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- PDB-7ezj: Crystal structure of p73 DNA binding domain complex bound with 1 ... -

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基本情報

登録情報
データベース: PDB / ID: 7ezj
タイトルCrystal structure of p73 DNA binding domain complex bound with 1 bp and 2 bp spacer DNA response elements.
要素
  • 12-mer DNA
  • Tumor protein p73
キーワードDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
機能・相同性
機能・相同性情報


positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Caspase Activators and Caspases / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of oligodendrocyte differentiation / negative regulation of neuron differentiation ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Caspase Activators and Caspases / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of oligodendrocyte differentiation / negative regulation of neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / mismatch repair / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / regulation of cell cycle / ciliary basal body / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / centrosome / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
類似検索 - 分子機能
Tumour protein p73, SAM domain / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / SAM domain (Sterile alpha motif) ...Tumour protein p73, SAM domain / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Tumor protein p73
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: 2.9 Å
データ登録者Koley, T. / Roy Chowdhury, S. / Kumar, M. / Kaur, P. / Singh, T.P. / Viadiu, H. / Ethayathulla, A.S.
引用ジャーナル: Int.J.Biol.Macromol. / 年: 2022
タイトル: Deciphering the mechanism of p73 recognition of p53 response elements using the crystal structure of p73-DNA complexes and computational studies.
著者: Koley, T. / Roy Chowdhury, S. / Kushwaha, T. / Kumar, M. / Inampudi, K.K. / Kaur, P. / Singh, T.P. / Viadiu, H. / Ethayathulla, A.S.
履歴
登録2021年6月1日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年4月13日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Tumor protein p73
B: Tumor protein p73
C: Tumor protein p73
D: Tumor protein p73
I: Tumor protein p73
J: Tumor protein p73
K: Tumor protein p73
L: Tumor protein p73
a: Tumor protein p73
b: Tumor protein p73
c: Tumor protein p73
d: Tumor protein p73
i: Tumor protein p73
j: Tumor protein p73
k: Tumor protein p73
l: Tumor protein p73
E: 12-mer DNA
F: 12-mer DNA
G: 12-mer DNA
H: 12-mer DNA
M: 12-mer DNA
N: 12-mer DNA
O: 12-mer DNA
P: 12-mer DNA
e: 12-mer DNA
f: 12-mer DNA
g: 12-mer DNA
h: 12-mer DNA
m: 12-mer DNA
n: 12-mer DNA
o: 12-mer DNA
p: 12-mer DNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)440,07648
ポリマ－439,03032
非ポリマー1,04716
水1,51384
1
A: Tumor protein p73
B: Tumor protein p73
C: Tumor protein p73
D: Tumor protein p73
E: 12-mer DNA
F: 12-mer DNA
G: 12-mer DNA
H: 12-mer DNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,01912
ポリマ－109,7578
非ポリマー2624
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
I: Tumor protein p73
J: Tumor protein p73
K: Tumor protein p73
L: Tumor protein p73
M: 12-mer DNA
N: 12-mer DNA
O: 12-mer DNA
P: 12-mer DNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,01912
ポリマ－109,7578
非ポリマー2624
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
3
a: Tumor protein p73
b: Tumor protein p73
c: Tumor protein p73
d: Tumor protein p73
e: 12-mer DNA
f: 12-mer DNA
g: 12-mer DNA
h: 12-mer DNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,01912
ポリマ－109,7578
非ポリマー2624
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
4
i: Tumor protein p73
j: Tumor protein p73
k: Tumor protein p73
l: Tumor protein p73
m: 12-mer DNA
n: 12-mer DNA
o: 12-mer DNA
p: 12-mer DNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,01912
