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- PDB-7dct: 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: 7dct
タイトルCrystal structure of HSF1 DNA-binding domain in complex with 3-site HSE DNA (24 bp)
要素
  • DNA (5'-D(*AP*CP*TP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*AP*G)-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 / response to hypobaric hypoxia / sequence-specific single stranded DNA binding / cellular response to diamide / cellular response to L-glutamine / negative regulation of double-strand break repair via nonhomologous end joining / positive regulation of stress granule assembly / positive regulation of apoptotic DNA fragmentation / translation elongation factor binding / negative regulation of inclusion body assembly ...cellular response to nitroglycerin / response to hypobaric hypoxia / sequence-specific single stranded DNA binding / cellular response to diamide / cellular response to L-glutamine / negative regulation of double-strand break repair via nonhomologous end joining / positive regulation of stress granule assembly / positive regulation of apoptotic DNA fragmentation / translation elongation factor binding / negative regulation of inclusion body assembly / positive regulation of inclusion body assembly / nuclear stress granule / cellular response to sodium arsenite / cellular response to potassium ion / positive regulation of macrophage differentiation / cellular response to angiotensin / protein folding chaperone complex / negative regulation of cardiac muscle cell apoptotic process / response to psychosocial stress / STAT family protein binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / response to testosterone / mitotic spindle pole / general transcription initiation factor binding / HSF1-dependent transactivation / Regulation of HSF1-mediated heat shock response / HSF1 activation / Attenuation phase / cellular response to unfolded protein / mRNA transport / negative regulation of protein-containing complex assembly / heterochromatin / regulation of cellular response to heat / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to copper ion / heat shock protein binding / cellular response to cadmium ion / positive regulation of mitotic cell cycle / response to nutrient / response to activity / cellular response to estradiol stimulus / promoter-specific chromatin binding / Hsp90 protein binding / euchromatin / chromatin DNA binding / cellular response to gamma radiation / mRNA processing / PML body / kinetochore / defense response / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / Aggrephagy / cellular response to hydrogen peroxide / : / MAPK cascade / sequence-specific double-stranded DNA binding / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / cellular response to heat / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / DNA repair / centrosome / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / 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 / cytoplasm / cytosol
類似検索 - 分子機能
Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / 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: 2.36 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

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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*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*AP*G)-3')
H: DNA (5'-D(*AP*CP*TP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*AP*C)-3')
I: DNA (5'-D(*TP*GP*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*AP*G)-3')
