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- PDB-7la9: Crystal structure of the first bromodomain (BD1) of human BRD4 (B... -

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IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7la9
タイトルCrystal structure of the first bromodomain (BD1) of human BRD4 (BRD4-1) in complex with bivalent inhibitor NC-III-49-1
要素Bromodomain-containing protein 4
キーワードTRANSCRIPTION/TRANSCRIPTION INHIBITOR / BET / ERK5 / dual BRD-kinase inhibitor / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
機能・相同性
機能・相同性情報


histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / histone H3K9ac reader activity / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription ...histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / histone H3K9ac reader activity / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
類似検索 - 分子機能
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / Chem-XR7 / Bromodomain-containing protein 4
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 分子置換 / 解像度: 2.2 Å
データ登録者Karim, M.R. / Schonbrunn, E.
引用ジャーナル: J.Med.Chem. / 年: 2022
タイトル: Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity.
著者: Guan, X. / Cheryala, N. / Karim, R.M. / Chan, A. / Berndt, N. / Qi, J. / Georg, G.I. / Schonbrunn, E.
履歴
登録2021年1月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年1月12日Provider: repository / タイプ: Initial release
改定 1.12022年8月3日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22022年8月24日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.32023年10月18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: Bromodomain-containing protein 4
B: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
D: Bromodomain-containing protein 4
E: Bromodomain-containing protein 4
F: Bromodomain-containing protein 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,19333
ポリマ－89,2876
非ポリマー3,90727
水4,828268
1
A: Bromodomain-containing protein 4
D: Bromodomain-containing protein 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,32015
ポリマ－29,7622
非ポリマー1,55713
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 4
F: Bromodomain-containing protein 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)30,8948
ポリマ－29,7622
非ポリマー1,1326
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 4
E: Bromodomain-containing protein 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)30,97910
ポリマ－29,7622
非ポリマー1,2178
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)114.126, 114.126, 94.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 60 through 98 or resid 100...
21(chain B and (resid 60 through 98 or resid 100...
31(chain C and (resid 60 through 98 or resid 100...
41(chain D and (resid 60 through 98 or resid 100...
51(chain E and (resid 60 through 98 or resid 100...
61(chain F and (resid 60 through 98 or resid 100...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTYRTYR(chain A and (resid 60 through 98 or resid 100...AA60 - 9817 - 55
12ILEILEILEILE(chain A and (resid 60 through 98 or resid 100...AA100 - 10157 - 58
13LYSLYSLYSLYS(chain A and (resid 60 through 98 or resid 100...AA10259
14THRTHRLEULEU(chain A and (resid 60 through 98 or resid 100...AA60 - 16417 - 121
15THRTHRLEULEU(chain A and (resid 60 through 98 or resid 100...AA60 - 16417 - 121
16THRTHRLEULEU(chain A and (resid 60 through 98 or resid 100...AA60 - 16417 - 121
17THRTHRLEULEU(chain A and (resid 60 through 98 or resid 100...AA60 - 16417 - 121
21THRTHRTYRTYR(chain B and (resid 60 through 98 or resid 100...BB60 - 9817 - 55
22ILEILEILEILE(chain B and (resid 60 through 98 or resid 100...BB100 - 10157 - 58
23LYSLYSLYSLYS(chain B and (resid 60 through 98 or resid 100...BB10259
24THRTHRLEULEU(chain B and (resid 60 through 98 or resid 100...BB60 - 16417 - 121
25THRTHRLEULEU(chain B and (resid 60 through 98 or resid 100...BB60 - 16417 - 121
26THRTHRLEULEU(chain B and (resid 60 through 98 or resid 100...BB60 - 16417 - 121
27THRTHRLEULEU(chain B and (resid 60 through 98 or resid 100...BB60 - 16417 - 121
31THRTHRTYRTYR(chain C and (resid 60 through 98 or resid 100...CC60 - 9817 - 55
32ILEILEILEILE(chain C and (resid 60 through 98 or resid 100...CC100 - 12657 - 83
33ASPASPASNASN(chain C and (resid 60 through 98 or resid 100...CC128 - 14085 - 97
34PROPROALAALA(chain C and (resid 60 through 98 or resid 100...CC142 - 15099 - 107
35ALAALALEULEU(chain C and (resid 60 through 98 or resid 100...CC152 - 164109 - 121
41THRTHRTYRTYR(chain D and (resid 60 through 98 or resid 100...DD60 - 9817 - 55
42ILEILEILEILE(chain D and (resid 60 through 98 or resid 100...DD100 - 10157 - 58
43LYSLYSLYSLYS(chain D and (resid 60 through 98 or resid 100...DD10259
44THRTHRLEULEU(chain D and (resid 60 through 98 or resid 100...DD60 - 16417 - 121
45THRTHRLEULEU(chain D and (resid 60 through 98 or resid 100...DD60 - 16417 - 121
46THRTHRLEULEU(chain D and (resid 60 through 98 or resid 100...DD60 - 16417 - 121
47THRTHRLEULEU(chain D and (resid 60 through 98 or resid 100...DD60 - 16417 - 121
51THRTHRTYRTYR(chain E and (resid 60 through 98 or resid 100...EE60 - 9817 - 55
52ILEILEILEILE(chain E and (resid 60 through 98 or resid 100...EE100 - 10157 - 58
53LYSLYSLYSLYS(chain E and (resid 60 through 98 or resid 100...EE10259
54THRTHRLEULEU(chain E and (resid 60 through 98 or resid 100...EE60 - 16417 - 121
55THRTHRLEULEU(chain E and (resid 60 through 98 or resid 100...EE60 - 16417 - 121
56THRTHRLEULEU(chain E and (resid 60 through 98 or resid 100...EE60 - 16417 - 121
57THRTHRLEULEU(chain E and (resid 60 through 98 or resid 100...EE60 - 16417 - 121
61THRTHRTYRTYR(chain F and (resid 60 through 98 or resid 100...FF60 - 9817 - 55
62ILEILEILEILE(chain F and (resid 60 through 98 or resid 100...FF100 - 10157 - 58
63LYSLYSLYSLYS(chain F and (resid 60 through 98 or resid 100...FF10259
64THRTHRLEULEU(chain F and (resid 60 through 98 or resid 100...FF60 - 16417 - 121
65THRTHRLEULEU(chain F and (resid 60 through 98 or resid 100...FF60 - 16417 - 121
66THRTHRLEULEU(chain F and (resid 60 through 98 or resid 100...FF60 - 16417 - 121
67THRTHRLEULEU(chain F and (resid 60 through 98 or resid 100...FF60 - 16417 - 121

