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- PDB-9gej: Crystal structure of CREBBP bromodomain in complex with (2R,13S,E... -

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基本情報

登録情報
データベース: PDB / ID: 9gej
タイトルCrystal structure of CREBBP bromodomain in complex with (2R,13S,E)-2-methyl-1,2,3,5,10,11,13,14,20,21,24,25-dodecahydro-19H,23H-16,18-etheno-9,13-methano-7,28-(metheno)[1,4]diazepino[2,3-k]pyrido[1,2-s][1,4]dioxa[7,19]diazacyclodocosine-4,8-dione
要素CREBBP
キーワードTRANSFERASE / bromodomain / protein-inhibitor complex / macrocycle
機能・相同性
機能・相同性情報


peptide lactyltransferase (CoA-dependent) activity / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...peptide lactyltransferase (CoA-dependent) activity / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / embryonic digit morphogenesis / protein acetylation / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / histone acetyltransferase activity / FOXO-mediated transcription of cell death genes / stimulatory C-type lectin receptor signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / homeostatic process / histone acetyltransferase complex / Attenuation phase / cAMP/PKA signal transduction / protein-lysine-acetyltransferase activity / histone acetyltransferase / positive regulation of double-strand break repair via homologous recombination / regulation of cellular response to heat / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / canonical NF-kappaB signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / Transcriptional and post-translational regulation of MITF-M expression and activity / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / SUMOylation of transcription cofactors / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / CD209 (DC-SIGN) signaling / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / cellular response to nutrient levels / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Formation of the beta-catenin:TCF transactivating complex / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / Pre-NOTCH Transcription and Translation / NOTCH1 Intracellular Domain Regulates Transcription / Evasion by RSV of host interferon responses / protein destabilization / tau protein binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription coactivator binding / p53 binding / cellular response to UV / transcription corepressor activity / rhythmic process / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-containing complex assembly / TRAF3-dependent IRF activation pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor binding / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / response to hypoxia / transcription coactivator activity / nuclear body / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II
類似検索 - 分子機能
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
類似検索 - ドメイン・相同性
: / CREB-binding protein
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: 1.84 Å
データ登録者Amann, M. / Boyd, A. / Einsle, O. / Guenther, S. / Moroglu, M. / Conway, S.
資金援助 ドイツ, 2件
組織認可番号国
German Research Foundation (DFG)RTG2202 ドイツ
Other governmentDMT0001
引用ジャーナル: To Be Published
タイトル: Crystal structure of CREBBP bromodomain in complex with (2R,13S,E)-2-methyl-1,2,3,5,10,11,13,14,20,21,24,25-dodecahydro-19H,23H-16,18-etheno-9,13-methano-7,28-(metheno)[1,4] ...タイトル: Crystal structure of CREBBP bromodomain in complex with (2R,13S,E)-2-methyl-1,2,3,5,10,11,13,14,20,21,24,25-dodecahydro-19H,23H-16,18-etheno-9,13-methano-7,28-(metheno)[1,4]diazepino[2,3-k]pyrido[1,2-s][1,4]dioxa[7,19]diazacyclodocosine-4,8-dione
著者: Amann, M. / Boyd, A. / Einsle, O. / Guenther, S. / Moroglu, M. / Conway, S.
履歴
登録2024年8月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年8月20日Provider: repository / タイプ: Initial release

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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: CREBBP
B: CREBBP
C: CREBBP
D: CREBBP
E: CREBBP
F: CREBBP
G: CREBBP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)104,23725
ポリマ－99,5637
非ポリマー4,67318
水14,736818
1
A: CREBBP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)15,0285
ポリマ－14,2231
非ポリマー8054
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: CREBBP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,9324
ポリマ－14,2231
非ポリマー7093
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: CREBBP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,3192
ポリマ－14,2231
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: CREBBP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,9324
ポリマ－14,2231
非ポリマー7093
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: CREBBP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8363
ポリマ－14,2231
非ポリマー6132
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: CREBBP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8363
ポリマ－14,2231
非ポリマー6132
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: CREBBP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)15,3534
ポリマ－14,2231
非ポリマー1,1293
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)162.160, 50.189, 144.461
Angle α, β, γ (deg.)90.00, 101.38, 90.00
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質
CREBBP