ポリマ－109,7578
非ポリマー2624
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)139.697, 105.496, 155.504
Angle α, β, γ (deg.)90.000, 112.360, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Tumor protein p73 / p53-like transcription factor / p53-related protein


分子量: 23775.955 Da / 分子数: 16 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TP73, P73 / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: O15350
#2: DNA鎖
12-mer DNA


分子量: 3663.392 Da / 分子数: 16 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 16 / 由来タイプ: 合成 / 式: Zn
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 84 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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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: 2.54 Å3/Da / 溶媒含有率: 51.67 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6
詳細: 100 mM MES, pH-6.0, 0.1 M Ammonium acetate, 12% w/v PEg20K

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データ収集

回折平均測定温度: 200 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRL / ビームライン: BL7-1 / 波長: 0.97 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2011年2月15日
放射モノクロメーター: M / 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: 0.97 Å / 相対比: 1
反射解像度: 2.9→100 Å / Num. obs: 91900 / % possible obs: 99.5 % / 冗長度: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.5
反射 シェル解像度: 2.9→3 Å / Rmerge(I) obs: 0.08 / Num. unique obs: 91900

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.18.2_3874: ???)精密化
PDB_EXTRACT3.27データ抽出
HKL-2000データ削減
SCALEPACKデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3VD0

3vd0


解像度: 2.9→40.93 Å / SU ML: 0.43 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 40.69 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3061 4363 4.97 %
Rwork0.2406 --
obs0.2438 87805 95.05 %
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: 217.08 Å2 / Biso mean: 90.1508 Å2 / Biso min: 30 Å2
精密化ステップサイクル: final / 解像度: 2.9→40.93 Å
タンパク質核酸リガンド溶媒全体
原子数21994 6975 16 84 29069
Biso mean--74.13 63.59 -
残基数----3387
LS精密化 シェル解像度: 2.9→2.94 Å
Rfactor反射数%反射
Rfree0.4207 160 -
Rwork0.3435 2775 -
obs--96 %
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)
10.1267-0.1592-0.38070.93361.36172.2070.5241-0.7184-1.05710.48350.6640.60871.1698-0.2980.44760.78310.1365-0.19270.73640.48551.010282.144512.5475-0.2544
20.84470.3236-0.32560.54550.41640.8416-0.27810.37130.04540.15170.042-0.8101-0.49820.7454-0.00510.6082-0.10290.14840.81010.25250.964191.826925.6717-15.0771
30.1727-0.2715-0.08140.4350.10321.1111-0.21320.801-0.6769-0.20860.8264-0.2427-0.16020.21690.02350.6204-0.33860.08830.7505-0.0150.733583.215128.6748-18.5443
40.8996-0.09570.85450.26620.58462.54060.39990.4954-0.52850.22310.1969-0.26850.17730.45460.25280.4975-0.08330.14840.5068-0.01871.154992.282415.5297-12.5237
50.3259-0.4042-0.50320.71680.46421.2003-0.12640.1453-1.2338-0.0073-0.11340.01580.1913-1.8757-0.02820.6291-0.17780.02460.5802-0.07380.787370.158617.2591-11.1897
63.5644-0.62980.93210.1558-0.03960.61750.12651.2422-1.2825-0.0594-0.15730.69840.55160.3383-0.01160.7798-0.08890.30540.6838-0.34111.150178.42518.9462-19.8437
76.90941.79041.03962.1964-1.89422.8350.16411.1611-1.4417-0.7956-0.1176-0.39020.51510.72190.55470.4335-0.07660.48730.6622-0.08771.658395.782213.9129-18.9568
80.1883-0.12120.25290.1203-0.2140.453-0.39540.0607-0.6809-0.16780.1624-0.32110.2079-0.0957-0.00040.5201-0.01680.21010.622-0.00460.545876.067120.9411-17.2376
90.97390.72980.0060.90130.53971.0547-0.01690.0873-0.22840.0168-0.0224-0.41060.8444-0.2399-0.00680.70650.02050.27120.5040.12310.751386.646817.9132-9.7498
100.37820.34240.62620.33390.63821.23650.12950.00860.5149-1.0589-0.30740.0341-1.7943-0.5338-0.03341.19610.10390.12610.66020.11410.480379.617640.0291-14.0864
