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- PDB-7dcs: Crystal structure of HSF1 DNA-binding domain in complex with 3-si... -

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基本情報

登録情報
データベース: PDB / ID: 7dcs
タイトルCrystal structure of HSF1 DNA-binding domain in complex with 3-site HSE DNA (23 bp)
要素
  • DNA (5'-D(*AP*TP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*GP*A)-3')
  • Heat shock factor protein 1
キーワードDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
機能・相同性
機能・相同性情報


cellular response to nitroglycerin / embryonic process involved in female pregnancy / sequence-specific single stranded DNA binding / cellular response to diamide / response to hypobaric hypoxia / negative regulation of double-strand break repair via nonhomologous end joining / cellular response to L-glutamine / positive regulation of stress granule assembly / positive regulation of apoptotic DNA fragmentation / response to peptide ...cellular response to nitroglycerin / embryonic process involved in female pregnancy / sequence-specific single stranded DNA binding / cellular response to diamide / response to hypobaric hypoxia / negative regulation of double-strand break repair via nonhomologous end joining / cellular response to L-glutamine / positive regulation of stress granule assembly / positive regulation of apoptotic DNA fragmentation / response to peptide / cellular response to sodium arsenite / translation elongation factor binding / negative regulation of inclusion body assembly / nuclear stress granule / female meiotic nuclear division / positive regulation of macrophage differentiation / positive regulation of inclusion body assembly / positive regulation of multicellular organism growth / pronucleus / cellular response to potassium ion / protein folding chaperone complex / negative regulation of cardiac muscle cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / STAT family protein binding / response to psychosocial stress / mitotic spindle pole / response to testosterone / cellular response to cadmium ion / cellular response to angiotensin / negative regulation of tumor necrosis factor production / general transcription initiation factor binding / HSF1-dependent transactivation / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / mRNA transport / Mitochondrial unfolded protein response (UPRmt) / HSF1 activation / embryonic placenta development / Attenuation phase / negative regulation of protein-containing complex assembly / heterochromatin / regulation of cellular response to heat / heat shock protein binding / response to nutrient / positive regulation of mitotic cell cycle / cellular response to copper ion / positive regulation of apoptotic signaling pathway / epithelial cell proliferation / response to activity / cellular response to estradiol stimulus / Hsp90 protein binding / chromatin DNA binding / promoter-specific chromatin binding / euchromatin / cellular response to gamma radiation / defense response / PML body / kinetochore / Aggrephagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / mRNA processing / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / MAPK cascade / positive regulation of cold-induced thermogenesis / cellular response to heat / cellular response to lipopolysaccharide / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / ribonucleoprotein complex / DNA repair / centrosome / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / 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) / Heat shock factor protein 1
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: 2.4 Å
データ登録者Feng, N. / Liu, W.
引用ジャーナル: Iscience / 年: 2021
タイトル: Structures of heat shock factor trimers bound to DNA.
著者: Feng, N. / Feng, H. / Wang, S. / Punekar, A.S. / Ladenstein, R. / Wang, D.C. / Zhang, Q. / Ding, J. / Liu, W.
履歴
登録2020年10月27日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年7月14日Provider: repository / タイプ: Initial release
改定 1.12021年9月15日Group: Database references / Structure summary
カテゴリ: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Heat shock factor protein 1
B: Heat shock factor protein 1
C: Heat shock factor protein 1
D: Heat shock factor protein 1
E: Heat shock factor protein 1
F: Heat shock factor protein 1
G: DNA (5'-D(*TP*GP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*GP*A)-3')
H: DNA (5'-D(*AP*TP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*C)-3')
I: DNA (5'-D(*TP*GP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*GP*A)-3')
J: DNA (5'-D(*AP*TP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,64115
ポリマ－107,52610
非ポリマー1155
水7,044391
1
A: Heat shock factor protein 1
B: Heat shock factor protein 1
C: Heat shock factor protein 1
G: DNA (5'-D(*TP*GP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*GP*A)-3')
H: DNA (5'-D(*AP*TP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)53,8328
ポリマ－53,7635
非ポリマー693
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-59 kcal/mol
Surface area20430 Å2
手法PISA
2
D: Heat shock factor protein 1
E: Heat shock factor protein 1
F: Heat shock factor protein 1
I: DNA (5'-D(*TP*GP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*GP*A)-3')
J: DNA (5'-D(*AP*TP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)53,8097
ポリマ－53,7635
非ポリマー462
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-53 kcal/mol
Surface area20650 Å2
手法PISA
単位格子
Length a, b, c (Å)86.720, 93.720, 142.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain G and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))
21(chain H and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))
12(chain A and (resid 15 through 83 or resid 97 through 119))
22(chain B and (resid 15 through 83 or resid 97 through 119))
32(chain C and (resid 15 through 83 or resid 97 through 119))
42(chain D and (resid 15 through 83 or resid 97 through 119))
52(chain E and (resid 15 through 83 or resid 97 through 119))
62(chain F and (resid 15 through 83 or resid 97 through 119))
13(chain I and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))
23(chain J and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DTDTDTDT(chain G and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))GG56
121DCDCDCDC(chain G and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))GG78
131DGDGDCDC(chain G and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))GG10 - 1711 - 18
141DGDGDGDG(chain G and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))GG2021
151DADADADA(chain G and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))GG2223
211DTDTDTDT(chain H and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))HH12
221DCDCDCDC(chain H and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))HH34
231DGDGDCDC(chain H and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))HH6 - 137 - 14
241DGDGDGDG(chain H and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))HH1617
251DADADADA(chain H and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))HH1819
112VALVALHISHIS(chain A and (resid 15 through 83 or resid 97 through 119))AA15 - 838 - 76
122THRTHRVALVAL(chain A and (resid 15 through 83 or resid 97 through 119))AA97 - 11990 - 112
212VALVALHISHIS(chain B and (resid 15 through 83 or resid 97 through 119))BB15 - 838 - 76
222THRTHRVALVAL(chain B and (resid 15 through 83 or resid 97 through 119))BB97 - 11990 - 112
312VALVALHISHIS(chain C and (resid 15 through 83 or resid 97 through 119))CC15 - 838 - 76
322THRTHRVALVAL(chain C and (resid 15 through 83 or resid 97 through 119))CC97 - 11990 - 112
412VALVALHISHIS(chain D and (resid 15 through 83 or resid 97 through 119))DD15 - 838 - 76
422THRTHRVALVAL(chain D and (resid 15 through 83 or resid 97 through 119))DD97 - 11990 - 112
512VALVALHISHIS(chain E and (resid 15 through 83 or resid 97 through 119))EE15 - 838 - 76
522THRTHRVALVAL(chain E and (resid 15 through 83 or resid 97 through 119))EE97 - 11990 - 112
612VALVALHISHIS(chain F and (resid 15 through 83 or resid 97 through 119))FF15 - 838 - 76
622THRTHRVALVAL(chain F and (resid 15 through 83 or resid 97 through 119))FF97 - 11990 - 112
113DTDTDTDT(chain I and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))II56
123DCDCDCDC(chain I and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))II78
133DGDGDCDC(chain I and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))II10 - 1711 - 18
143DGDGDGDG(chain I and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))II2021
153DADADADA(chain I and (resid 5 or resid 7 or resid 10 through 17 or resid 20 or resid 22))II2223
213DTDTDTDT(chain J and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))JJ12
223DCDCDCDC(chain J and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))JJ34
233DGDGDCDC(chain J and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))JJ6 - 137 - 14
243DGDGDGDG(chain J and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))JJ1617
253DADADADA(chain J and (resid 1 or resid 3 or resid 6 through 13 or resid 16 or resid 18))JJ1819