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要素

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タンパク質 , 1種, 6分子 ABCDEF

#1: タンパク質
Bromodomain-containing protein 4 / Protein HUNK1


分子量: 14881.105 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BRD4, HUNK1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O60885

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非ポリマー , 6種, 295分子

#2: 化合物 ChemComp-XR7 / N,N'-(oxybis{(ethane-2,1-diyl)oxyethane-2,1-diyloxy[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)-4,1-phenylene]})di(ethane-1-sulfonamide)


分子量: 875.018 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C44H50N4O11S2 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


分子量: 62.068 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C2H6O2
#4: 化合物
ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Cl
#5: 化合物 ChemComp-NA / SODIUM ION


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Na
#6: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER


分子量: 106.120 Da / 分子数: 1 / 由来タイプ: 天然 / 式: C4H10O3
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 268 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.94 Å3/Da / 溶媒含有率: 68.75 %
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: 0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate (pH 5.6), 10% v/v Jeffamine M-600

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: 回転陽極 / タイプ: RIGAKU MICROMAX-007 HF / 波長: 1.5417 Å
検出器タイプ: RIGAKU SATURN 944+ / 検出器: CCD / 日付: 2018年9月8日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.5417 Å / 相対比: 1
反射解像度: 2.2→98.84 Å / Num. obs: 139185 / % possible obs: 100 % / 冗長度: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.028 / Rrim(I) all: 0.065 / Net I/σ(I): 18.2
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.255.52.6492520745500.4351.2482.930.7100
10.55-98.8450.024304560410.0110.02757.996.2

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2-3874_3874精密化
Aimless0.7.4データスケーリング
PDB_EXTRACT3.27データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7K6H