J: DNA (5'-D(*AP*CP*TP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*AP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)108,80712
ポリマ－108,76110
非ポリマー462
水2,882160
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*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*AP*G)-3')
H: DNA (5'-D(*AP*CP*TP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*AP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)54,4046
ポリマ－54,3815
非ポリマー231
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-60 kcal/mol
Surface area20820 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*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*AP*G)-3')
J: DNA (5'-D(*AP*CP*TP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*AP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)54,4046
ポリマ－54,3815
非ポリマー231
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-55 kcal/mol
Surface area21150 Å2
手法PISA
単位格子
Length a, b, c (Å)85.559, 94.710, 142.259
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 A and (resid 15 through 82 or resid 96 through 119))
21(chain B and (resid 15 through 82 or resid 96 through 119))
31(chain C and (resid 15 through 82 or resid 96 through 119))
41(chain D and (resid 15 through 82 or resid 96 through 119))
51(chain E and (resid 15 through 82 or resid 96 through 119))
61(chain F and resid 15 through 119)
12chain H
22chain J
13chain G
23chain I

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
111VALVALVALVAL(chain A and (resid 15 through 82 or resid 96 through 119))AA15 - 828 - 75
121ASPASPVALVAL(chain A and (resid 15 through 82 or resid 96 through 119))AA96 - 11989 - 112
211VALVALVALVAL(chain B and (resid 15 through 82 or resid 96 through 119))BB15 - 828 - 75
221ASPASPVALVAL(chain B and (resid 15 through 82 or resid 96 through 119))BB96 - 11989 - 112
311VALVALVALVAL(chain C and (resid 15 through 82 or resid 96 through 119))CC15 - 828 - 75
321ASPASPVALVAL(chain C and (resid 15 through 82 or resid 96 through 119))CC96 - 11989 - 112
411VALVALVALVAL(chain D and (resid 15 through 82 or resid 96 through 119))DD15 - 828 - 75
421ASPASPVALVAL(chain D and (resid 15 through 82 or resid 96 through 119))DD96 - 11989 - 112
511VALVALVALVAL(chain E and (resid 15 through 82 or resid 96 through 119))EE15 - 828 - 75
521ASPASPVALVAL(chain E and (resid 15 through 82 or resid 96 through 119))EE96 - 11989 - 112
611VALVALVALVAL(chain F and resid 15 through 119)FF15 - 1198 - 112
112DADADCDCchain HHH0 - 231 - 24
212DADADCDCchain JJJ0 - 231 - 24
113DTDTDGDGchain GGG0 - 231 - 24
213DTDTDGDGchain III0 - 231 - 24

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*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*AP*G)-3')


分子量: 7415.787 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*CP*TP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP*AP*C)-3')


分子量: 7322.756 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: 2 / 由来タイプ: 合成 / 式: Na
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 160 / 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: 2.91 Å3/Da / 溶媒含有率: 57.7 %
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 6.5 and 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: BL17U1 / 波長: 0.97949 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2018年1月5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: 0.97949 Å / 相対比: 1
反射解像度: 2.36→85.56 Å / Num. obs: 43397 / % possible obs: 99.9 % / 冗長度: 13.1 % / Rpim(I) all: 0.028 / Net I/σ(I): 14.5
反射 シェル解像度: 2.36→2.49 Å / 冗長度: 13.8 % / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.383 / % possible all: 100