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
Heat shock factor protein 1 / HSF 1 / Heat shock transcription factor 1 / HSTF 1


分子量: 13214.025 Da / 分子数: 6 / 断片: UNP residues 15-120 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HSF1, HSTF1 / 発現宿主: Escherichia coli K-12 (大腸菌) / 株 (発現宿主): K-12 / 参照: UniProt: Q00613
#2: DNA鎖 DNA (5'-D(*TP*GP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*GP*A)-3')


分子量: 7111.594 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: DNA satellites (ウイルス)
#3: DNA鎖 DNA (5'-D(*AP*TP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*C)-3')


分子量: 7009.549 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: DNA satellites (ウイルス)
#4: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 5 / 由来タイプ: 合成 / 式: Na
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 391 / 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: 2.69 Å3/Da / 溶媒含有率: 58.94 %
解説: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 2% v/v Tacsimate pH 6.0, 0.1 M Bis-Tris pH 6.4, 21% (w/v) PEG 3350

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データ収集

回折平均測定温度: 80 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL18U1 / 波長: 0.97778 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年11月22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: 0.97778 Å / 相対比: 1
反射解像度: 2.4→86.72 Å / Num. obs: 41724 / % possible obs: 99.7 % / 冗長度: 12.1 % / Rpim(I) all: 0.03 / Net I/σ(I): 14.5
反射 シェル解像度: 2.4→2.53 Å / Mean I/σ(I) obs: 2.2 / Rpim(I) all: 0.317

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
PDB_EXTRACT3.25データ抽出
HKL-2000データ削減
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: 5HDG

