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- PDB-5u2b: 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: 5u2b
タイトルCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the phenylamino-substituted estrogen, (8R,9S,13S,14S,17S)-13-methyl-17-(phenylamino)-7,8,9,11,12,13,14,15,16,17-decahydro-6H-cyclopenta[a]phenanthren-3-ol, without a coactivator peptide
要素Estrogen receptor
キーワードTRANSCRIPTION / 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 / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / 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 / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X Receptor / 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-6WV / Estrogen receptor
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: 2.22 Å
データ登録者Nwachukwu, J.C. / Nowak, J. / Carlson, K.E. / Katzenellenbogen, J.A. / Nettles, K.W.
引用ジャーナル: Mol. Cell / 年: 2017
タイトル: Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells.
著者: Stender, J.D. / Nwachukwu, J.C. / Kastrati, I. / Kim, Y. / Strid, T. / Yakir, M. / Srinivasan, S. / Nowak, J. / Izard, T. / Rangarajan, E.S. / Carlson, K.E. / Katzenellenbogen, J.A. / Yao, X. ...著者: Stender, J.D. / Nwachukwu, J.C. / Kastrati, I. / Kim, Y. / Strid, T. / Yakir, M. / Srinivasan, S. / Nowak, J. / Izard, T. / Rangarajan, E.S. / Carlson, K.E. / Katzenellenbogen, J.A. / Yao, X.Q. / Grant, B.J. / Leong, H.S. / Lin, C.Y. / Frasor, J. / Nettles, K.W. / Glass, C.K.
履歴
登録2016年11月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年4月26日Provider: repository / タイプ: Initial release
改定 1.12017年11月22日Group: Refinement description / カテゴリ: software
改定 1.22024年3月6日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Estrogen receptor
D: Estrogen receptor
E: Estrogen receptor
F: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)177,88212
ポリマ－175,7976
非ポリマー2,0856
水12,611700
1
A: Estrogen receptor
B: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,2944
ポリマ－58,5992
非ポリマー6952
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-13 kcal/mol
Surface area19790 Å2
手法PISA
2
C: Estrogen receptor
D: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,2944
ポリマ－58,5992
非ポリマー6952
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-10 kcal/mol
Surface area19550 Å2
手法PISA
3
E: Estrogen receptor
F: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,2944
ポリマ－58,5992
非ポリマー6952
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-10 kcal/mol
Surface area19590 Å2
手法PISA
単位格子
Length a, b, c (Å)60.584, 64.440, 135.406
Angle α, β, γ (deg.)83.11, 75.20, 61.99
Int Tables number1
Space group name H-MP1

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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: 6 / 断片: ligand-binding domain, UNP residues 125-381 / 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: 化合物
ChemComp-6WV / (8~{R},9~{S},13~{S},14~{S},17~{S})-13-methyl-17-phenylazanyl-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-3-ol


分子量: 347.493 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C24H29NO
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 700 / 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: 2.57 Å3/Da / 溶媒含有率: 52.08 % / Mosaicity: 0.422 °
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: APS / ビームライン: 23-ID-B / 波長: 1.033 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2010年12月18日
放射モノクロメーター: Double crystal cryo-cooled Si(111)
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: 1.033 Å / 相対比: 1