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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: 2.36→63.489 Å / SU ML: 0.33 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 25.85 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2236 2199 5.07 %
Rwork0.1862 41198 -
obs0.1882 43397 89.94 %
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: 161.26 Å2 / Biso mean: 63.3424 Å2 / Biso min: 24.3 Å2
精密化ステップサイクル: final / 解像度: 2.36→63.489 Å
タンパク質核酸リガンド溶媒全体
原子数4808 1956 2 160 6926
Biso mean--41.73 47.84 -
残基数----679
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0077137
X-RAY DIFFRACTIONf_angle_d1.10810054
X-RAY DIFFRACTIONf_chiral_restr0.0581080
X-RAY DIFFRACTIONf_plane_restr0.007956
X-RAY DIFFRACTIONf_dihedral_angle_d17.8073848
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2688X-RAY DIFFRACTION12.112TORSIONAL
12B2688X-RAY DIFFRACTION12.112TORSIONAL
13C2688X-RAY DIFFRACTION12.112TORSIONAL
14D2688X-RAY DIFFRACTION12.112TORSIONAL
15E2688X-RAY DIFFRACTION12.112TORSIONAL
16F2688X-RAY DIFFRACTION12.112TORSIONAL
21H472X-RAY DIFFRACTION12.112TORSIONAL
22J472X-RAY DIFFRACTION12.112TORSIONAL
31G472X-RAY DIFFRACTION12.112TORSIONAL
32I472X-RAY DIFFRACTION12.112TORSIONAL
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 (%)
2.36-2.41130.3602850.2949160257
2.4113-2.46740.3641990.2679174462
2.4674-2.52910.2755920.2589191368
2.5291-2.59750.30031260.2506213075
2.5975-2.67390.30981330.2476234883
2.6739-2.76020.32071190.2458271495
2.7602-2.85890.30631510.2542282099
2.8589-2.97340.30751510.26542839100
2.9734-3.10870.31471580.24012830100
3.1087-3.27260.2371560.20792840100
3.2726-3.47760.22381490.18312847100
3.4776-3.74610.21451510.18272876100
3.7461-4.1230.20871590.1542861100
4.123-4.71940.17951550.1395288499
4.7194-5.94530.17711460.15342936100
5.9453-630.17661690.1664301499
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)
10.0189-0.0776-0.01220.3248-0.01820.0043-0.1154-0.218-0.3890.77370.2006-0.1223-0.0807-0.08620.00410.54260.1950.11740.63210.18410.4371-20.2174-1.3878-7.2716
20.04370.0785-0.00350.1531-0.0470.0395-0.1638-0.0851-0.04820.4253-0.1117-0.1974-0.0001-0.22960.00140.57730.1512-0.07570.96880.18170.5543-11.14923.98611.0313
30.0284-0.01170.01420.10740.01130.0579-0.0147-0.48830.11680.459-0.0292-0.1426-0.03590.0734-0.01780.83580.30940.03271.28350.0670.3484-17.54549.16813.1219
40.1648-0.05820.13890.0189-0.06540.3509-0.3199-0.4406-0.30450.11850.2125-0.68320.13540.5395-0.07540.28060.3255-0.03230.8525-0.14490.548-8.41047.857-9.3646
50.02160.00870.01590.0604-0.00210.0137-0.127-0.45560.14070.10290.04660.0598-0.17240.1343-0.00070.50.22230.04980.6017-0.04490.3546-12.67897.0599-16.1554
60.1242-0.07480.0230.1338-0.07510.0401-0.217-0.1826-0.0130.16920.24080.1714-0.00550.17720.02570.34410.05320.11840.53210.03940.2755-21.654110.6423-12.0988
70.380.02840.28910.1935-0.00340.2684-0.7047-0.3488-0.14310.3660.31750.1355-0.1901-0.2533-0.20020.44910.33310.45010.67910.0366-0.2145-24.405813.1915-2.6225
80.2949-0.154-0.16150.52990.05580.83150.0553-0.42280.22760.4770.20830.2293-0.1178-0.30231.17290.69920.2390.27230.84830.24770.4238-24.37724.91620.7574
90.01010.0281-0.00610.0614-0.05470.05520.0866-0.0412-0.23130.25740.03780.07280.0233-0.05110.16020.74280.05920.38980.76270.43760.6967-28.2303-5.0316-3.2693
100.08580.0412-0.00840.017-0.00040.0006-0.1841-0.092-0.16340.03010.04460.15950.143-0.1994-0.0060.54970.01690.1940.6440.02030.7227-31.39143.7358-13.0103
110.1881-0.06630.00070.5270.34030.8014-0.1547-0.2220.2946-0.33260.4511-0.5911-0.68640.54170.06680.5102-0.09820.03630.4903-0.18440.4838-6.778833.0265-19.9774
