-0.0025-0.00190.13370.11170.088-0.06430.1239-0.10610.4453-0.1955-0.17120.24440.17360.00010.82620.18810.07330.62460.18870.968276.051458.337436.32
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'I' and (resid 121 through 138 )I121 - 138
2X-RAY DIFFRACTION2chain 'I' and (resid 139 through 153 )I139 - 153
3X-RAY DIFFRACTION3chain 'I' and (resid 154 through 190 )I154 - 190
4X-RAY DIFFRACTION4chain 'I' and (resid 191 through 208 )I191 - 208
5X-RAY DIFFRACTION5chain 'I' and (resid 209 through 325 )I209 - 325
6X-RAY DIFFRACTION6chain 'I' and (resid 326 through 345 )I326 - 345
7X-RAY DIFFRACTION7chain 'I' and (resid 346 through 369 )I346 - 369
8X-RAY DIFFRACTION8chain 'J' and (resid 2 through 10 )J2 - 10
9X-RAY DIFFRACTION9chain 'O' and (resid 121 through 153 )O121 - 153
10X-RAY DIFFRACTION10chain 'O' and (resid 154 through 174 )O154 - 174
11X-RAY DIFFRACTION11chain 'O' and (resid 175 through 208 )O175 - 208
12X-RAY DIFFRACTION12chain 'O' and (resid 209 through 225 )O209 - 225
13X-RAY DIFFRACTION13chain 'O' and (resid 226 through 259 )O226 - 259
14X-RAY DIFFRACTION14chain 'O' and (resid 260 through 369 )O260 - 369
15X-RAY DIFFRACTION15chain 'P' and (resid 2 through 10 )P2 - 10
16X-RAY DIFFRACTION16chain 'Q' and (resid 13 through 23 )Q13 - 23
17X-RAY DIFFRACTION17chain 'Q' and (resid 24 through 28 )Q24 - 28
18X-RAY DIFFRACTION18chain 'Q' and (resid 29 through 71 )Q29 - 71
19X-RAY DIFFRACTION19chain 'Q' and (resid 72 through 76 )Q72 - 76
20X-RAY DIFFRACTION20chain 'Q' and (resid 77 through 81 )Q77 - 81
21X-RAY DIFFRACTION21chain 'Q' and (resid 82 through 88 )Q82 - 88
22X-RAY DIFFRACTION22chain 'E' and (resid 121 through 138 )E121 - 138
23X-RAY DIFFRACTION23chain 'E' and (resid 139 through 174 )E139 - 174
24X-RAY DIFFRACTION24chain 'E' and (resid 175 through 190 )E175 - 190
25X-RAY DIFFRACTION25chain 'E' and (resid 191 through 208 )E191 - 208
26X-RAY DIFFRACTION26chain 'E' and (resid 209 through 303 )E209 - 303
27X-RAY DIFFRACTION27chain 'E' and (resid 304 through 325 )E304 - 325
28X-RAY DIFFRACTION28chain 'E' and (resid 326 through 345 )E326 - 345
29X-RAY DIFFRACTION29chain 'E' and (resid 346 through 370 )E346 - 370
30X-RAY DIFFRACTION30chain 'F' and (resid 2 through 10 )F2 - 10
31X-RAY DIFFRACTION31chain 'G' and (resid 121 through 138 )G121 - 138
32X-RAY DIFFRACTION32chain 'G' and (resid 139 through 153 )G139 - 153
33X-RAY DIFFRACTION33chain 'G' and (resid 154 through 190 )G154 - 190
34X-RAY DIFFRACTION34chain 'G' and (resid 191 through 208 )G191 - 208
35X-RAY DIFFRACTION35chain 'G' and (resid 209 through 225 )G209 - 225
36X-RAY DIFFRACTION36chain 'G' and (resid 226 through 240 )G226 - 240
37X-RAY DIFFRACTION37chain 'G' and (resid 241 through 296 )G241 - 296
38X-RAY DIFFRACTION38chain 'G' and (resid 297 through 325 )G297 - 325
39X-RAY DIFFRACTION39chain 'G' and (resid 326 through 345 )G326 - 345
40X-RAY DIFFRACTION40chain 'G' and (resid 346 through 369 )G346 - 369
41X-RAY DIFFRACTION41chain 'H' and (resid 2 through 10 )H2 - 10
42X-RAY DIFFRACTION42chain 'B' and (resid 117 through 190 )B117 - 190
43X-RAY DIFFRACTION43chain 'B' and (resid 191 through 208 )B191 - 208
44X-RAY DIFFRACTION44chain 'B' and (resid 209 through 370 )B209 - 370
45X-RAY DIFFRACTION45chain 'C' and (resid 2 through 10 )C2 - 10
46X-RAY DIFFRACTION46chain 'A' and (resid 121 through 138 )A121 - 138
47X-RAY DIFFRACTION47chain 'A' and (resid 139 through 153 )A139 - 153
48X-RAY DIFFRACTION48chain 'A' and (resid 154 through 174 )A154 - 174
49X-RAY DIFFRACTION49chain 'A' and (resid 175 through 240 )A175 - 240
50X-RAY DIFFRACTION50chain 'A' and (resid 241 through 260 )A241 - 260
51X-RAY DIFFRACTION51chain 'A' and (resid 261 through 345 )A261 - 345
52X-RAY DIFFRACTION52chain 'A' and (resid 346 through 369 )A346 - 369
53X-RAY DIFFRACTION53chain 'D' and (resid 2 through 10 )D2 - 10
54X-RAY DIFFRACTION54chain 'K' and (resid 121 through 153 )K121 - 153
55X-RAY DIFFRACTION55chain 'K' and (resid 154 through 174 )K154 - 174
56X-RAY DIFFRACTION56chain 'K' and (resid 175 through 208 )K175 - 208
57X-RAY DIFFRACTION57chain 'K' and (resid 209 through 296 )K209 - 296
58X-RAY DIFFRACTION58chain 'K' and (resid 297 through 325 )K297 - 325
59X-RAY DIFFRACTION59chain 'K' and (resid 326 through 369 )K326 - 369
60X-RAY DIFFRACTION60chain 'L' and (resid 2 through 10 )L2 - 10
61X-RAY DIFFRACTION61chain 'M' and (resid 121 through 138 )M121 - 138
62X-RAY DIFFRACTION62chain 'M' and (resid 139 through 174 )M139 - 174
63X-RAY DIFFRACTION63chain 'M' and (resid 175 through 190 )M175 - 190
64X-RAY DIFFRACTION64chain 'M' and (resid 191 through 208 )M191 - 208
65X-RAY DIFFRACTION65chain 'M' and (resid 209 through 282 )M209 - 282
66X-RAY DIFFRACTION66chain 'M' and (resid 283 through 296 )M283 - 296
67X-RAY DIFFRACTION67chain 'M' and (resid 297 through 345 )M297 - 345
68X-RAY DIFFRACTION68chain 'M' and (resid 346 through 370 )M346 - 370
69X-RAY DIFFRACTION69chain 'N' and (resid 2 through 10 )N2 - 10

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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