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- PDB-5krh: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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基本情報

登録情報
データベース: PDB / ID: 5krh
タイトルCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with 16-benzylidene estrone
要素
  • Estrogen receptor
  • NCOA2
キーワードTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
機能・相同性
機能・相同性情報


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / nitric-oxide synthase regulator activity / TBP-class protein binding / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / euchromatin / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
類似検索 - 分子機能
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / : / Estrogen receptor/oestrogen-related receptor ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / : / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Chem-6WN / Estrogen receptor / Nuclear receptor coactivator 2
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: 2.243 Å
データ登録者Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
引用ジャーナル: Cell Chem Biol / 年: 2017
タイトル: Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
著者: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / ...著者: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
履歴
登録2016年7月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年2月15日Provider: repository / タイプ: Initial release
改定 1.12024年3月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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: Estrogen receptor
B: Estrogen receptor
C: NCOA2
D: NCOA2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,6506
ポリマ－61,9334
非ポリマー7172
水1,76598
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-30 kcal/mol
Surface area20580 Å2
手法PISA
単位格子
Length a, b, c (Å)55.530, 81.903, 58.665
Angle α, β, γ (deg.)90.00, 110.67, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質 Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


分子量: 29299.535 Da / 分子数: 2 / 断片: ligand-binding domain / 変異: Y537S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ESR1, ESR, NR3A1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P03372
#2: タンパク質・ペプチド NCOA2


分子量: 1666.943 Da / 分子数: 2 / 断片: Nuclear receptor-interacting peptide / 由来タイプ: 合成 / 詳細: This sequence occurs naturally in humans / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q15596*PLUS
#3: 化合物 ChemComp-6WN / (8~{R},9~{S},13~{S},14~{S},16~{E})-13-methyl-3-oxidanyl-16-(phenylmethylidene)-6,7,8,9,11,12,14,15-octahydrocyclopenta[ a]phenanthren-17-one / 16-benzylidene estrone / (16E)-16-ベンジリデン-3β-ヒドロキシエストラ-1,3,5(10)-トリエン-17-オン


分子量: 358.473 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C25H26O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 98 / 由来タイプ: 天然 / 式: H2O