120.120.1345-0.10470.1778-0.12150.1005-0.1306-0.41190.15270.78960.2065-0.2639-0.2780.37260.07770.44640.0763-0.2240.7119-0.19680.338-9.34828.2024-8.4824
130.06530.0422-0.01140.08010.04040.0236-0.30870.0313-0.0466-0.18280.24560.0808-0.2404-0.2611-0.00180.391-0.0302-0.00730.3826-0.05530.3158-17.971726.9884-19.6049
140.03150.0212-0.01370.02470.00440.00440.1027-0.33340.1856-0.107-0.1159-0.15330.07510.44-0.00070.6096-0.0161-00.6902-0.13960.7816-7.207512.2661-26.1046
150.0343-0.023-0.05190.2538-0.00840.529-0.340.3535-0.2457-0.37480.3554-0.3833-0.6928-0.06540.00490.6634-0.10860.02980.3263-0.04670.4035-14.480434.9561-25.8384
160.40310.07560.21280.1836-0.1420.3542-0.22790.17750.1093-0.0036-0.0256-0.15050.1650.3089-0.06080.34530.0660.07050.274-0.00970.3956-8.10083.02-42.2449
170.1138-0.0442-0.07790.01790.06330.0872-0.1238-0.42790.0609-0.34120.0841-0.17760.59430.5965-0.00460.45540.14020.12640.37790.0030.454-4.9624-2.6509-31.2934
180.0255-0.0075-0.03820.05340.0330.04130.0083-0.01060.0489-0.0101-0.01790.07330.360.35960.00150.50890.00680.08910.34260.04170.4506-11.4575-0.2118-27.2536
190.02870.0129-0.03670.02-0.03390.0318-0.12390.3168-0.27460.1843-0.11370.1140.071-0.0064-0.00060.42420.02270.08540.2432-0.01350.4205-18.3968-1.7938-34.7055
200.1278-0.0714-0.24690.04830.08470.5539-0.41460.0683-0.2892-0.05080.3380.28920.435-0.3368-0.02450.49710.00370.11990.3078-0.09140.5543-16.2067-4.8024-43.3925
210.020.02350.01670.0323-0.0030.01680.20540.45150.2649-0.2506-0.32760.30860.01230.21620.00030.324-0.01010.02240.45090.02450.426-15.0855.8267-49.0597
220.06010.0659-0.03490.0930.01460.09940.0041-0.01370.38660.2334-0.03520.1077-0.3576-0.294300.37410.06350.0080.31070.00690.4754-20.910210.6887-42.4023
231.0102-0.54760.28551.46180.02420.13480.32090.95410.5648-0.47590.1586-0.0496-0.1752-0.53690.70590.39550.150.04930.62520.29880.4379-37.3053-46.9059-76.3245
240.03990.03870.09850.16080.12880.27590.17610.51480.21360.001-0.0073-0.26560.03090.63540.02190.34380.03420.05030.62830.18610.4211-26.3515-51.8165-71.9453
250.1240.14420.0530.16480.05070.02840.06510.18430.11550.30660.139-0.1073-0.2185-0.25830.01730.34430.0869-0.02990.59710.20430.4248-36.9331-54.2849-65.416
260.26630.09160.08260.02710.03550.0291-0.0480.19960.1042-0.0111-0.06710.08440.0014-0.23210.00860.39960.017-0.02650.85040.2470.6242-44.8979-56.3937-71.0876
270.43330.3443-0.04010.20810.00790.00710.14380.7983-0.04550.05750.1002-0.00090.1309-0.63420.02820.5830.0597-0.07950.9240.280.6541-43.8758-53.2253-76.8153
280.0263-0.0014-0.00760.0298-0.02280.055-0.0597-0.1949-0.04160.1518-0.00230.0324-0.0439-0.1236-0.040.50360.79830.17070.79140.78460.8621-46.6031-39.4968-70.0494
290.2627-0.04080.12090.04360.02580.09990.01440.11150.02310.38310.1070.1317-0.0968-0.12540.02370.54440.01660.26770.92130.26330.751-44.4777-48.2201-59.9064
300.074-0.15580.0820.2111-0.04070.13280.09870.42110.0333-0.8154-0.2328-0.24630.33350.4999-0.00070.5448-0.00120.07780.5540.02420.4799-18.8958-76.7547-67.0059
310.876-0.2003-0.0580.09750.00460.01720.22940.8730.2031-0.38960.05990.0199-0.0350.05160.03651.1316-0.0297-0.02360.6882-0.02090.0559-24.8148-71.7523-75.9548
320.03410-0.00360.016-0.07110.24280.15330.2177-0.3006-0.57940.29550.44180.0230.20060.00020.4942-0.0363-0.14970.45020.05730.4267-31.7201-72.1235-67.4678
330.12570.1755-0.12850.4257-0.19160.16610.0614-0.2762-0.01430.1042-0.21810.14720.2804-0.36850.00840.49350.00850.04120.42740.07210.5122-26.0523-72.0275-57.5233