Reflection twinOperator: -h,-h+k,-l / Fraction: 0.5
反射解像度: 2.22→34.625 Å / Num. obs: 84041 / % possible obs: 98 % / 冗長度: 2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 10.7
反射 シェル解像度: 2.22→2.26 Å / 冗長度: 2 % / Rmerge(I) obs: 0.396 / % possible all: 96.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155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
DENZOデータ削減
SCALEPACKデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 2.22→34.63 Å / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 29.01
Rfactor反射数%反射
Rfree0.229 2047 2.44 %
Rwork0.201 --
obs0.217 84041 97.8 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 51.95 Å2
精密化ステップサイクル: LAST / 解像度: 2.22→34.63 Å
タンパク質核酸リガンド溶媒全体
原子数10767 0 133 700 11600
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00211131
X-RAY DIFFRACTIONf_angle_d0.51815075
X-RAY DIFFRACTIONf_dihedral_angle_d17.8134044
X-RAY DIFFRACTIONf_chiral_restr0.0331802
X-RAY DIFFRACTIONf_plane_restr0.0031862
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2234-2.2790.41421400.37375546X-RAY DIFFRACTION91
2.279-2.34060.421410.34025843X-RAY DIFFRACTION95
2.3406-2.40940.33251420.32855821X-RAY DIFFRACTION95
2.4094-2.48720.3511420.30965838X-RAY DIFFRACTION95
2.4872-2.5760.37321400.28485863X-RAY DIFFRACTION96
2.576-2.67910.30221380.26835907X-RAY DIFFRACTION96
2.6791-2.80090.28991500.25645857X-RAY DIFFRACTION96
2.8009-2.94840.29811410.23695845X-RAY DIFFRACTION96
2.9484-3.13290.27471360.22335899X-RAY DIFFRACTION96
3.1329-3.37450.20271430.20995937X-RAY DIFFRACTION96
3.3745-3.71340.19331470.18835865X-RAY DIFFRACTION96
3.7134-4.24920.22571490.1675940X-RAY DIFFRACTION96
4.2492-5.34770.1711460.16095960X-RAY DIFFRACTION97
5.3477-28.44820.24841450.19015899X-RAY DIFFRACTION96
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)
17.2141-0.85364.76675.2262-2.3368.61130.69830.6171-0.3947-0.3012-0.0022-0.01861.06140.2169-0.58340.3160.0227-0.08110.4161-0.06550.3027-4.62720.0407-5.7716
25.6141-1.34934.46510.3373-1.02743.92130.6679-0.1664-0.84230.41510.3022-0.63011.10690.4022-0.980.72740.2717-0.32070.5394-0.1590.643318.6636-5.127915.4854
36.7626-1.26494.02290.7041-1.24272.90630.13190.17090.07130.30510.1531-0.46650.67310.7405-0.32560.45640.2424-0.1310.5886-0.12370.390517.22362.23119.1641
41.90960.60510.18691.28040.33834.51620.11490.33230.05550.13210.2642-0.11660.16820.0171-0.35410.18170.0974-0.01350.3892-0.05160.25787.68968.00043.1288
53.9748-1.26971.90781.0484-0.29383.22220.2091-0.4786-0.83670.39820.17-0.02110.97210.0316-0.42820.83690.1143-0.24660.51170.09040.476410.4547-3.067822.4433
63.34021.04261.88753.84930.37217.12050.292-0.7041-0.34090.77030.1539-0.38220.531-0.1668-0.41740.54470.1162-0.11890.48450.0140.27719.35386.750425.4388
74.83420.47460.18144.2825-2.06347.60650.0934-0.0027-0.0079-0.00160.02250.25240.3694-0.4486-0.12430.1730.0401-0.01870.326-0.04490.1877-4.41188.30782.6231
85.53871.4729-0.48693.5870.15192.83850.0702-0.38790.09780.47120.1155-0.19990.1575-0.3361-0.18370.29130.044-0.00250.42230.00850.14470.88412.079515.2982
94.8688-2.9894-1.35446.9427-1.09264.3390.1892-0.0110.50370.42610.1446-1.1535-0.09761.1291-0.31990.25250.0646-0.02590.8004-0.12440.436121.050714.36967.2406
102.03560.42910.10874.9559-1.46382.2634-0.3216-0.33510.180.62310.1161-0.1074-0.3789-0.82990.16590.44010.1961-0.03790.8851-0.24350.4958-13.887232.486319.1625
111.302-1.04310.27623.2248-0.38440.6297-0.4577-0.35690.66670.51930.0238-0.4576-0.7508-0.63110.29530.78220.2708-0.29380.6961-0.31190.4089-3.19237.298221.3441