7k6h


解像度: 2.2→37.36 Å / SU ML: 0.3 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 27.57 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2077 4004 2.88 %
Rwork0.1846 135181 -
obs0.1853 139185 99.26 %
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: 128.87 Å2 / Biso mean: 62.8059 Å2 / Biso min: 40.47 Å2
精密化ステップサイクル: final / 解像度: 2.2→37.36 Å
タンパク質核酸リガンド溶媒全体
原子数5313 0 255 268 5836
Biso mean--65.62 59.11 -
残基数----630
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0095697
X-RAY DIFFRACTIONf_angle_d1.0417710
X-RAY DIFFRACTIONf_chiral_restr0.056801
X-RAY DIFFRACTIONf_plane_restr0.007942
X-RAY DIFFRACTIONf_dihedral_angle_d10.569746
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1740X-RAY DIFFRACTION6.103TORSIONAL
12B1740X-RAY DIFFRACTION6.103TORSIONAL
13C1740X-RAY DIFFRACTION6.103TORSIONAL
14D1740X-RAY DIFFRACTION6.103TORSIONAL
15E1740X-RAY DIFFRACTION6.103TORSIONAL
16F1740X-RAY DIFFRACTION6.103TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.43411140.39314076419088
2.23-2.250.4091460.35194562470896
2.25-2.280.34541450.31634706485199
2.28-2.310.29821390.31954602474199
2.31-2.340.29371320.301846794811100
2.34-2.380.37921520.281147714923100
2.38-2.410.30691280.27546404768100
2.41-2.450.31971320.280746534785100
2.45-2.490.27051520.27247554907100
2.49-2.530.33491240.237747114835100
2.53-2.580.26031400.229246654805100
2.58-2.630.28291320.220346044736100
2.63-2.680.26571400.218247644904100
2.68-2.740.25621400.211147444884100
2.74-2.80.27121320.207246464778100
2.8-2.870.25981400.221247344874100
2.87-2.950.26981360.215746824818100
2.95-3.040.19291440.214146884832100
3.04-3.140.28961400.206546504790100
3.14-3.250.23071560.206347224878100
3.25-3.380.20241280.177947364864100
3.38-3.530.20931480.17546774825100
3.53-3.720.24351320.1746964828100
3.72-3.950.1751360.161846734809100
3.95-4.250.16961360.153647024838100
4.26-4.680.13141360.133446774813100
4.68-5.360.15851360.149347354871100
5.36-6.740.16571400.15947004840100
6.75-37.360.15181480.14854531467997
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)
18.4768-0.16460.51874.7443.98513.3918-0.11010.1960.9138-0.7631-0.06890.1779-0.9030.04010.31190.64-0.0172-0.05480.3830.01670.57483.702757.9393-10.5333
23.8484-0.3441-1.34589.6103-0.04253.8969-0.1318-0.0533-0.1707-0.03540.00520.41430.1864-0.47590.12370.4355-0.0216-0.04040.41160.08340.3782-6.214439.3779-8.4015
38.04523.35390.67234.52640.05050.4968-0.16270.45050.2048-0.5310.27420.0534-0.0447-0.1374-0.09590.5422-0.005-0.03710.43920.03530.3175-1.846144.1714-18.2416
45.69631.38282.24487.342.27044.2902-0.206-0.08220.3155-0.54760.16990.6847-0.2388-0.39040.01750.45420.0587-0.03330.49780.11170.3979-13.482948.512-11.0624
56.42274.41653.34157.13812.08857.39120.66460.9009-0.9003-0.8594-0.42550.14530.56570.5047-0.22210.6980.1404-0.07340.5206-0.0150.6197-17.384349.5594-39.5869
63.4424-1.6645-3.29345.79173.974.84190.14860.0752-0.5744-0.0552-0.06260.36730.1392-0.5356-0.13290.55140.0186-0.14070.52060.11770.6379-28.073951.8365-26.0178
74.5665-2.1767-4.58792.49971.68214.770.5593-1.87840.70331.16820.35940.0351-0.52350.8883-0.96230.7347-0.0001-0.0370.8709-0.04680.6572-28.380865.708-11.5569
82.3545-0.5302-2.23171.0475-1.82347.46030.14330.01690.0746-0.05530.0456-0.2934-0.13450.2907-0.16550.53160.019-0.08990.46930.05250.5918-18.670961.8607-27.9182
90.9367-0.3145-0.52181.8114-1.73312.37380.0642-0.043-0.109-0.090.0272-0.07110.21090.0848-0.10030.55830.0061-0.1010.54340.08630.628-15.907855.345-22.7787
103.2839-1.33010.08093.72830.16564.5727-0.0988-0.1919-0.53920.1420.09090.16290.6539-0.0152-0.01220.5266-0.0216-0.12970.40560.12060.5976-20.682746.3604-20.3644
116.5193-0.29273.94837.8875-1.67389.3068-0.2811-0.3215-0.4661.42180.4563-0.53620.68090.4608-0.18550.64050.1479-0.06130.5149-0.04840.586722.80816.8878-0.8968
125.6156-2.54171.04637.0895-4.77125.20780.08580.4190.1426-0.25020.0845-0.362-0.29780.3587-0.24530.5603-0.00250.04510.5112-0.16390.511423.181919.178-18.2122
130.6445-0.3451-1.14552.05330.89575.5721-0.02260.0137-0.2031-0.01330.1602-0.03410.16970.0305-0.11030.48440.01960.00990.5238-0.11310.583414.714911.8297-14.5834