340.0116-0.05190.03240.1309-0.10490.05740.44020.15310.0956-0.4954-0.1996-0.18080.1612-0.17840.00040.7581-0.0736-0.00090.65960.13860.7996-16.5616-56.9767-61.977
350.0666-0.00140.09540.07830.0010.0825-0.30660.0257-0.19070.08580.2723-0.54460.0360.2972-0.00090.5229-0.01410.00010.4226-0.04510.4555-19.1172-76.9363-58.3275
360.1727-0.0681-0.0190.0931-0.03560.01650.294-0.055-0.26480.0029-0.10410.3350.5224-0.2180.00110.5571-0.1212-0.00880.5613-0.00280.5696-27.8883-84.0194-56.5766
370.2794-0.24180.15520.2361-0.14470.28020.15440.07060.11430.029-0.3624-0.0907-0.04690.8197-0.10770.4295-0.2451-0.06820.57990.08180.5378-9.4453-48.3163-46.5509
380.8642-0.03420.24350.07810.02270.0816-0.04740.59250.5884-0.2095-0.18510.1193-0.53020.5977-0.11050.5926-0.211-0.07230.40440.20810.6372-14.6038-42.9686-56.9769
390.02240.03190.00740.04410.0060.00490.0867-0.28090.74690.01750.0475-0.0471-0.1584-0.1473-0.00120.5981-0.08190.00110.35450.10490.7344-22.1716-42.8745-47.5007
400.2361-0.17030.21820.152-0.23220.4301-0.1542-0.09780.34830.640.3641-0.0365-0.6133-0.23040.02911.0154-0.6093-0.0695-0.3928-0.28590.6182-15.8455-41.0019-40.2379
410.0120.0227-0.0220.0326-0.01350.07790.0612-0.34370.07770.3725-0.4228-0.0139-0.36520.5185-0.0010.5051-0.1719-0.02460.51010.04780.4567-11.9375-51.38-37.4479
420.0940.15610.14880.26150.27470.27940.3809-0.3249-0.0343-0.05720.08030.17740.3287-0.25570.04510.6332-0.2412-0.07350.49560.15580.4508-20.5993-55.764-40.294
430.0805-0.09880.12280.0621-0.11520.2117-0.20190.13180.54720.18130.34271.3204-0.3515-0.1549-0.0330.78420.3367-0.14110.6291-0.25451.3175-33.393241.8809-12.2859
440.87270.06530.22580.4378-0.09570.0765-0.1401-0.8005-0.0584-0.1820.09330.3962-0.3626-0.38540.01350.64630.22550.14420.6175-0.1470.2481-24.014425.7093-8.8547
450.0626-0.0303-0.00240.05870.01860.00350.34440.16340.0812-0.2316-0.09890.0870.267-0.28260.00090.31280.02690.07430.4487-0.01670.3763-27.662313.8324-23.305
460.90490.12330.61150.7636-0.31040.6681-0.03630.0245-0.5495-0.2661-0.54980.25930.9204-0.0361-1.12030.7282-0.13980.19130.2998-0.22810.6762-25.8061-8.0754-30.3564
471.1341-0.17211.46310.0626-0.28241.94440.2933-0.2009-1.0583-0.081-0.2346-0.17150.646-0.8770.74040.5126-0.17030.19150.2691-0.18140.8377-26.3443-8.7287-32.2907
480.81650.07880.42150.59330.0380.7575-0.1655-0.09940.27430.1689-0.0280.1001-0.1784-0.1775-0.17260.37140.08640.10580.377-0.05310.3649-26.249124.7945-13.6584
490.18830.1604-0.16610.1098-0.0850.5266-0.349-0.3461-0.49850.16690.0720.79010.44620.0547-0.01240.9969-0.6-0.06740.75590.19251.3239-45.9496-86.7484-60.7259
500.44760.1339-0.44980.29380.03090.55290.27620.38220.0328-0.1530.05440.30590.1414-0.47010.29650.4543-0.1385-0.25360.56340.19530.5092-39.7608-70.1918-67.6555
510.0704-0.0025-0.00590.0519-0.04510.07420.2314-0.33560.31010.2653-0.16520.0571-0.6617-0.5496-0.00280.3543-0.1293-0.00940.53260.10990.3485-36.047-58.4096-52.9974
520.07420.0136-0.09720.0428-0.00830.05960.33730.110.53760.2151-0.2640.0972-1.0074-0.3677-0.00050.69080.06140.06040.35890.07720.7029-29.0315-41.5579-53.7351
530.02460.00630.01020.0217-0.05540.50960.5372-0.36260.10320.52580.13250.1934-0.5647-0.42240.05921.5559-0.07230.26180.8444-0.43181.4821-33.2317-29.8138-40.5724
540.16190.2187-0.24340.4439-0.78742.72910.7595-0.31480.90530.40690.2608-0.0255-1.0806-0.45591.42750.8009-0.06720.31240.3908-0.31530.9348-30.4787-35.5905-46.0384
550.748-0.4062-0.20760.87840.73680.84660.3776-0.5698-0.139-0.6487-0.1530.7457-0.0761-0.740.630.2422-0.2194-0.35230.55410.290.6355-39.4262-69.3836-62.4206
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 27 )A14 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 37 )A28 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 48 )A38 - 48