分子量: 14223.349 Da / 分子数: 7 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli BL21 (大腸菌)
参照: UniProt: Q92793, histone acetyltransferase, 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの
#2: 化合物
ChemComp-A1IKJ / 2R,13S,E)-2-methyl-1,2,3,5,10,11,13,14,20,21,24,25-dodecahydro-19H,23H-16,18-etheno-9,13-methano-7,28-(metheno)[1,4]diazepino[2,3-k]pyrido[1,2-s][1,4]dioxa[7,19]diazacyclodocosine-4,8-dione


分子量: 516.631 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C30H36N4O4 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 11 / 由来タイプ: 合成 / 式: SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 818 / 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Y
Has protein modificationN

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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: 2.89 Å3/Da / 溶媒含有率: 57.51 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.3 M LiSO4, 0.1 M Tris pH 8, PEG 3350

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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: シンクロトロン / サイト: ESRF / ビームライン: BM07 / 波長: 0.9798 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2024年2月1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: 0.9798 Å / 相対比: 1
反射解像度: 1.837→141.62 Å / Num. obs: 52607 / % possible obs: 90.7 % / 冗長度: 6.8 % / Biso Wilson estimate: 20.06 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.5
反射 シェル解像度: 1.837→2.042 Å / Num. unique obs: 2630 / CC1/2: 0.784