112.0665-0.5555-0.04091.0857-0.83050.7990.28710.1724-0.2259-0.0790.1985-0.0871-0.2709-0.76360.0390.59480.0805-0.05140.85210.30590.515637.871128.4316-22.6763
120.3588-0.00660.08371.58980.42551.118-0.06140.78380.2679-0.2674-0.0465-0.05690.1648-0.2925-0.0010.7468-0.1027-0.10331.02030.26030.484640.994519.225-25.109
131.78870.66420.79571.18150.53241.2827-0.04830.4982-0.02560.18910.06340.02140.3915-0.4945-0.01450.6929-0.18-0.18510.7310.2150.458339.914114.1001-17.028
141.7987-1.0049-0.45051.1953-0.59882.27980.31680.92370.4173-0.042-0.1523-0.4393-0.3477-0.26130.18050.612-0.0714-0.02940.86120.44650.532142.786227.4838-24.4781
150.91560.0964-0.34820.1278-0.2610.54910.45670.51971.1878-0.23060.05380.3586-0.2539-0.17930.08580.2470.1769-0.03650.62550.25171.233723.173330.68894.9434
160.2975-0.1-0.20460.15220.04060.27470.47590.40430.41210.27390.20871.1598-0.8332-0.51870.00360.57310.1130.04010.5422-0.04841.030230.430136.322511.8806
170.92941.00480.39781.5467-0.32271.1070.0070.39860.51010.26120.0360.1165-0.2674-0.0840.00030.59670.0362-0.01550.57750.13170.594428.768423.34326.4908
182.26740.1992-0.5110.9014-0.19140.13890.5508-0.61460.8540.84960.7296-0.17980.0590.79611.25150.4233-0.0246-0.3070.6087-0.18260.582535.444816.321319.9669
191.08960.73-0.10860.5949-0.40460.9244-0.1963-0.19010.29650.4285-0.39150.15660.2528-0.826-0.02160.5787-0.0116-0.05870.57550.0230.608621.411819.763412.0823
201.6061-0.9822-0.09850.7303-0.66733.12820.59530.00730.75250.2691-0.3341-0.0928-0.4482-0.22920.00360.59540.04310.06790.34490.14190.642231.388231.38076.9884
210.9389-0.1638-0.66652.07280.94860.82640.0025-1.2611-0.24510.674-0.5908-0.40680.778-0.3314-0.02440.680.0086-0.15131.68490.54640.40179.48717.366426.9563
220.76670.5435-0.46470.5732-0.09620.49050.1312-0.35540.7589-0.1398-0.2382-0.3223-0.45230.181-0.00030.4873-0.0437-0.00620.72920.18530.719972.322930.213910.9316
231.19321.62660.53322.45450.31090.7448-0.0748-1.2256-0.25720.2337-0.3217-0.04290.4286-0.09760.00310.4811-0.02050.14040.8070.25570.415369.107417.506619.5656
241.2032-1.3435-0.38081.99060.10250.34720.28060.0061-0.4435-0.3864-0.6505-0.22830.74460.1675-0.4321.0522-0.36-0.18060.83780.40730.461558.032612.67188.0723
251.0865-0.35750.61211.40490.64840.8991-0.264-0.6579-0.3841-0.45540.1383-0.12460.6949-0.02830.00090.6860.0539-0.02480.660.29540.722473.753911.176113.4512
261.33131.063-0.06011.01-0.32280.65390.2344-1.08040.00410.0473-0.185-0.1050.12660.17280.00130.5137-0.1029-0.04010.77290.19650.533269.247720.399118.4027
270.7172-0.48510.54410.3269-0.37280.4255-0.5278-1.90940.9471.1676-0.3415-0.2598-0.3595-0.6709-0.05211.0659-0.124-0.05610.9277-0.13771.171868.271141.144217.6012
280.4411-0.321-0.79034.135-1.14875.57410.4311-0.4967-0.02780.1046-0.3218-0.8207-1.22331.38970.06440.7231-0.1628-0.29210.6392-0.15560.303950.8693-0.55-6.1079
290.1009-0.2331-0.16940.55110.40010.26730.35111.2260.3831-1.08410.14110.0285-0.03330.27380.09310.9104-0.0601-0.26240.6891-0.0140.579236.6961-3.552-24.3763
300.30110.00690.00390.1172-0.20410.383-0.38020.4016-0.1202-0.629-0.10770.6405-0.1610.1169-0.00050.5894-0.0927-0.02390.67740.01690.654335.1727-6.3483-19.054
311.9987-1.76190.35611.698-0.43372.2398-0.5649-0.2833-0.8341-0.2733-0.3772-0.00150.26470.3744-0.0440.7166-0.0247-0.04860.7485-0.02960.566744.4076-13.0362-11.2436
320.7432-0.107-0.20320.0971-0.11410.256-0.2229-0.1235-0.88030.0928-0.4785-0.28790.1188-0.1308-0.00440.67930.20070.19870.80530.07611.009549.0383-20.6372-13.5074
330.1214-0.2464-0.19160.44650.3110.20140.13730.8978-0.0687-0.58080.08410.4317-0.30430.1839-0.00110.7554-0.04460.07750.9258-0.03920.581854.5395-6.4112-21.6823
340.4111-0.0755-0.11320.69940.2530.4995-0.1769-0.1356-0.48470.0073-0.3068-0.65730.19480.4054-0.00020.5765-0.02950.03580.71070.11890.611543.4762-11.9912-11.6627