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 60 )A49 - 60
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 65 )A61 - 65
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 75 )A66 - 75
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 96 )A76 - 96
8X-RAY DIFFRACTION8chain 'A' and (resid 97 through 108 )A97 - 108
9X-RAY DIFFRACTION9chain 'A' and (resid 109 through 114 )A109 - 114
10X-RAY DIFFRACTION10chain 'A' and (resid 115 through 119 )A115 - 119
11X-RAY DIFFRACTION11chain 'B' and (resid 14 through 48 )B14 - 48
12X-RAY DIFFRACTION12chain 'B' and (resid 49 through 65 )B49 - 65
13X-RAY DIFFRACTION13chain 'B' and (resid 66 through 81 )B66 - 81
14X-RAY DIFFRACTION14chain 'B' and (resid 82 through 95 )B82 - 95
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 119 )B96 - 119
16X-RAY DIFFRACTION16chain 'C' and (resid 14 through 48 )C14 - 48
17X-RAY DIFFRACTION17chain 'C' and (resid 49 through 60 )C49 - 60
18X-RAY DIFFRACTION18chain 'C' and (resid 61 through 65 )C61 - 65
19X-RAY DIFFRACTION19chain 'C' and (resid 66 through 75 )C66 - 75
20X-RAY DIFFRACTION20chain 'C' and (resid 76 through 99 )C76 - 99
21X-RAY DIFFRACTION21chain 'C' and (resid 100 through 108 )C100 - 108
22X-RAY DIFFRACTION22chain 'C' and (resid 109 through 119 )C109 - 119
23X-RAY DIFFRACTION23chain 'D' and (resid 13 through 48 )D13 - 48
24X-RAY DIFFRACTION24chain 'D' and (resid 49 through 65 )D49 - 65
25X-RAY DIFFRACTION25chain 'D' and (resid 66 through 76 )D66 - 76
26X-RAY DIFFRACTION26chain 'D' and (resid 77 through 81 )D77 - 81
27X-RAY DIFFRACTION27chain 'D' and (resid 82 through 108 )D82 - 108
28X-RAY DIFFRACTION28chain 'D' and (resid 109 through 114 )D109 - 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 60 )E49 - 60
32X-RAY DIFFRACTION32chain 'E' and (resid 61 through 75 )E61 - 75
33X-RAY DIFFRACTION33chain 'E' and (resid 76 through 81 )E76 - 81
34X-RAY DIFFRACTION34chain 'E' and (resid 82 through 96 )E82 - 96
35X-RAY DIFFRACTION35chain 'E' and (resid 97 through 108 )E97 - 108
36X-RAY DIFFRACTION36chain 'E' and (resid 109 through 119 )E109 - 119
37X-RAY DIFFRACTION37chain 'F' and (resid 14 through 48 )F14 - 48
38X-RAY DIFFRACTION38chain 'F' and (resid 49 through 65 )F49 - 65
39X-RAY DIFFRACTION39chain 'F' and (resid 66 through 75 )F66 - 75
40X-RAY DIFFRACTION40chain 'F' and (resid 76 through 99 )F76 - 99
41X-RAY DIFFRACTION41chain 'F' and (resid 100 through 108 )F100 - 108
42X-RAY DIFFRACTION42chain 'F' and (resid 109 through 119 )F109 - 119
43X-RAY DIFFRACTION43chain 'G' and (resid 0 through 4 )G0 - 4
44X-RAY DIFFRACTION44chain 'G' and (resid 5 through 9 )G5 - 9
45X-RAY DIFFRACTION45chain 'G' and (resid 10 through 14 )G10 - 14
46X-RAY DIFFRACTION46chain 'G' and (resid 15 through 23 )G15 - 23
47X-RAY DIFFRACTION47chain 'H' and (resid 0 through 9 )H0 - 9
48X-RAY DIFFRACTION48chain 'H' and (resid 10 through 23 )H10 - 23
49X-RAY DIFFRACTION49chain 'I' and (resid 0 through 4 )I0 - 4
50X-RAY DIFFRACTION50chain 'I' and (resid 5 through 9 )I5 - 9
51X-RAY DIFFRACTION51chain 'I' and (resid 10 through 14 )I10 - 14
52X-RAY DIFFRACTION52chain 'I' and (resid 15 through 19 )I15 - 19
53X-RAY DIFFRACTION53chain 'I' and (resid 20 through 23 )I20 - 23
54X-RAY DIFFRACTION54chain 'J' and (resid 0 through 9 )J0 - 9
55X-RAY DIFFRACTION55chain 'J' and (resid 10 through 23 )J10 - 23

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万見について

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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