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21_5207精密化
STARANISOデータスケーリング
XDSデータ削減
MOLREP位相決定
PDB_EXTRACTデータ抽出
精密化構造決定の手法: 分子置換 / 解像度: 1.84→141.62 Å / SU ML: 0.17 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 27.23 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2199 2581 4.91 %
Rwork0.1918 --
obs0.1932 52583 52.59 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 1.84→141.62 Å
タンパク質核酸リガンド溶媒全体
原子数6652 0 321 818 7791
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0057516
X-RAY DIFFRACTIONf_angle_d0.75110275
X-RAY DIFFRACTIONf_dihedral_angle_d23.0342977
X-RAY DIFFRACTIONf_chiral_restr0.0431022
X-RAY DIFFRACTIONf_plane_restr0.0051300
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.870.106420.322194X-RAY DIFFRACTION2
1.87-1.910.1935180.2593271X-RAY DIFFRACTION5
1.91-1.950.359280.2812464X-RAY DIFFRACTION9
1.95-20.2564380.2712747X-RAY DIFFRACTION14
2-2.050.3149500.26711043X-RAY DIFFRACTION20
2.05-2.10.2626650.26211233X-RAY DIFFRACTION24
2.1-2.170.3121780.24311441X-RAY DIFFRACTION27
2.17-2.230.225900.21911685X-RAY DIFFRACTION32
2.23-2.310.23161020.2341949X-RAY DIFFRACTION37
2.31-2.410.27651210.23342292X-RAY DIFFRACTION43
2.41-2.520.30841460.24512980X-RAY DIFFRACTION56
2.52-2.650.24682330.24434231X-RAY DIFFRACTION80
2.65-2.820.28772650.24195134X-RAY DIFFRACTION98
2.82-3.030.23512760.20975233X-RAY DIFFRACTION99
3.03-3.340.23032570.19425267X-RAY DIFFRACTION99
3.34-3.820.20382530.16575239X-RAY DIFFRACTION98
3.82-4.810.16592760.13795305X-RAY DIFFRACTION99
4.82-141.620.18462830.17435394X-RAY DIFFRACTION98
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)
17.3277-0.9144-2.28041.04640.37140.71820.67161.2790.2591-0.64060.345-0.6391-0.71360.781-0.89920.60430.16480.28070.5699-0.11630.8206-23.394-30.1655-87.1761
23.8328-1.1472-1.82285.68472.58076.34280.1499-0.3399-0.4708-0.35640.0697-1.1899-0.50460.9275-0.24340.1016-0.06520.05120.1799-0.02680.4378-25.6717-22.0874-73.6375
35.22234.1943-2.22326.9924-1.85794.07030.2183-0.599-0.10110.0975-0.3901-0.4089-0.60180.24290.16270.1375-0.0146-0.02150.1189-0.00990.142-37.1987-21.7323-61.8928
49.49489.58655.78952.02634.07245.76820.9409-0.7716-1.11010.6441-0.4129-0.38820.4865-0.5532-0.3440.2703-0.0896-0.02810.231-0.01510.2554-46.7189-34.0236-55.8945
54.78540.4342-0.53222.7973-0.60982.9804-0.22290.0314-0.3775-0.20840.0131-0.42780.1862-0.04460.18540.1058-0.00090.01790.0219-0.01840.2139-36.8161-30.6259-71.8512
67.58231.1843-4.33764.4602-0.24895.57150.24260.27110.3764-0.1815-0.10650.0492-1.0425-0.3938-0.21770.22050.045-0.07490.0766-0.01570.1655-41.2839-18.4786-73.0541
75.11310.8175-3.03682.00560.02421.8037-0.05862.6895-0.2351-2.0550.62570.8027-0.129-1.7638-0.61260.4665-0.0996-0.110.96090.00960.4705-78.584-39.2546-89.9069
82.0292-1.84820.90284.8349-1.52072.44810.3437-0.6067-0.3550.2742-0.16360.64620.1832-0.6701-0.17670.1673-0.02470.01140.2834-0.05130.2487-65.641-40.0014-80.6036
93.30220.85611.03361.798-0.12791.9191-0.0228-0.09240.2318-0.0665-0.07410.2346-0.2245-0.31820.09310.14840.07270.00560.1525-0.06830.1545-54.5442-26.5616-82.0182
105.12512.1171-1.94612.4451-1.51292.1713-0.17150.2260.1178-0.23640.34620.4970.1934-0.60470.01280.17140.16890.0140.2378-0.19010.1273-61.1464-32.016-89.9526
116.8466.8698-0.02539.6529-0.05473.12190.11240.0494-0.35530.0048-0.2239-0.09310.4207-0.08410.09460.19190.06870.0080.1436-0.06590.1694-52.5344-39.0415-88.8025