121.94041.5276-1.93731.92750.19287.3684-0.0964-0.5670.39990.21930.24930.2894-0.1598-0.5427-0.05710.38040.214-0.07520.6114-0.12730.2729-5.051928.499318.5713
139.792-4.13232.65416.31811.09795.1366-0.55670.98661.8385-0.429-0.3095-1.7919-1.30310.72680.86450.6523-0.0746-0.1340.65470.33171.12884.944139.73034.6197
149.54186.13734.26936.73843.08064.5876-0.03610.740.3403-0.317-0.1157-0.2179-0.0923-0.13220.14750.29060.11440.06710.44730.05370.2849-1.167527.6512.8027
150.59710.2535-0.17441.09370.75491.6127-0.1677-0.38110.00930.6191-0.0660.06290.005-0.62350.12210.25370.08380.12531.0228-0.06380.1994-14.342718.521616.0944
161.7412-0.65770.03472.61370.65142.8401-0.1036-0.24310.35850.44690.2737-0.5638-0.2552-0.0389-0.16630.33280.1347-0.05340.4655-0.08910.26512.482925.492715.1947
175.77551.03894.02312.15221.06146.16930.5236-0.2212-0.4718-0.3582-0.05690.27741.1504-0.4346-0.46530.4902-0.0826-0.1460.38660.10110.380518.3471-0.5548-19.9269
183.25080.11061.01732.575-0.15194.91830.19790.3684-0.3204-0.70710.2340.20360.5227-0.1451-0.4180.3752-0.0198-0.10370.40160.00160.290220.44845.4123-28.4014
194.84340.67890.65671.7081-1.2721.90550.17080.0012-0.2588-0.17950.085-0.03130.30320.448-0.25760.24370.1468-0.03150.4417-0.02130.214434.08317.4031-16.8162
208.9699-1.2563-0.28643.0529-0.10993.7365-0.01510.0486-0.0551-0.28610.18250.38950.0713-0.1802-0.20180.30380.0252-0.04090.37370.01130.177521.484112.7174-26.0704
212.2793-0.0716-0.52971.76840.54111.51630.10610.63250.013-0.82140.354-0.39910.07330.4702-0.25090.5393-0.20150.2291.41650.06280.38451.281522.5496-36.4713
222.1470.74580.33833.46630.80914.8489-0.57650.81860.7747-0.46070.10020.2898-0.81440.48630.35550.4582-0.1599-0.15140.58390.18790.342433.653533.5053-31.6272
238.0574.2143-3.06527.37373.34482.0011-0.6353-0.07681.0984-0.1456-0.18391.7888-1.5915-1.7780.77570.63430.2968-0.09750.762-0.13680.741819.116437.9176-17.7678
247.2337-2.15891.53727.7055-0.62947.2118-0.3036-0.22890.25340.55560.09650.1736-0.43010.25430.22830.3293-0.0094-0.01120.3908-0.06220.159130.481527.7473-16.331
251.80980.1008-0.13522.86770.04251.2555-0.21280.77030.0464-0.5671-0.02570.3838-0.21220.7390.10690.26430.03020.09080.81780.024-0.008438.082119.3064-27.5734
263.0596-0.1927-1.05534.36141.35021.9482-0.26221.23821.2755-0.40820.1513-0.032-0.4454-0.3630.14950.5668-0.0429-0.20311.00450.32410.636519.922532.5688-38.6446
271.87131.45733.00825.46281.99944.8108-0.2955-0.28270.35131.56090.2325-0.82940.0715-0.16450.09570.5328-0.31160.10440.8104-0.08760.525921.686536.71471.1622
283.2764-0.2968-0.00843.0706-0.52532.83980.10360.3336-0.22990.0127-0.0873-0.3467-0.14160.0295-0.01860.28350.0137-0.02440.68560.010.31316.494627.387363.5726
291.83020.5357-0.15714.10020.21893.4619-0.0864-0.51310.42620.64250.05860.1618-0.2497-0.40050.07310.58380.0911-0.05660.7275-0.11310.33079.387644.197566.7043
301.06160.50820.28123.18250.68230.57820.12550.0275-0.09260.3856-0.1149-0.1035-0.1657-0.2178-0.01190.5070.069-0.02020.801-0.01610.24547.596930.477161.4964
312.0026-3.44544.48616.71611.33422.0041-0.20170.82160.8295-0.10910.5516-0.6933-1.3086-0.189-0.41040.64680.05250.00890.5760.18580.57452.864449.559936.4479
324.63914.9665-3.80936.1905-4.53423.3643-0.25690.45440.58110.09070.58680.3704-0.858-1.1006-0.30270.73970.1801-0.06250.7297-0.03590.4193-8.95350.408643.7275
330.3442-0.19810.0040.1102-0.0084-0.00760.00610.268-0.1662-0.02890.086-0.3624-0.0749-0.4573-0.0460.4640.19850.07971.4855-0.09810.8781-20.967634.338748.0603
343.95084.2284-1.91416.7894-1.90642.7275-0.23421.03910.23070.1950.67330.4819-0.1437-1.1-0.44560.36140.1202-0.03291.0372-0.02110.3751-14.958929.94845.4784