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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: 2.02 Å3/Da / 溶媒含有率: 39.14 % / Mosaicity: 0.713 °
結晶化温度: 294 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.3 / 詳細: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SSRL / ビームライン: BL11-1 / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年7月27日
放射モノクロメーター: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
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 Å / 相対比: 1
反射解像度: 2.24→50 Å / Num. obs: 23260 / % possible obs: 98.6 % / 冗長度: 6.8 % / Rmerge(I) obs: 0.139 / Χ2: 1.261 / Net I/av σ(I): 18.939 / Net I/σ(I): 4.4 / Num. measured all: 158488
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsDiffraction-ID% possible all
2.24-2.286.90.983199.4
2.28-2.326.90.85198.6
2.32-2.366.90.752199.4
2.36-2.416.90.665199.2
2.41-2.476.90.552199
2.47-2.526.80.507199.3
2.52-2.596.80.431199.2
2.59-2.666.80.378198.5
2.66-2.736.60.331198.2
2.73-2.8260.272195.6
2.82-2.9270.238199.2
2.92-3.047.20.199199.4
3.04-3.187.10.179199.5
3.18-3.3570.162199.1
3.35-3.566.90.147199.2
3.56-3.836.70.131199.3
3.83-4.226.10.119194.8
4.22-4.827.20.11199.5
4.82-6.0870.107199
6.08-506.50.092196.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1690精密化
HKL-2000データスケーリング
PDB_EXTRACT3.2データ抽出
HKL-2000データ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.243→46.89 Å / SU ML: 0.31 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 28.83 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2433 1840 8.49 %
Rwork0.206 --
obs0.2092 21665 91.61 %
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
精密化ステップサイクル: LAST / 解像度: 2.243→46.89 Å
タンパク質核酸リガンド溶媒全体
原子数3788 0 54 98 3940
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0063934
X-RAY DIFFRACTIONf_angle_d0.9155339
X-RAY DIFFRACTIONf_dihedral_angle_d13.2951439
X-RAY DIFFRACTIONf_chiral_restr0.044640
X-RAY DIFFRACTIONf_plane_restr0.004657
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2427-2.30330.3411990.32231250X-RAY DIFFRACTION74
2.3033-2.37110.2851380.26221376X-RAY DIFFRACTION85
2.3711-2.44760.28881260.25721451X-RAY DIFFRACTION86
2.4476-2.53510.30521370.24541489X-RAY DIFFRACTION89
2.5351-2.63660.29731380.23471476X-RAY DIFFRACTION90
2.6366-2.75650.27471370.24171519X-RAY DIFFRACTION91
2.7565-2.90190.2981540.24241514X-RAY DIFFRACTION92
2.9019-3.08360.30541520.23351600X-RAY DIFFRACTION97
3.0836-3.32170.27431430.22431608X-RAY DIFFRACTION97
3.3217-3.65580.27051600.20561646X-RAY DIFFRACTION98
3.6558-4.18450.2111470.17511584X-RAY DIFFRACTION95
4.1845-5.27090.17261550.16321651X-RAY DIFFRACTION99
5.2709-46.90010.22741540.19291661X-RAY DIFFRACTION97
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)
10.83950.55790.11711.1669-0.34130.59530.6303-0.49290.56210.6034-0.35270.2223-0.43580.36720.130.668-0.2009-0.0690.5956-0.03660.4316-3.2737-6.99915.4608
20.473-0.0639-0.61790.20580.21130.8945-0.2232-0.2665-0.25470.0565-0.3173-0.16940.6996-0.5095-0.11750.3175-0.13050.02880.8034-0.07660.4735-21.7422-27.75719.4093
30.0997-0.0596-0.190.06740.20480.9211-0.1220.1987-0.18210.10560.1428-0.239-0.16990.15450.02311.20220.1379-0.21611.2133-0.3571.8785-25.2679-39.63775.2707
40.01250.00560.01030.12850.10430.2038-0.18250.1861-0.2131-0.2617-0.0078-0.3812-0.03950.0735-0.0030.6089-0.05930.04280.51040.05460.6926-26.6065-34.4217-3.0666
50.03770.01070.00610.0197-0.00830.0050.1184-0.4673-0.17440.00920.0411-0.1980.00270.0469-0.00050.428-0.0389-0.0310.36990.04970.4431-22.1484-21.27391.9069
60.25310.12210.13630.06990.05440.1281-0.2261-0.46550.80560.101-0.4248-0.2271-0.6116-0.15920.00390.7341-0.0469-0.01240.4032-0.07990.6817-13.6735-5.09610.1534
70.6259-0.1654-0.41951.14680.11280.58990.14970.2759-0.1372-0.097-0.18970.6185-0.26410.0146-0.02750.3694-0.02380.09160.28430.0030.352-13.7799-16.9178-4.8569