128.7343-5.79242.75839.5733-2.52048.8173-0.1619-0.86510.13620.28610.42260.9873-1.1282-0.6719-0.21540.3070.04790.0680.4606-0.09040.3521-56.3598-14.8903-43.182
134.99740.7756-0.69242.4202-1.1434.56730.0735-0.6310.29320.2687-0.16370.0939-0.32660.04510.07930.1992-0.01930.00920.215-0.0530.1245-37.363-16.1914-42.9407
147.938-1.103-1.09593.50010.8963.9186-0.15210.26290.54210.197-0.0420.2371-0.307-0.27940.18280.2059-0.01420.00720.1798-0.0140.1304-45.6962-16.4959-50.8581
152.1385-2.80442.61966.4078-1.55634.60020.2566-0.4048-0.7438-0.1918-0.17550.33290.3944-0.3695-0.06070.2351-0.06620.05210.243-0.01290.1393-44.4047-27.4812-47.0457
162.90621.45210.68085.32170.41640.1583-0.01230.1480.1629-0.56060.58930.2916-1.38481.0125-0.53341.01790.02040.30521.04780.20120.5318-44.0355-17.5594-129.1774
178.4599-0.6228-6.6441.8042-1.09356.6290.1242-0.37130.9550.1286-0.0836-0.1085-1.50680.8334-0.14280.66030.036-0.12750.285-0.06830.2982-50.5885-16.6986-113.324
184.9225-3.9972-1.3388.31661.12581.8166-0.4260.65560.3476-0.32730.0796-0.0112-0.5407-0.23820.21940.1060.3418-0.02930.0811-0.18040.1837-54.2192-28.1304-101.9144
191.53190.5684-0.67634.1367-2.64254.2331-0.11410.0795-0.1501-0.2296-0.1421-0.24930.16220.35720.23210.23680.1156-0.00650.1951-0.05710.1863-48.6978-35.4135-107.9811
202.0102-0.29112.00312.0068-1.84992.00420.48041.5814-0.439-1.7763-0.4677-0.93920.3212.00410.01650.56240.12560.12130.59980.01870.4896-43.1288-24.035-120.9778
210.6758-0.37960.18812.25910.16211.20390.1190.03230.1014-0.5034-0.20630.2624-0.17120.02160.07060.3970.095-0.10860.1943-0.09270.2179-57.4765-32.2831-114.0549
222.91721.3832-1.69817.1408-6.50929.7111-0.02050.1640.4458-0.19370.01430.3359-0.9632-0.4865-0.06520.49880.15-0.14140.2436-0.10940.3231-61.6372-23.2354-113.1435
233.1718-0.99640.07892.81111.5373.45610.1839-0.0048-0.54930.09830.07470.09591.1464-0.071-0.26090.69390.0742-0.160.3145-0.02850.2529-64.959-51.1776-123.5988
242.36991.83521.51466.75241.98352.5198-0.1141-0.2940.39280.2499-0.23750.4389-0.3247-0.77660.30880.3340.2037-0.06330.4392-0.11960.2463-73.0709-32.1162-123.2375
252.01488.12654.38976.85080.16545.5621-0.0504-0.7528-0.44471.06930.15120.08070.8169-0.4357-0.12510.51470.1346-0.00850.32760.00950.3258-71.4859-50.3536-120.8957
262.00632.2889-1.28667.6329.40912.00180.21430.6885-0.5331-0.4872-0.67781.1999-0.3603-0.22260.40080.41380.0191-0.04530.4518-0.0310.4182-77.2389-55.3796-126.634
273.1924-1.0493-0.45042.3823-2.50263.63170.00980.2376-0.2448-0.84190.17920.52440.4285-0.3669-0.14860.44350.1153-0.16040.3207-0.09020.2094-69.54-43.7454-131.9686
282.00846.0293-6.59148.19143.22372.00530.25180.47011.28520.0560.4932-0.3386-1.8654-0.0069-0.71980.52190.0035-0.03790.25680.01170.5251-60.7152-28.692-132.3798
293.4581.42880.46967.18324.39363.6930.20870.4832-0.51350.20860.2282-0.48530.73930.5723-0.47670.53520.2173-0.12120.4879-0.09210.2407-59.9833-47.2488-132.6808
301.97661.57110.37811.61260.82886.22790.0274-0.4085-0.4740.05580.0878-0.41930.58850.7885-0.14420.32190.1533-0.05930.71570.06980.2806-17.7636-27.7183-27.4852
312.1197-1.53-0.54164.31583.93147.0388-0.0557-0.6146-0.26780.3726-0.29380.76190.5263-0.99610.19130.2828-0.03490.05050.98250.06160.104-36.52-22.3053-20.2879
329.6912.41490.18788.0947.17576.8144-0.0769-1.2013-1.2651.29640.1747-1.06671.04240.6556-0.1190.36340.063-0.07080.58270.13960.3259-22.1134-33.4632-24.4604
337.7706-3.99653.30946.14130.30747.13580.0509-0.689-1.56540.80540.38210.47221.1728-0.2623-0.35410.5301-0.009-0.02180.42630.13380.481-24.3972-39.265-32.7737