350.5033-0.2834-0.15431.2553-0.72290.6160.37450.5272-0.23710.5511-0.13920.36710.18280.53-0.00220.5163-0.182-0.02240.6315-0.05250.548140.8534-5.9724-12.5452
360.44680.53730.09680.64880.13920.0684-0.24010.40340.5914-0.37730.34581.66150.2055-0.8030.00830.60630.0712-0.04070.9153-0.10950.701224.59-1.3076-16.1928
370.5463-1.11260.73232.2615-1.50410.9914-0.5830.1998-0.34360.3848-0.7655-0.8361.1363-0.539-0.2442.2226-0.6533-0.22551.08960.13151.218911.2104-54.8297-13.1716
380.2824-0.3071-0.14050.34880.01720.47680.1768-0.6365-0.12340.26830.22450.22820.7907-1.18520.0020.7191-0.2314-0.05061.08120.15440.87326.2487-34.7313-5.5514
390.39340.10360.32820.30270.22590.2916-0.3253-0.1039-1.23220.34210.4160.06711.0699-0.32630.00112.1759-0.2665-0.09790.7720.25361.251411.1946-50.6768-3.0039
401.0441-0.1583-0.49320.6763-0.32530.5070.06710.2507-0.7347-0.61720.1264-0.9250.70340.08210.00141.13120.1260.14820.7261-0.04480.973126.5098-36.5999-7.1247
410.43710.27130.410.652-0.19230.705-0.10050.1342-0.3402-0.26140.4382-0.0271.3138-0.87960.01661.1476-0.1089-0.03580.81420.37821.095317.4723-48.60350.9122
420.11-0.3392-0.0841.02780.31940.10580.4162-0.1868-0.2343-0.63110.6826-0.56391.02660.1540.37450.9059-0.2196-0.05330.57930.03740.873818.6893-35.465-8.071
430.06980.0006-0.04090.04060.08630.19030.3295-0.149-0.3401-0.23991.0167-0.23020.63791.06510.02421.48690.0588-0.11690.68870.05330.94916.2457-53.6943-6.9181
441.33830.0620.1718-0.00370.00310.03560.0398-0.1091-0.37970.2794-0.575-0.52580.8529-0.6206-0.3931.3004-0.31950.19790.41910.14420.635911.6219-41.563-10.235
450.3204-0.12910.02890.2720.0123-0.0014-0.6367-0.4074-0.0328-1.09790.50710.92220.6974-0.6529-0.01510.8073-0.1636-0.18671.0850.31520.60133.6348-27.2607-15.3978
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510.6222-0.17630.3040.2574-0.27150.3464-0.1349-0.4731-0.4731-0.14840.20680.130.74890.4412-0.00151.0002-0.3207-0.02091.36310.25821.0426.0772-38.927624.3613
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540.37350.0486-0.33440.2903-0.14380.3809-0.41691.0417-0.1222-0.88620.0370.1550.15740.0290.00060.8520.2176-0.17070.7715-0.19190.542423.5548-1.624315.0746
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570.08530.3012-0.05570.94410.31030.4311-0.36640.9397-0.2959-1.0160.0630.10810.73340.3775-0.87710.50860.5950.3693-1.1449-1.9405-1.194441.3773-10.196716.9833
581.00740.22651.08411.70790.25581.4791-0.44910.065-0.5709-0.3973-0.11050.09840.0838-0.2808-0.01470.480.1457-0.05130.4373-0.26350.460633.1596-8.903823.2482
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620.51890.0507-0.72510.0285-0.12531.0506-0.08971.1697-1.25740.25380.43350.2540.61910.02850.08490.8795-0.13150.30030.8971-0.47421.2545118.207310.056247.2744
631.231-0.08980.2850.8894-0.17032.5198-0.45450.3444-1.14580.37720.1564-0.42090.02570.0359-00.5245-0.0910.10.5954-0.08251.1441124.681315.977457.7242
640.23020.17190.09170.10460.06040.0744-0.49480.04540.4844-0.2503-0.1072-0.2752-1.01180.70140.00191.0292-0.18510.13130.72970.09730.9564119.780339.469757.1226
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660.1768-0.1308-0.0690.1528-0.05450.18730.2927-0.29350.33390.49030.06610.081-0.2848-0.43780.00160.6881-0.233-0.02150.9325-0.03770.689791.260212.881758.6135
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680.1552-0.1053-0.36240.79730.38760.84950.4160.4454-0.00790.07620.1225-0.2651-0.50190.04810.06330.5398-0.0425-0.30070.9480.13890.876367.113719.593167.2912
690.21490.2284-0.06670.3808-0.37840.47320.2672-0.21440.1134-0.31030.57410.0298-0.9992-1.00390.00680.8135-0.06070.08420.96240.11731.33661.575234.796381.5009
700.6789-0.37480.76680.6959-1.29412.51750.02-0.49931.47150.23850.6570.9925-1.2061-1.1392-0.01021.0058-0.02390.1920.43610.11441.255670.779935.995284.1192