80.27880.05140.68520.01290.14511.747-0.2202-0.31580.2276-0.18780.2384-0.19520.3182-0.69950.00940.50530.01290.1710.34510.0630.5505-12.4438-33.15463.7116
90.3207-0.1236-0.1730.06990.05670.104-0.30530.1261-0.17850.36180.32880.19510.1043-0.013-0.00421.0805-0.20620.06220.6271-0.05221.493-18.6523-39.2579-6.7528
100.0217-0.0161-0.00810.0255-0.00010.0043-0.22170.2968-0.1601-0.4775-0.1069-0.1795-0.02430.0759-00.9515-0.0152-0.00330.5517-0.08680.512-14.6448-34.3613-9.7457
110.9390.0539-0.66350.06770.24961.74120.1976-0.2812-0.15840.28130.1918-0.1870.06770.55370.04440.69380.02750.10490.39090.01990.4404-5.0807-30.6167-6.7158
120.0124-0.01070.00530.04110.02430.03120.1681-0.12670.35680.23610.1787-0.21490.338-0.5186-0.00180.65960.057-0.13630.61410.14940.55071.9431-29.3382-2.6687
130.52830.2595-0.50760.2041-0.22170.44380.1983-0.05340.22950.1122-0.13240.147-0.36530.73810.00520.4252-0.10350.0230.36480.04140.3063-4.0288-15.5586-2.8851
140.3491-0.53440.40310.8805-0.65190.4819-0.5810.58320.1584-0.4279-0.1913-0.5004-0.64820.0275-0.10051.4066-0.180.23980.8135-0.2820.9346-9.559-3.5033-13.9276
150.0163-0.02480.00390.0325-0.00490.00190.51190.5504-0.0251-0.70810.33510.1951-0.45520.0303-0.00070.6007-0.06270.05780.4566-0.02610.5428-3.1264-3.3475-9.1185
161.5314-1.89780.09292.3606-0.10180.05260.5896-0.34340.0974-0.0734-0.514-0.0302-0.11040.05760.07130.5162-0.2342-0.08610.5790.07350.40627.3966-12.0758-1.0573
170.0589-0.0625-0.08040.07110.08790.14810.0988-0.1074-0.4430.3568-0.0576-0.1693-0.14350.265300.53810.0065-0.0360.49820.05470.39587.2497-19.1948-8.2897
180.0351-0.0337-0.03430.0409-0.00340.06870.15670.14030.5356-0.2848-0.00550.1163-0.5836-0.08360.00080.3978-0.07120.04920.2977-0.04680.366-9.6928-23.0738-13.4827
190.01890.01040.02960.11650.01760.03260.54820.9012-0.7633-0.71540.2176-0.07210.3638-0.11310.00270.5504-0.0888-0.15540.5365-0.04960.5762-22.9365-26.0332-14.1654
200.4149-0.31-0.60617.8752.97751.79610.0860.3685-0.20071.0228-0.24681.62940.7677-0.62120.02390.2882-0.05880.03740.5242-0.0280.5653-28.8791-20.5063-9.4238
210.1104-0.1410.05610.1761-0.070.0213-0.1005-0.01460.1040.0109-0.0233-0.12710.04880.09270.24820.25410.3949-0.87861.32140.25690.360918.603-26.7475-22.023
220.08250.03270.02730.99890.6670.4964-0.11680.3437-0.0828-0.4392-0.1446-0.1577-0.40450.3001-0.11930.3243-0.05180.0110.61090.08640.45628.8289-18.0567-33.8451
230.36140.2751-0.28120.28190.00520.8570.1513-0.0471-0.3699-0.005-0.0557-0.2070.0644-0.29350.0590.43950.1077-0.07720.87590.19260.8811-15.3733-10.9937-48.7715
241.9796-0.7712.26422.006-1.4022.749-0.0366-0.20470.430.01340.04060.6115-0.0889-0.46340.1841-0.08030.0522-0.21411.17650.09840.6527-20.2268-15.148-40.1667
251.004-0.03790.00470.5875-0.54750.8316-0.3747-0.013-0.4298-0.05770.1875-0.14640.5698-0.057-0.10.43970.05760.03860.334-0.00860.4660.3986-27.151-33.4797
260.3018-0.0457-0.09650.31510.49810.72770.0595-0.0531-0.3917-0.0705-0.26740.17750.2420.103800.40780.04730.00020.3502-0.01020.3622-3.037-21.5858-27.9837
270.0932-0.09990.0210.1493-0.08070.057-0.54630.040.24870.39650.4247-0.2306-1.33950.20670.00080.6458-0.0368-0.08350.52170.01440.4676-5.8249-6.4855-36.4136
280.10970.1085-0.20930.9307-0.07280.9454-0.1029-0.1880.41170.00410.01550.3441-0.5754-0.4011-0.04580.42310.1334-0.07270.85170.01940.6854-13.1443-5.5965-36.7912
290.02750.034-0.01450.0482-0.03760.03580.21050.0424-0.38340.22140.17880.2477-0.0016-0.2175-0.00111.4310.1930.00981.2580.2221.379-20.854-10.4013-33.6846
300.0098-0.00260.01750.0369-0.01670.03080.06610.0126-0.14810.14520.16670.13990.3109-0.60460.00140.89250.20920.14770.82880.16860.6302-16.9099-11.068-28.3054
310.0471-0.02520.14310.11260.07680.6236-0.2328-0.3059-0.11460.10790.1825-0.2755-0.7186-0.19280.01740.60410.1722-0.02830.3220.02540.428-8.9898-7.4748-25.1768