5hdg


解像度: 2.4→19.876 Å / SU ML: 0.27 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 24.78 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2251 2091 5.01 %
Rwork0.1951 39633 -
obs0.1966 41724 90.77 %
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: 166.29 Å2 / Biso mean: 51.9289 Å2 / Biso min: 19.02 Å2
精密化ステップサイクル: final / 解像度: 2.4→19.876 Å
タンパク質核酸リガンド溶媒全体
原子数4820 1874 5 391 7090
Biso mean--43.27 45.71 -
残基数----676
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0067058
X-RAY DIFFRACTIONf_angle_d0.9719930
X-RAY DIFFRACTIONf_chiral_restr0.0591065
X-RAY DIFFRACTIONf_plane_restr0.006955
X-RAY DIFFRACTIONf_dihedral_angle_d17.383818
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11G210X-RAY DIFFRACTION11.523TORSIONAL
12H210X-RAY DIFFRACTION11.523TORSIONAL
21A2706X-RAY DIFFRACTION11.523TORSIONAL
22B2706X-RAY DIFFRACTION11.523TORSIONAL
23C2706X-RAY DIFFRACTION11.523TORSIONAL
24D2706X-RAY DIFFRACTION11.523TORSIONAL
25E2706X-RAY DIFFRACTION11.523TORSIONAL
26F2706X-RAY DIFFRACTION11.523TORSIONAL
31I210X-RAY DIFFRACTION11.523TORSIONAL
32J210X-RAY DIFFRACTION11.523TORSIONAL
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 (%)
2.4001-2.45580.32771000.2689185765
2.4558-2.51710.3019940.2506196468
2.5171-2.5850.30761140.2563213474
2.585-2.66090.27411070.2586229780
2.6609-2.74660.26531180.249245185
2.7466-2.84450.33141510.2508266992
2.8445-2.9580.28911300.2572282598
2.958-3.09220.2881580.24732919100
3.0922-3.25450.21681630.2145284699
3.2545-3.45750.23051820.19122878100
3.4575-3.72280.23691580.2007285999
3.7228-4.09450.20731490.1722936100
4.0945-4.68020.1891490.14632952100
4.6802-5.87130.18561600.1586295899
5.8713-19.870.17281580.17553088100
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)
10.00460.0016-0.01110.0051-0.00150.016-0.0114-0.1364-0.07670.0132-0.175-0.08220.1660.1045-0.00010.2251-0.0612-0.00750.46120.10290.3627-16.57011.3219-3.8737
20.0053-0.0032-0.00460.0098-0.00580.0177-0.0451-0.05510.07030.0563-0.0282-0.02910.020.0005-0.00040.4093-0.1622-0.03540.52960.03490.4022-17.40279.89812.9443
30.0388-0.0187-0.00240.03030.00610.00170.0001-0.0053-0.01850.0066-0.0109-0.0351-0.00730.01520.0070.13430.0454-0.06280.54050.0140.4357-7.63811.5162-8.3638
40.02380.0207-0.03040.0258-0.02240.0430.0033-0.02380.001-0.00830.0075-0.0403-0.00640.0503-0.01680.1770.0480.10650.41350.04820.4371-11.65075.4495-13.713
50.00910.00280.00820.01140.00120.0090.0012-0.03010.0106-0.0062-0.01110.0062-0.00730.01440.00150.0651-0.10860.16640.4007-0.05640.2975-22.349310.5565-11.9815
60.0005-0.00080.00340.0027-0.00840.0348-0.0074-0.0231-0.00210.0213-0.05140.0071-0.0573-0.01120.00020.2681-0.04630.0940.3678-0.10270.3482-26.276713.4513-3.6537
70.0128-0.00810.01240.0130.00230.01280.0823-0.14870.0757-0.01560.0219-0.0590.019-0.09520.00020.3458-0.14610.07150.5085-0.04080.3378-22.7029.1340.9647
80.0113-0.0060.00360.0117-0.00260.00270.02430.0137-0.04310.0286-0.0124-0.02190.0148-0.0489-00.4117-0.14640.08730.53020.05620.2951-28.4269-3.8597-2.8197