350.93090.3416-1.24032.07750.58282.30360.0364-0.53740.16150.0963-0.0270.3408-0.3265-0.5544-0.04270.42670.20870.01041.0735-0.02630.3439-10.326334.043450.9801
362.12441.7909-0.85565.9988-3.43462.00130.189-0.738-0.02270.359-0.32440.35550.0286-0.30460.16260.7261-0.00670.03391.34810.0080.3612-12.874230.126265.8627
375.08551.41330.0683.77420.1485.079-0.3479-0.19990.04130.11270.29070.329-0.8902-0.03110.07570.62410.2064-0.080.7267-0.03090.2723-3.358342.03550.9176
381.26390.69880.29683.05271.23164.8383-0.0414-0.1870.18430.0587-0.05770.1539-0.8686-0.2510.10690.40390.1518-0.04580.6406-0.01940.2803-0.091341.342954.9386
392.7742-1.23662.68666.7326-1.88615.54440.42060.0805-0.3061-0.447-0.39070.4090.9767-0.7965-0.04630.49-0.1276-0.03720.8647-0.01310.3169-7.218119.084946.3353
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 299 THROUGH 321 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 322 THROUGH 338 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 339 THROUGH 363 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 364 THROUGH 394 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 395 THROUGH 411 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 412 THROUGH 437 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 438 THROUGH 496 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 497 THROUGH 528 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 529 THROUGH 548 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 304 THROUGH 341 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 342 THROUGH 363 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 364 THROUGH 404 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 405 THROUGH 421 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 422 THROUGH 438 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 439 THROUGH 496 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 497 THROUGH 548 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 300 THROUGH 363 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 364 THROUGH 437 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 438 THROUGH 496 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 497 THROUGH 549 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 304 THROUGH 321 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 322 THROUGH 411 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 412 THROUGH 421 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 422 THROUGH 438 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 439 THROUGH 528 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 529 THROUGH 550 )
27X-RAY DIFFRACTION27CHAIN 'E' AND (RESID 306 THROUGH 338 )
28X-RAY DIFFRACTION28CHAIN 'E' AND (RESID 339 THROUGH 438 )
29X-RAY DIFFRACTION29CHAIN 'E' AND (RESID 439 THROUGH 496 )
30X-RAY DIFFRACTION30CHAIN 'E' AND (RESID 497 THROUGH 548 )
31X-RAY DIFFRACTION31CHAIN 'F' AND (RESID 302 THROUGH 311 )
32X-RAY DIFFRACTION32CHAIN 'F' AND (RESID 312 THROUGH 322 )
33X-RAY DIFFRACTION33CHAIN 'F' AND (RESID 323 THROUGH 341 )
34X-RAY DIFFRACTION34CHAIN 'F' AND (RESID 342 THROUGH 363 )
35X-RAY DIFFRACTION35CHAIN 'F' AND (RESID 364 THROUGH 411 )
36X-RAY DIFFRACTION36CHAIN 'F' AND (RESID 412 THROUGH 437 )
37X-RAY DIFFRACTION37CHAIN 'F' AND (RESID 438 THROUGH 468 )
38X-RAY DIFFRACTION38CHAIN 'F' AND (RESID 469 THROUGH 529 )
39X-RAY DIFFRACTION39CHAIN 'F' AND (RESID 530 THROUGH 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