710.7020.5190.5811.9172-0.51261.2894-0.16840.5350.3582-0.14080.243-0.0636-0.1130.05880.00020.5941-0.07960.12220.5766-0.02080.797968.996523.017978.7267
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830.44030.3394-0.23460.79020.52030.88340.0806-0.80630.61490.4330.17080.2120.34480.4724-0.0020.6326-0.11380.02640.8305-0.02820.9998110.462732.210389.9049
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922.9947-0.3527-0.83810.69490.19250.26920.54590.28631.0544-0.21340.06770.09270.3115-1.27120.18390.7169-0.3505-0.10081.07280.15840.368346.4228-35.144766.2288
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940.5584-0.1379-0.43950.20610.06240.34530.05960.8549-0.0462-1.2309-0.3257-0.6339-0.33920.0559-0.00540.9706-0.02050.06640.56530.01190.864865.6867-37.883257.9283
950.02120.05590.08290.24640.0940.4124-0.18910.2609-0.32241.1386-0.3744-0.9940.58251.6186-0.00260.7648-0.0630.05210.70170.02221.15467.9741-35.940373.4561
962.5655-0.2165-1.87020.01530.14981.3644-0.7745-0.9337-0.29840.7706-0.5882-0.41220.8063-0.1935-0.29091.0931-0.3462-0.21360.46610.01910.674859.8998-44.252676.5132
972.51672.24161.89342.00091.68451.42320.67160.3274-1.0565-0.09630.2022-0.86440.72950.24441.83511.8343-0.02810.27660.3127-0.15530.765.4232-49.888266.6552
983.9435-1.361-0.75283.2031-0.34570.82780.29260.16870.8477-0.2781-0.2459-0.70891.0986-0.781-0.16610.9187-0.4763-0.13630.4644-0.3332-0.172453.9861-40.906868.6053
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1000.1949-0.30170.04530.49050.17410.3493-0.45690.5750.6965-0.69660.90050.0520.0591-0.00190.03040.866-0.2436-0.01231.19960.26050.647746.6401-31.034757.7602
1011.53170.5377-0.89351.9274-0.43681.2133-0.15120.16240.8567-0.81510.93010.53680.087-0.66370.18320.7611-0.2853-0.11910.91220.32030.422139.0525-44.229493.148
1021.6174-0.77-0.57962.4883-0.40871.66180.03380.53460.4429-0.67120.5320.1507-0.1097-0.75760.37280.3534-0.1587-0.19620.67860.25040.316943.6681-37.860396.4364
1032.7343-1.30010.47690.6179-0.22780.0846-0.1449-1.1193-0.51070.90920.3898-0.2043-0.45710.41350.00020.5686-0.1209-0.07560.84060.01180.417256.711-36.6002107.0334
1041.75160.2088-0.44492.0054-0.48332.0068-0.36760.10330.22280.13230.69030.0356-0.0033-0.70930.14810.3784-0.1159-0.09850.50490.1290.321645.8035-43.462899.4595
1052.97890.9576-1.3170.3394-0.30341.23840.40190.67791.1386-0.35080.37670.8778-0.267-0.94540.80650.59630.0838-0.19830.74840.42270.484736.5344-28.516993.0129
1060.47130.01920.27390.61350.62360.73330.5058-0.74850.19180.5614-0.0530.1763-0.19221.08490.00870.7338-0.0257-0.01640.89410.08160.831581.31780.079699.5247
1070.30760.2428-0.41710.1568-0.2960.50330.04560.07720.9177-0.09130.26270.488-0.886-0.07640.00040.6857-0.08920.01720.53010.17880.682163.8512-2.080687.1258
1081.336-0.83560.75412.02030.80591.7041-0.2738-0.4726-0.20110.22090.3074-0.31640.0892-0.3217-0.00770.56480.0826-0.05310.6510.17580.481976.7867-6.57996.3778
1090.3127-0.04670.13840.0354-0.08940.2806-0.4932-0.3404-0.4189-0.7401-0.0128-0.31870.64420.0425-0.05050.7651-0.0220.02680.56570.29760.781369.8831-22.605391.0663
1102.5939-0.24480.60681.96050.51580.7263-0.0443-0.4686-0.4062-0.26030.2341-0.24650.00390.31560.00290.54360.0271-0.02470.65520.23310.471877.7214-9.79192.2501
1110.93110.4082-0.59280.93-0.35060.6984-0.2712-0.49051.02260.13380.27320.22750.00070.14460.00750.55610.1315-0.18940.70370.16590.599863.01070.634394.5864
1120.3043-0.19930.10440.4693-0.15770.04940.1935-0.12321.05280.08330.64790.12860.10830.43180.01950.9826-0.36560.21761.04110.20660.809565.04937.6742-22.2954
1130.4611-0.47970.14970.4554-0.16750.04480.56030.32731.2299-0.0383-0.06560.3713-0.3279-0.08440.00120.9348-0.16880.14480.92990.00820.920464.067737.9211-22.3119