343.264-2.3730.20957.07080.6390.81810.0549-0.0567-0.1387-0.2686-0.09350.1436-0.0451-0.06380.06010.21560.0227-0.02560.52390.03740.1545-29.167-21.9979-31.6126
359.9837-7.0903-4.41037.47085.62816.26440.17590.2711-0.0627-0.4997-0.1686-0.2368-0.24960.4484-0.05890.2702-0.01210.00310.60820.04460.2015-19.64-20.4563-34.6655
363.93790.3756-0.77860.1774-0.03862.53630.12720.26880.65-0.1177-0.08710.1394-0.8263-0.7773-0.06030.58250.3015-0.07180.5825-0.03380.3172-25.0833-5.2262-2.0065
375.1242-3.148-1.66667.62670.16527.33160.15430.68420.2993-0.1793-0.1015-0.3435-0.51220.3794-0.07120.2513-0.0147-0.04760.4571-0.03930.1591-13.3161-10.435-7.4136
382.660.7424-1.06432.538-0.17720.4321-0.3411.17910.9396-0.5632-0.3155-0.2953-0.99890.13980.67541.1980.36910.11530.79280.25780.6131-21.20853.7166-15.1987
392.529-0.0289-0.18482.23641.58541.64490.04720.32150.1725-0.1645-0.08030.0285-0.3439-0.82950.03740.35310.1329-0.03350.6394-0.02890.1601-23.1195-13.5911-11.4587
405.7294-3.40542.45557.8569-2.98432.7065-0.04760.02280.2351-0.0389-0.0170.5135-0.5875-1.2950.01430.49360.2307-0.03360.9042-0.07920.261-31.7501-11.6065-6.9348
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 38 )
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 46 )
5X-RAY DIFFRACTION5chain 'A' and (resid 47 through 89 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 119 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 8 )
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 24 )
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 89 )
11X-RAY DIFFRACTION11chain 'B' and (resid 90 through 119 )
12X-RAY DIFFRACTION12chain 'C' and (resid 5 through 24 )
13X-RAY DIFFRACTION13chain 'C' and (resid 25 through 65 )
14X-RAY DIFFRACTION14chain 'C' and (resid 66 through 89 )
15X-RAY DIFFRACTION15chain 'C' and (resid 90 through 119 )
16X-RAY DIFFRACTION16chain 'D' and (resid 4 through 8 )
17X-RAY DIFFRACTION17chain 'D' and (resid 9 through 25 )
18X-RAY DIFFRACTION18chain 'D' and (resid 26 through 38 )
19X-RAY DIFFRACTION19chain 'D' and (resid 39 through 65 )
20X-RAY DIFFRACTION20chain 'D' and (resid 66 through 71 )
21X-RAY DIFFRACTION21chain 'D' and (resid 72 through 94 )
22X-RAY DIFFRACTION22chain 'D' and (resid 95 through 119 )
23X-RAY DIFFRACTION23chain 'E' and (resid 5 through 38 )
24X-RAY DIFFRACTION24chain 'E' and (resid 39 through 56 )
25X-RAY DIFFRACTION25chain 'E' and (resid 57 through 65 )
26X-RAY DIFFRACTION26chain 'E' and (resid 66 through 71 )
27X-RAY DIFFRACTION27chain 'E' and (resid 72 through 89 )
28X-RAY DIFFRACTION28chain 'E' and (resid 90 through 94 )
29X-RAY DIFFRACTION29chain 'E' and (resid 95 through 118 )
30X-RAY DIFFRACTION30chain 'F' and (resid 5 through 38 )
31X-RAY DIFFRACTION31chain 'F' and (resid 39 through 56 )
32X-RAY DIFFRACTION32chain 'F' and (resid 57 through 65 )
33X-RAY DIFFRACTION33chain 'F' and (resid 66 through 71 )
34X-RAY DIFFRACTION34chain 'F' and (resid 72 through 94 )
35X-RAY DIFFRACTION35chain 'F' and (resid 95 through 119 )
36X-RAY DIFFRACTION36chain 'G' and (resid 11 through 38 )
37X-RAY DIFFRACTION37chain 'G' and (resid 39 through 65 )
38X-RAY DIFFRACTION38chain 'G' and (resid 66 through 71 )
39X-RAY DIFFRACTION39chain 'G' and (resid 72 through 94 )
40X-RAY DIFFRACTION40chain 'G' and (resid 95 through 117 )

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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