90.00310.0067-0.02610.0199-0.03410.21230.04640.0141-0.0181-0.01190.0116-0.02380.012-0.04420.02290.1319-0.02810.030.40670.0110.4159-31.93445.2692-12.5072
100.01910.03620.02350.11690.24370.7871-0.16550.07150.06-0.2149-0.0019-0.1962-0.18810.1753-0.06010.198-0.05840.02650.3214-0.06970.32-6.756433.1876-20.853
110.04790.0088-0.04040.0405-0.02920.10410.0067-0.0516-0.02910.0385-0.024-0.05970.03780.1321-0.07010.1973-0.0058-0.13540.4091-0.03810.3698-6.538628.1978-10.0345
120.0007-0.0031-0.00150.0187-0.00470.0149-0.047-0.03980.00070.00970.00090.0126-0.0141-0.0091-0.00010.2936-0.01380.03650.3591-0.05420.1613-14.115730.0026-7.7158
130.00860.00460.00810.0206-0.00540.011-0.0835-0.0107-0.01410.0647-0.05820.10270.0185-0.0266-0.02730.18410.0026-0.02590.3117-0.04370.2869-18.381127.2155-16.9178
140.0281-0.02670.01530.0404-0.01310.0074-0.1085-0.0118-0.0278-0.0148-0.0441-0.0246-0.0471-0.05120.00050.21180.0308-0.08250.3898-0.0130.34-17.363527.6571-25.1278
150.00420.0010.00230.0004-0.00080.00060.0434-0.02770.0003-0.04-0.0080.0073-0.05180.02110.00010.53690.1628-0.01070.7153-0.03090.8075-7.58212.3444-26.4388
160.01-0.0010.00750.01250.00450.0114-0.22770.0468-0.0547-0.03160.008-0.0640.00130.053-0.00040.3471-0.12410.00380.3879-0.04670.3733-10.593231.4322-27.7713
170.0151-0.013-0.00090.01040.001-0.0005-0.04230.0278-0.0001-0.03650.04660.0541-0.1785-0.07450.00030.5466-0.0103-0.19940.37420.00750.3583-19.462639.5703-25.1361
180.56740.24760.12970.14070.10490.0971-0.0890.06030.0146-0.1027-0.17010.05750.29830.2268-0.37320.41890.46630.260.35330.05130.2807-8.58362.7669-41.9345
190.01630.0177-0.00190.02730.01090.02910.02540.01140.0152-0.0160.0171-0.05670.02860.07140.04270.48260.42480.2420.38160.04720.5774-6.0652-2.801-31.4234
200.12240.01060.01770.05260.08080.1164-0.04710.0212-0.058-0.0202-0.08610.05080.1247-0.0609-0.13440.42570.12340.23770.293-0.02420.4094-16.7294-1.1087-31.9555
210.02970.01560.02470.01230.01570.0176-0.02530.0303-0.0536-0.07720.0074-0.01230.0783-0.01070.00390.44570.15670.17070.3418-0.06850.4678-18.3274-4.6571-43.9468
220.22570.00780.1360.01110.00320.0845-0.010.18560.0847-0.0295-0.14790.04660.21310.0858-0.08170.50330.12350.15230.41960.02010.3374-14.8772.656-47.6231
230.01450.0215-0.00970.053-0.02720.0188-0.00150.06720.05340.0521-0.05940.033-0.042-0.0393-0.00370.32730.1002-0.0070.39570.03970.4987-21.190510.5805-42.4367
240.0176-0.00330.00510.0074-0.01390.02880.10670.30160.1442-0.0182-0.0066-0.13840.0181-0.11240.00020.2121-0.009-0.01370.40110.06920.2556-37.8148-47.9122-77.9899
250.10540.0346-0.01440.0224-0.0160.0155-0.00610.02120.0027-0.0437-0.0064-0.0263-0.02630.05150.00060.2508-0.05570.04350.56360.05640.218-26.4525-55.2841-77.0273
260.05040.01320.05550.00320.01240.05760.040.0262-0.00740.00230.0345-0.0281-0.020.00490.06040.1525-0.23770.00080.31760.10140.2609-27.2923-49.3764-70.2823
270.0306-0.01110.00030.0173-0.01970.0597-0.01910.0722-0.1351-0.05770.09440.06480.0973-0.1390.02180.2565-0.08050.01050.31870.00180.2213-40.616-57.2347-71.5789