143.1383-1.1630.10113.62970.57692.7680.01520.0463-0.2086-0.28790.0958-0.38140.25320.3643-0.06370.45320.02970.04650.522-0.17350.635127.25258.1779-20.1217
158.4464-0.4884-0.91112.50332.10636.0329-0.181-0.1555-1.08210.2994-0.2879-0.14541.20580.3660.47090.70610.01140.06610.42020.03870.60233.70027.96771.6611
163.3858-0.06761.02167.27460.23653.5804-0.092-0.20410.23970.10160.03860.2241-0.4006-0.35120.06340.45950.02550.03130.45630.07790.4129-6.055527.56653.06
174.9232-2.51960.87294.3019-0.09710.9104-0.19-0.3535-0.26430.530.25120.09270.1697-0.1522-0.06510.5259-0.00720.03580.41460.03640.3582-0.701319.11138.3736
185.3393-1.3673-2.56336.93792.23054.0942-0.11870.2966-0.20390.40130.07720.57750.1725-0.41940.05760.5092-0.06230.01750.5470.11060.4433-13.312717.21862.1054
198.09990.72182.43518.9411.46737.72240.46671.2761.2064-0.1819-0.0056-0.1629-0.645-0.1332-0.39610.79570.00660.11460.56420.11380.607215.579552.3215-24.6074
209.3729-4.72212.86763.9277-3.31223.85060.11711.2629-0.5545-1.4796-0.32180.39730.33210.2637-0.0440.7139-0.08820.10260.5378-0.05450.412918.104138.4907-28.6378
216.4706-3.9323.96283.2362-2.99643.06060.07040.3682-0.0099-0.04080.0365-1.44980.32550.63230.04120.6054-0.01670.07260.5497-0.17860.869730.530229.5792-18.9233
222.9775-2.8053-0.72986.40951.29362.01030.01780.09760.2727-0.38550.1714-1.034-0.31660.4992-0.14810.5749-0.13590.15410.6287-0.08490.708929.216543.8382-19.6436
234.4556-1.72581.29736.7457-1.96613.52450.51180.94990.1027-1.5015-0.399-0.80010.15190.4173-0.09070.9418-0.0940.29840.7445-0.0960.556427.674739.7131-33.1019
249.2775.07422.53264.5434-0.05367.00810.3006-0.12490.7360.98610.16860.9548-0.559-0.6507-0.45430.62930.14660.16660.76780.05010.6402-53.105978.5679-15.8974
256.0908-5.7036-1.03669.46194.53626.3115-0.0549-0.4015-0.74520.86340.06730.25030.59040.0036-0.01750.4514-0.04280.0050.57770.20620.533-41.500260.8903-17.3078
263.6489-3.26980.87637.231-1.3172.1796-0.0248-0.3354-0.72980.0330.260.87110.2627-0.5467-0.1770.4814-0.09160.00150.70210.17530.6931-52.589562.5173-20.8602
273.9173-1.3555-0.98047.31041.8873.1195-0.5367-0.9975-0.59451.52050.64230.47550.6239-0.1095-0.12970.74810.02440.0791.0210.28470.5593-48.312461.7487-7.4052
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 60 through 68 )A60 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 96 )A69 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 139 )A97 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 164 )A140 - 164
5X-RAY DIFFRACTION5chain 'B' and (resid 60 through 68 )B60 - 68
6X-RAY DIFFRACTION6chain 'B' and (resid 69 through 88 )B69 - 88
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 96 )B89 - 96
8X-RAY DIFFRACTION8chain 'B' and (resid 97 through 121 )B97 - 121
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 139 )B122 - 139
10X-RAY DIFFRACTION10chain 'B' and (resid 140 through 164 )B140 - 164
11X-RAY DIFFRACTION11chain 'C' and (resid 60 through 68 )C60 - 68
12X-RAY DIFFRACTION12chain 'C' and (resid 69 through 96 )C69 - 96
13X-RAY DIFFRACTION13chain 'C' and (resid 97 through 139 )C97 - 139
14X-RAY DIFFRACTION14chain 'C' and (resid 140 through 164 )C140 - 164
15X-RAY DIFFRACTION15chain 'D' and (resid 60 through 68 )D60 - 68
16X-RAY DIFFRACTION16chain 'D' and (resid 69 through 106 )D69 - 106
17X-RAY DIFFRACTION17chain 'D' and (resid 107 through 139 )D107 - 139
18X-RAY DIFFRACTION18chain 'D' and (resid 140 through 164 )D140 - 164
19X-RAY DIFFRACTION19chain 'E' and (resid 60 through 68 )E60 - 68
20X-RAY DIFFRACTION20chain 'E' and (resid 69 through 80 )E69 - 80
21X-RAY DIFFRACTION21chain 'E' and (resid 81 through 96 )E81 - 96
22X-RAY DIFFRACTION22chain 'E' and (resid 97 through 139 )E97 - 139
23X-RAY DIFFRACTION23chain 'E' and (resid 140 through 164 )E140 - 164
24X-RAY DIFFRACTION24chain 'F' and (resid 60 through 68 )F60 - 68
25X-RAY DIFFRACTION25chain 'F' and (resid 69 through 96 )F69 - 96
26X-RAY DIFFRACTION26chain 'F' and (resid 97 through 139 )F97 - 139
27X-RAY DIFFRACTION27chain 'F' and (resid 140 through 164 )F140 - 164

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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://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