1141.0808-0.19530.12890.8419-0.07840.00070.3832-0.40921.00620.4191-0.175-0.40270.22580.0679-0.00090.819-0.11710.12030.758-0.05331.086451.989840.661813.4259
1150.62260.073-0.38520.46380.06120.25210.0595-0.49571.26190.12120.16430.2658-0.3781-0.2723-0.00010.97810.1120.13980.8393-0.02351.129150.608941.085112.5976
1160.251-0.2058-0.09920.4278-0.05020.1508-0.00770.52540.9336-0.33460.8866-0.1688-0.49-0.63270.00260.941-0.11290.08810.9661-0.12590.853716.6131-15.1457-15.9035
1170.8591-0.32590.39030.9125-0.31180.1890.36670.10.4688-0.53790.30670.53540.1259-0.6164-0.00031.0377-0.02260.12251.1787-0.15590.859316.1935-16.3072-16.2356
1181.7032-0.9303-0.02261.2466-0.15590.03250.4386-1.1038-0.48691.3477-0.41660.7754-0.4946-0.0791-0.00781.269-0.0152-0.08781.5968-0.84361.19145.5939-10.552223.0928
1190.2805-0.12870.29720.90410.19390.34870.6432-0.1121-0.08530.2106-0.35641.1017-0.0116-1.14480.00121.0217-0.13030.15041.4187-0.5351.13185.1985-11.634622.6285
1200.74820.20360.20440.5295-0.31360.2987-0.1778-0.05061.45820.0160.58070.25580.11760.8869-0.00040.94470.01190.20261.0264-0.02591.0963105.227337.485749.8136
1210.4298-0.02440.29270.3697-0.25070.3-0.07580.61691.8027-0.83910.63020.886-0.3696-0.04050.00220.9341-0.27090.23461.083-0.13161.1562104.281937.707149.7326
1221.4201-0.10490.71130.5881-0.19530.36280.8875-1.64412.2040.6607-0.3816-0.0290.1210.7168-0.01161.2432-0.22750.08240.9518-0.07931.197292.330540.142585.7028
1230.33050.0687-0.2240.19260.05210.19460.3744-0.75681.17491.0146-0.67780.7339-0.4661-0.755-0.00181.029-0.15240.18761.1323-0.3151.414490.65940.420886.4995
1240.45950.0303-0.15940.8293-0.27010.124-0.09450.41570.5445-0.19690.65320.122-0.4557-0.3768-0.00050.99980.04370.23370.92340.14610.716256.7294-15.505556.0647
1250.75780.02640.13190.99580.29620.5328-0.07250.79940.3304-0.00020.91570.2109-0.0985-1.52090.01331.0886-0.27930.24241.05280.03420.846156.3442-16.66355.7377
1260.48320.26980.22320.79160.20440.0927-0.2415-0.19220.84260.50560.57210.1387-0.59460.21340.00621.05820.20410.03990.83360.27650.696345.8279-11.066795.2259
1270.1852-0.6742-0.60132.58721.51552.2961-0.75510.74680.30990.0651-0.17221.78560.0184-0.3062-0.84590.50220.456-0.3920.59681.19010.126945.3124-12.144694.5768
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 111 through 119 )A111 - 119
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 141 )A120 - 141
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 158 )A142 - 158
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 181 )A159 - 181
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 199 )A182 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 233 )A200 - 233
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 249 )A234 - 249
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 270 )A250 - 270
9X-RAY DIFFRACTION9chain 'A' and (resid 271 through 297 )A271 - 297
10X-RAY DIFFRACTION10chain 'A' and (resid 298 through 312 )A298 - 312
11X-RAY DIFFRACTION11chain 'B' and (resid 112 through 158 )B112 - 158
12X-RAY DIFFRACTION12chain 'B' and (resid 159 through 199 )B159 - 199
13X-RAY DIFFRACTION13chain 'B' and (resid 200 through 249 )B200 - 249
14X-RAY DIFFRACTION14chain 'B' and (resid 250 through 312 )B250 - 312
15X-RAY DIFFRACTION15chain 'C' and (resid 112 through 141 )C112 - 141
16X-RAY DIFFRACTION16chain 'C' and (resid 142 through 158 )C142 - 158
17X-RAY DIFFRACTION17chain 'C' and (resid 159 through 199 )C159 - 199
18X-RAY DIFFRACTION18chain 'C' and (resid 200 through 214 )C200 - 214
19X-RAY DIFFRACTION19chain 'C' and (resid 215 through 249 )C215 - 249
20X-RAY DIFFRACTION20chain 'C' and (resid 250 through 312 )C250 - 312
21X-RAY DIFFRACTION21chain 'D' and (resid 113 through 127 )D113 - 127
22X-RAY DIFFRACTION22chain 'D' and (resid 128 through 158 )D128 - 158
23X-RAY DIFFRACTION23chain 'D' and (resid 159 through 199 )D159 - 199