280.0021-0.00430.00080.0133-0.00280.0019-0.00620.05630.1110.0533-0.05790.0042-0.0884-0.115-0.00330.2650.03930.04320.49870.08780.3298-47.3208-43.4719-74.1453
290.0367-0.01180.02670.0161-0.0160.02770.0082-0.01490.0310.036-0.016-0.0101-0.0422-0.0412-0.00110.3513-0.01120.1060.49810.13980.4082-45.5531-49.3564-61.0817
300.0079-0.0026-0.00090.0266-0.00030.00770.00790.1374-0.0551-0.21780.0578-0.09680.26340.30750.00060.57260.08550.16860.50060.00830.3377-18.4774-76.4669-67.0661
310.0068-0.003-0.00180.06150.00090.0035-0.05340.1107-0.0325-0.0589-0.02490.0894-0.01070.0777-0.00220.7595-0.0845-0.03340.5064-0.00540.2681-26.7203-72.3915-75.6992
320.0047-0.00710.00110.019-0.00380.0014-0.0746-0.0474-0.0261-0.05850.08160.10770.04160.1195-0.00050.4011-0.0543-0.00390.30710.04380.2972-29.4798-71.5653-62.0335
33-0.00030.00040.000400.00030.0039-0.0630.01370.05150.0135-0.039-0.0345-0.02990.0121-0.00010.3508-0.2430.01410.3976-0.05760.3914-16.3168-60.4564-58.3264
340.009-0.0254-0.00820.1493-0.02010.03020.04140.0018-0.043-0.00780.0183-0.00660.0095-0.0022-0.00230.608-0.1459-0.04850.5640.1430.5305-18.1861-51.3588-62.9455
350.00350.005-0.00420.0094-0.00320.0040.02250.01270.0947-0.05910.0234-0.0150.01210.02970.00050.4382-0.1760.04280.33870.14030.5036-16.6678-61.542-66.0882
360.00140.00120.00220.0033-0.00050.0035-0.012-0.01930.0092-0.0166-0.0327-0.00010.07830.0719-00.38530.15770.12360.41110.01370.3817-18.523-79.4321-57.2192
370.01480.00440.00350.0112-0.00550.00430.0299-0.04-0.0265-0.0308-0.0050.03310.08890.0251-0.00030.58360.03670.01750.32010.0260.4556-27.6684-83.5311-56.6807
380.13980.13420.02530.11340.0207-0.0009-0.0119-0.10140.17030.1321-0.0332-0.2083-0.19650.2788-0.06580.4912-0.8-0.47210.6150.01050.4237-10.2348-46.0613-47.277
390.00760.00160.01220.02520.01010.0317-0.01190.0047-0.0127-0.0048-0.0013-0.0309-0.01080.0124-0.01570.7655-0.414-0.00920.44750.13970.6342-12.6901-37.4999-57.3087
400.0168-0.0346-0.00150.0730.00110.01820.01910.0070.0354-0.0193-0.0039-0.0305-0.03980.02370.01580.5581-0.4807-0.01820.36720.18380.2745-17.6573-44.8592-58.3125
410.0092-0.00960.00470.0111-0.00390.00120.0105-0.01560.11430.0414-0.0083-0.0331-0.02280.0206-0.01070.7131-0.2893-0.12160.25230.09670.3752-23.4513-42.3044-48.5354
42-0.00020.0016-0.00220.0009-0.00050.0024-0.0047-0.03610.09570.01460.0446-0.05380.0187-0.02230.04440.6421-0.3966-0.08510.4418-0.06660.5117-18.2848-39.3245-40.3354
430.0134-0.009-0.01430.0266-0.01140.0411-0.0493-0.01420.0741-0.0061-0.05090.0366-0.10290.0408-0.07670.6523-0.4373-0.16650.6307-0.0430.4456-13.4662-46.7122-39.3254
440.03040.03230.01630.04640.02260.01070.0533-0.0555-0.041-0.02660.0346-0.0362-0.0028-0.0020.09750.5856-0.4162-0.09920.54650.14210.3296-21.2931-54.7659-40.9962
450.0146-0.0458-0.00230.13530.00260.01540.010.0150.05390.0414-0.01260.1724-0.0545-0.0503-0.00620.3510.11770.03440.3543-0.21770.5609-29.113939.7794-12.8853
460.0588-0.08570.11610.1687-0.21030.3780.12790.1238-0.0191-0.1267-0.18290.19640.3634-0.25670.22510.3211-0.01080.110.3541-0.14480.3527-26.37785.2615-23.5123