321.3826-0.74850.86690.4089-0.47450.5493-0.91630.10460.3369-0.1982-0.5026-0.001-0.47310.1945-0.10550.89490.13210.10420.42010.00560.5593-0.9303-3.6216-22.9927
330.6922-0.1499-0.30324.82251.98121.03190.1879-0.0933-0.07520.7532-0.38940.60.30610.7007-0.30410.2312-0.0074-0.0820.39380.05010.27384.5035-16.8075-23.1536
342.17920.31581.92180.83260.37451.76230.202-0.0948-0.38620.10330.59610.16260.3676-0.12840.31361.42040.13560.32791.46280.04961.36210.4941-38.3298-12.9533
350.52420.67341.2022.89151.26733.311-0.0941-0.2893-0.45790.21250.16880.96370.5545-0.5208-0.16731.04510.1973-0.05020.88610.09090.76627.6156-34.9527-15.576
362.9213-1.662-1.47147.6126-1.73033.5943-0.7552-0.19940.1920.468-0.1106-1.01380.32290.7879-0.80780.24680.0545-0.01990.5410.02910.293610.1266-25.5515-15.9723
371.39360.1441-0.36883.52010.3990.35810.17-0.52790.14610.6152-0.36160.1404-0.17110.7125-0.89330.3512-0.1651-0.1350.58050.10090.27639.9813-9.6254-14.8688
380.22740.0587-0.48540.0295-0.14071.015-0.6174-0.18910.25960.47340.4130.176-0.196-0.6370.00750.41810.07570.01550.2893-0.04480.3564-10.0887-18.5577-21.0521
390.8935-0.2056-0.01220.06930.10871.483-0.96690.21770.81140.0752-0.25590.39780.4769-0.4164-0.17250.5433-0.198-0.04930.9716-0.12670.6289-21.2882-24.9464-33.3955
400.2327-0.5517-0.02061.29940.08350.0397-0.29750.6535-0.53390.25020.48190.3390.5024-0.2659-0.00880.4457-0.13560.06350.5349-0.07270.568-12.7505-31.2226-30.7839
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 305:325)A305 - 325
2X-RAY DIFFRACTION2(chain A and resid 326:331)A326 - 331
3X-RAY DIFFRACTION3(chain A and resid 332:337)A332 - 337
4X-RAY DIFFRACTION4(chain A and resid 338:344)A338 - 344
5X-RAY DIFFRACTION5(chain A and resid 345:357)A345 - 357
6X-RAY DIFFRACTION6(chain A and resid 358:372)A358 - 372
7X-RAY DIFFRACTION7(chain A and resid 373:396)A373 - 396
8X-RAY DIFFRACTION8(chain A and resid 397:410)A397 - 410
9X-RAY DIFFRACTION9(chain A and resid 411:420)A411 - 420
10X-RAY DIFFRACTION10(chain A and resid 421:426)A421 - 426
11X-RAY DIFFRACTION11(chain A and resid 427:434)A427 - 434
12X-RAY DIFFRACTION12(chain A and resid 435:438)A435 - 438
13X-RAY DIFFRACTION13(chain A and resid 439:458)A439 - 458
14X-RAY DIFFRACTION14(chain A and resid 459:474)A459 - 474
15X-RAY DIFFRACTION15(chain A and resid 475:479)A475 - 479
16X-RAY DIFFRACTION16(chain A and resid 480:496)A480 - 496
17X-RAY DIFFRACTION17(chain A and resid 497:511)A497 - 511
18X-RAY DIFFRACTION18(chain A and resid 512:519)A512 - 519
19X-RAY DIFFRACTION19(chain A and resid 520:528)A520 - 528
20X-RAY DIFFRACTION20(chain A and resid 529:548)A529 - 548
21X-RAY DIFFRACTION21(chain B and resid 305:312)B305 - 312
22X-RAY DIFFRACTION22(chain B and resid 313:329)B313 - 329
23X-RAY DIFFRACTION23(chain B and resid 330:337)B330 - 337
24X-RAY DIFFRACTION24(chain B and resid 338:343)B338 - 343
25X-RAY DIFFRACTION25(chain B and resid 344:373)B344 - 373
26X-RAY DIFFRACTION26(chain B and resid 374:396)B374 - 396
27X-RAY DIFFRACTION27(chain B and resid 397:407)B397 - 407
28X-RAY DIFFRACTION28(chain B and resid 408:413)B408 - 413
29X-RAY DIFFRACTION29(chain B and resid 414:420)B414 - 420
30X-RAY DIFFRACTION30(chain B and resid 421:425)B421 - 425
31X-RAY DIFFRACTION31(chain B and resid 426:433)B426 - 433
32X-RAY DIFFRACTION32(chain B and resid 434:437)B434 - 437
33X-RAY DIFFRACTION33(chain B and resid 438:458)B438 - 458
34X-RAY DIFFRACTION34(chain B and resid 459:469)B459 - 469
35X-RAY DIFFRACTION35(chain B and resid 470:474)B470 - 474
36X-RAY DIFFRACTION36(chain B and resid 475:483)B475 - 483
37X-RAY DIFFRACTION37(chain B and resid 484:510)B484 - 510
38X-RAY DIFFRACTION38(chain B and resid 511:522)B511 - 522
39X-RAY DIFFRACTION39(chain B and resid 523:536)B523 - 536
40X-RAY DIFFRACTION40(chain B and resid 537:548)B537 - 548

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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