24X-RAY DIFFRACTION24chain 'D' and (resid 200 through 214 )D200 - 214
25X-RAY DIFFRACTION25chain 'D' and (resid 215 through 249 )D215 - 249
26X-RAY DIFFRACTION26chain 'D' and (resid 250 through 297 )D250 - 297
27X-RAY DIFFRACTION27chain 'D' and (resid 298 through 311 )D298 - 311
28X-RAY DIFFRACTION28chain 'I' and (resid 113 through 127 )I113 - 127
29X-RAY DIFFRACTION29chain 'I' and (resid 128 through 141 )I128 - 141
30X-RAY DIFFRACTION30chain 'I' and (resid 142 through 158 )I142 - 158
31X-RAY DIFFRACTION31chain 'I' and (resid 159 through 203 )I159 - 203
32X-RAY DIFFRACTION32chain 'I' and (resid 204 through 233 )I204 - 233
33X-RAY DIFFRACTION33chain 'I' and (resid 234 through 249 )I234 - 249
34X-RAY DIFFRACTION34chain 'I' and (resid 250 through 283 )I250 - 283
35X-RAY DIFFRACTION35chain 'I' and (resid 284 through 297 )I284 - 297
36X-RAY DIFFRACTION36chain 'I' and (resid 298 through 311 )I298 - 311
37X-RAY DIFFRACTION37chain 'J' and (resid 114 through 126 )J114 - 126
38X-RAY DIFFRACTION38chain 'J' and (resid 127 through 158 )J127 - 158
39X-RAY DIFFRACTION39chain 'J' and (resid 159 through 181 )J159 - 181
40X-RAY DIFFRACTION40chain 'J' and (resid 182 through 214 )J182 - 214
41X-RAY DIFFRACTION41chain 'J' and (resid 215 through 249 )J215 - 249
42X-RAY DIFFRACTION42chain 'J' and (resid 250 through 270 )J250 - 270
43X-RAY DIFFRACTION43chain 'J' and (resid 271 through 283 )J271 - 283
44X-RAY DIFFRACTION44chain 'J' and (resid 284 through 297 )J284 - 297
45X-RAY DIFFRACTION45chain 'J' and (resid 298 through 310 )J298 - 310
46X-RAY DIFFRACTION46chain 'K' and (resid 112 through 141 )K112 - 141
47X-RAY DIFFRACTION47chain 'K' and (resid 142 through 158 )K142 - 158
48X-RAY DIFFRACTION48chain 'K' and (resid 159 through 199 )K159 - 199
49X-RAY DIFFRACTION49chain 'K' and (resid 200 through 223 )K200 - 223
50X-RAY DIFFRACTION50chain 'K' and (resid 224 through 249 )K224 - 249
51X-RAY DIFFRACTION51chain 'K' and (resid 250 through 283 )K250 - 283
52X-RAY DIFFRACTION52chain 'K' and (resid 284 through 312 )K284 - 312
53X-RAY DIFFRACTION53chain 'L' and (resid 112 through 130 )L112 - 130
54X-RAY DIFFRACTION54chain 'L' and (resid 131 through 158 )L131 - 158
55X-RAY DIFFRACTION55chain 'L' and (resid 159 through 199 )L159 - 199
56X-RAY DIFFRACTION56chain 'L' and (resid 200 through 214 )L200 - 214
57X-RAY DIFFRACTION57chain 'L' and (resid 215 through 249 )L215 - 249
58X-RAY DIFFRACTION58chain 'L' and (resid 250 through 283 )L250 - 283
59X-RAY DIFFRACTION59chain 'L' and (resid 284 through 311 )L284 - 311
60X-RAY DIFFRACTION60chain 'a' and (resid 113 through 141 )a113 - 141
61X-RAY DIFFRACTION61chain 'a' and (resid 142 through 199 )a142 - 199
62X-RAY DIFFRACTION62chain 'a' and (resid 200 through 223 )a200 - 223
63X-RAY DIFFRACTION63chain 'a' and (resid 224 through 297 )a224 - 297
64X-RAY DIFFRACTION64chain 'a' and (resid 298 through 311 )a298 - 311
65X-RAY DIFFRACTION65chain 'b' and (resid 112 through 199 )b112 - 199
66X-RAY DIFFRACTION66chain 'b' and (resid 200 through 214 )b200 - 214
67X-RAY DIFFRACTION67chain 'b' and (resid 215 through 310 )b215 - 310
68X-RAY DIFFRACTION68chain 'c' and (resid 111 through 120 )c111 - 120
69X-RAY DIFFRACTION69chain 'c' and (resid 121 through 141 )c121 - 141
70X-RAY DIFFRACTION70chain 'c' and (resid 142 through 158 )c142 - 158
71X-RAY DIFFRACTION71chain 'c' and (resid 159 through 199 )c159 - 199
72X-RAY DIFFRACTION72chain 'c' and (resid 200 through 223 )c200 - 223
73X-RAY DIFFRACTION73chain 'c' and (resid 224 through 283 )c224 - 283
74X-RAY DIFFRACTION74chain 'c' and (resid 284 through 310 )c284 - 310
76X-RAY DIFFRACTION76chain 'd' and (resid 113 through 141 )d113 - 141
77X-RAY DIFFRACTION77chain 'd' and (resid 142 through 158 )d142 - 158