470.0221-0.0046-0.01540.01290.0130.019-0.00280.01070.0224-0.0081-0.02460.003-0.04740.023-0.09071.0726-0.0165-0.05130.4869-0.64280.8982-24.4557-15.9618-37.2828
480.0230.0228-0.00330.0254-0.02450.1107-0.0346-0.069-0.0845-0.0584-0.0171-0.01370.0239-0.07070.03520.2878-0.11340.18450.464-0.19290.3558-29.8411-1.7097-27.043
490.23090.07510.04070.1791-0.01710.06090.0459-0.05180.10970.0435-0.19620.1495-0.0444-0.0488-0.28740.06150.05380.15820.3846-0.2150.3245-25.589219.3352-17.2661
500.12180.05320.04250.10920.01680.0154-0.0101-0.01380.04420.025-0.0138-0.0167-0.0517-0.0325-0.04720.8857-0.08690.27360.6502-0.44960.8677-27.198438.3268-3.7386
510.00420.00420.00330.0018-0.00290.004-0.0403-0.0611-0.04580.0285-0.04160.11770.0582-0.019-00.6542-0.16820.00890.223-0.06940.8347-42.1795-84.0983-62.901
520.0123-0.01490.01970.0348-0.04930.04540.1461-0.2178-0.2088-0.0172-0.07840.23340.1076-0.0092-0.00030.4207-0.1178-0.04720.34890.03910.3282-36.9202-61.3041-59.578
530.1137-0.1425-0.01720.17050.01610.048-0.0015-0.18120.2572-0.0073-0.1240.0565-0.092-0.1056-0.19050.7693-0.0703-0.08960.0672-0.30910.3866-32.5645-34.3433-48.1626
540.0113-0.0512-0.0030.22830.01610.0017-0.01520.0345-0.0751-0.0262-0.0221-0.02650.0440.0486-0.17041.176-0.1455-0.07820.4827-0.50420.8354-26.4973-28.0763-43.6717
550.00210.0017-0.0020.00090.00110.00210.07480.04130.07010.11360.10060.0014-0.063-0.07870.00020.604-0.030.05610.3852-0.07450.3603-36.3897-42.288-49.7252
560.00050.00110.00270.01620.0040.00590.11820.03220.08710.02740.0377-0.04730.0283-0.005-00.3091-0.0987-0.02670.3369-0.00070.2354-30.742-56.5375-59.5069
570.00130.0049-0.00250.0036-0.00630.0077-0.0882-0.0955-0.103-0.0916-0.16180.13620.0374-0.0566-0.00020.3484-0.1134-0.00750.39840.01590.4782-43.5904-70.336-61.1694
580.0044-0.0064-0.00210.0070.00340.0031-0.01340.1168-0.0135-0.0781-0.0531-0.04440.04670.04780.00010.8578-0.0546-0.1020.5389-0.24071.0103-44.0061-81.5814-73.5508
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 37 )A14 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 48 )A38 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 55 )A49 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 65 )A56 - 65
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 76 )A66 - 76
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 81 )A77 - 81
7X-RAY DIFFRACTION7chain 'A' and (resid 82 through 108 )A82 - 108
8X-RAY DIFFRACTION8chain 'A' and (resid 109 through 114 )A109 - 114
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 119 )A115 - 119
10X-RAY DIFFRACTION10chain 'B' and (resid 14 through 48 )B14 - 48
11X-RAY DIFFRACTION11chain 'B' and (resid 49 through 60 )B49 - 60
12X-RAY DIFFRACTION12chain 'B' and (resid 61 through 65 )B61 - 65
13X-RAY DIFFRACTION13chain 'B' and (resid 66 through 75 )B66 - 75
14X-RAY DIFFRACTION14chain 'B' and (resid 76 through 81 )B76 - 81
15X-RAY DIFFRACTION15chain 'B' and (resid 82 through 95 )B82 - 95
16X-RAY DIFFRACTION16chain 'B' and (resid 96 through 108 )B96 - 108
17X-RAY DIFFRACTION17chain 'B' and (resid 109 through 119 )B109 - 119
18X-RAY DIFFRACTION18chain 'C' and (resid 14 through 48 )C14 - 48
19X-RAY DIFFRACTION19chain 'C' and (resid 49 through 60 )C49 - 60
20X-RAY DIFFRACTION20chain 'C' and (resid 61 through 75 )C61 - 75
21X-RAY DIFFRACTION21chain 'C' and (resid 76 through 96 )C76 - 96
22X-RAY DIFFRACTION22chain 'C' and (resid 97 through 108 )C97 - 108
23X-RAY DIFFRACTION23chain 'C' and (resid 109 through 119 )C109 - 119
24X-RAY DIFFRACTION24chain 'D' and (resid 14 through 48 )D14 - 48
25X-RAY DIFFRACTION25chain 'D' and (resid 49 through 55 )D49 - 55
26X-RAY DIFFRACTION26chain 'D' and (resid 56 through 65 )D56 - 65
27X-RAY DIFFRACTION27chain 'D' and (resid 66 through 100 )D66 - 100
28X-RAY DIFFRACTION28chain 'D' and (resid 101 through 114 )D101 - 114
29X-RAY DIFFRACTION29chain 'D' and (resid 115 through 119 )D115 - 119
30X-RAY DIFFRACTION30chain 'E' and (resid 15 through 48 )E15 - 48
31X-RAY DIFFRACTION31chain 'E' and (resid 49 through 65 )E49 - 65
32X-RAY DIFFRACTION32chain 'E' and (resid 66 through 80 )E66 - 80
33X-RAY DIFFRACTION33chain 'E' and (resid 81 through 85 )E81 - 85
34X-RAY DIFFRACTION34chain 'E' and (resid 86 through 90 )E86 - 90
35X-RAY DIFFRACTION35chain 'E' and (resid 91 through 99 )E91 - 99
36X-RAY DIFFRACTION36chain 'E' and (resid 100 through 108 )E100 - 108
37X-RAY DIFFRACTION37chain 'E' and (resid 109 through 119 )E109 - 119
38X-RAY DIFFRACTION38chain 'F' and (resid 15 through 48 )F15 - 48
39X-RAY DIFFRACTION39chain 'F' and (resid 49 through 55 )F49 - 55
40X-RAY DIFFRACTION40chain 'F' and (resid 56 through 65 )F56 - 65
41X-RAY DIFFRACTION41chain 'F' and (resid 66 through 75 )F66 - 75
42X-RAY DIFFRACTION42chain 'F' and (resid 76 through 96 )F76 - 96
43X-RAY DIFFRACTION43chain 'F' and (resid 97 through 108 )F97 - 108
44X-RAY DIFFRACTION44chain 'F' and (resid 109 through 119 )F109 - 119
45X-RAY DIFFRACTION45chain 'G' and (resid 0 through 4 )G0 - 4
46X-RAY DIFFRACTION46chain 'G' and (resid 5 through 22 )G5 - 22
47X-RAY DIFFRACTION47chain 'H' and (resid 0 through 4 )H0 - 4
48X-RAY DIFFRACTION48chain 'H' and (resid 5 through 9 )H5 - 9
49X-RAY DIFFRACTION49chain 'H' and (resid 10 through 19 )H10 - 19
50X-RAY DIFFRACTION50chain 'H' and (resid 20 through 22 )H20 - 22
51X-RAY DIFFRACTION51chain 'I' and (resid 0 through 4 )I0 - 4
52X-RAY DIFFRACTION52chain 'I' and (resid 5 through 14 )I5 - 14
53X-RAY DIFFRACTION53chain 'I' and (resid 15 through 22 )I15 - 22
54X-RAY DIFFRACTION54chain 'J' and (resid 0 through 4 )J0 - 4
55X-RAY DIFFRACTION55chain 'J' and (resid 5 through 9 )J5 - 9
56X-RAY DIFFRACTION56chain 'J' and (resid 10 through 14 )J10 - 14
57X-RAY DIFFRACTION57chain 'J' and (resid 15 through 19 )J15 - 19
58X-RAY DIFFRACTION58chain 'J' and (resid 20 through 22 )J20 - 22

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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