78X-RAY DIFFRACTION78chain 'd' and (resid 159 through 199 )d159 - 199
79X-RAY DIFFRACTION79chain 'd' and (resid 200 through 214 )d200 - 214
80X-RAY DIFFRACTION80chain 'd' and (resid 215 through 249 )d215 - 249
81X-RAY DIFFRACTION81chain 'd' and (resid 250 through 270 )d250 - 270
82X-RAY DIFFRACTION82chain 'd' and (resid 271 through 283 )d271 - 283
83X-RAY DIFFRACTION83chain 'd' and (resid 284 through 310 )d284 - 310
84X-RAY DIFFRACTION84chain 'i' and (resid 112 through 130 )i112 - 130
85X-RAY DIFFRACTION85chain 'i' and (resid 131 through 141 )i131 - 141
86X-RAY DIFFRACTION86chain 'i' and (resid 142 through 158 )i142 - 158
87X-RAY DIFFRACTION87chain 'i' and (resid 159 through 223 )i159 - 223
88X-RAY DIFFRACTION88chain 'i' and (resid 224 through 249 )i224 - 249
89X-RAY DIFFRACTION89chain 'i' and (resid 250 through 283 )i250 - 283
90X-RAY DIFFRACTION90chain 'i' and (resid 284 through 312 )i284 - 312
91X-RAY DIFFRACTION91chain 'j' and (resid 116 through 126 )j116 - 126
92X-RAY DIFFRACTION92chain 'j' and (resid 127 through 158 )j127 - 158
93X-RAY DIFFRACTION93chain 'j' and (resid 159 through 181 )j159 - 181
94X-RAY DIFFRACTION94chain 'j' and (resid 182 through 199 )j182 - 199
95X-RAY DIFFRACTION95chain 'j' and (resid 200 through 214 )j200 - 214
96X-RAY DIFFRACTION96chain 'j' and (resid 215 through 223 )j215 - 223
97X-RAY DIFFRACTION97chain 'j' and (resid 224 through 239 )j224 - 239
98X-RAY DIFFRACTION98chain 'j' and (resid 240 through 270 )j240 - 270
99X-RAY DIFFRACTION99chain 'j' and (resid 271 through 287 )j271 - 287
100X-RAY DIFFRACTION100chain 'j' and (resid 288 through 311 )j288 - 311
101X-RAY DIFFRACTION101chain 'k' and (resid 107 through 141 )k107 - 141
102X-RAY DIFFRACTION102chain 'k' and (resid 142 through 199 )k142 - 199
103X-RAY DIFFRACTION103chain 'k' and (resid 200 through 214 )k200 - 214
104X-RAY DIFFRACTION104chain 'k' and (resid 215 through 283 )k215 - 283
105X-RAY DIFFRACTION105chain 'k' and (resid 284 through 312 )k284 - 312
106X-RAY DIFFRACTION106chain 'l' and (resid 112 through 130 )l112 - 130
107X-RAY DIFFRACTION107chain 'l' and (resid 131 through 158 )l131 - 158
108X-RAY DIFFRACTION108chain 'l' and (resid 159 through 194 )l159 - 194
109X-RAY DIFFRACTION109chain 'l' and (resid 195 through 217 )l195 - 217
110X-RAY DIFFRACTION110chain 'l' and (resid 218 through 283 )l218 - 283
111X-RAY DIFFRACTION111chain 'l' and (resid 284 through 311 )l284 - 311
112X-RAY DIFFRACTION112chain 'E' and (resid 398 through 408 )E398 - 408
113X-RAY DIFFRACTION113chain 'F' and (resid 411 through 421 )F411 - 421
114X-RAY DIFFRACTION114chain 'G' and (resid 500 through 511 )G500 - 511
115X-RAY DIFFRACTION115chain 'H' and (resid 512 through 523 )H512 - 523
116X-RAY DIFFRACTION116chain 'M' and (resid 410 through 421 )M410 - 421
117X-RAY DIFFRACTION117chain 'N' and (resid 398 through 409 )N398 - 409
118X-RAY DIFFRACTION118chain 'O' and (resid 410 through 421 )O410 - 421
119X-RAY DIFFRACTION119chain 'P' and (resid 398 through 409 )P398 - 409
120X-RAY DIFFRACTION120chain 'e' and (resid 398 through 408 )e398 - 408
121X-RAY DIFFRACTION121chain 'f' and (resid 411 through 421 )f411 - 421
122X-RAY DIFFRACTION122chain 'g' and (resid 500 through 511 )g500 - 511
123X-RAY DIFFRACTION123chain 'h' and (resid 512 through 522 )h512 - 522
124X-RAY DIFFRACTION124chain 'm' and (resid 410 through 421 )m410 - 421
125X-RAY DIFFRACTION125chain 'n' and (resid 398 through 409 )n398 - 409
126X-RAY DIFFRACTION126chain 'o' and (resid 410 through 421 )o410 - 421
127X-RAY DIFFRACTION127chain 'p' and (resid 398 through 409 )p398 - 409

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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://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