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- PDB-3osa: Estrogen Receptor -

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基本情報

登録情報
データベース: PDB / ID: 3osa
タイトルEstrogen Receptor
要素Estrogen receptor
キーワードSIGNALING PROTEIN / Estrogen receptor 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 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 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 / negative regulation of miRNA transcription / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / ESR-mediated signaling / transcription corepressor binding / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / euchromatin / negative regulation of DNA-binding transcription factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / transcription coactivator binding / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / Regulation of RUNX2 expression and activity / male gonad development / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / regulation of inflammatory response / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / transcription regulator complex / Estrogen-dependent gene expression / 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 transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / 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 ...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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ligand-binding domain of nuclear hormone receptor / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Chem-KN3 / 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: 2.296 Å
データ登録者Bruning, J. / Parent, A.A. / Gil, G. / Zhao, M. / Nowak, J. / Pace, M.C. / Smith, C.L. / Afonine, P.V. / Adams, P.D. / Katzenellenbogen, J.A. / Nettles, K.W.
引用ジャーナル: Nat.Chem.Biol. / 年: 2010
タイトル: Coupling of receptor conformation and ligand orientation determine graded activity.
著者: Bruning, J.B. / Parent, A.A. / Gil, G. / Zhao, M. / Nowak, J. / Pace, M.C. / Smith, C.L. / Afonine, P.V. / Adams, P.D. / Katzenellenbogen, J.A. / Nettles, K.W.
履歴
登録2010年9月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年11月10日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22021年10月6日Group: Database references / Derived calculations / カテゴリ: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.32024年2月21日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,3128
ポリマ－117,8624
非ポリマー1,4494
水5,603311
1
A: Estrogen receptor
C: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,6564
ポリマ－58,9312
非ポリマー7252
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-14 kcal/mol
Surface area19390 Å2
手法PISA
2
B: Estrogen receptor
D: Estrogen receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,6564
ポリマ－58,9312
非ポリマー7252
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-15 kcal/mol
Surface area19200 Å2
手法PISA
単位格子
Length a, b, c (Å)53.559, 58.478, 93.319
Angle α, β, γ (deg.)85.88, 74.75, 62.76
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B
112chain C
212chain D

NCSアンサンブル:
ID
1
2

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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: 29465.605 Da / 分子数: 4 / 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) / 参照: UniProt: P03372
#2: 化合物
ChemComp-KN3 / 4-[1-(3-methylbut-2-en-1-yl)-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol


分子量: 362.346 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C19H17F3N2O2
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 311 / 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

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試料調製

結晶マシュー密度: 2.12 Å3/Da / 溶媒含有率: 42.08 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: see publication, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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データ収集

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: 0.9764 Å
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: 0.9764 Å / 相対比: 1
反射解像度: 2.296→38.15 Å / Num. all: 38048 / Num. obs: 38048 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
PHENIXモデル構築
PHENIX(phenix.refine)精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.296→38.15 Å / SU ML: 2.08 / σ(F): 0.15 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.24 1908 5.01 %RANDOM
Rwork0.1963 ---
obs0.1985 38048 87.83 %-
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 / Bsol: 55.96 Å2 / ksol: 0.379 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--3.512 Å2-2.3765 Å2-1.0069 Å2
2---10.774 Å20.1772 Å2
3---14.286 Å2
精密化ステップサイクル: LAST / 解像度: 2.296→38.15 Å
タンパク質核酸リガンド溶媒全体
原子数7315 0 104 311 7730
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0157633
X-RAY DIFFRACTIONf_angle_d1.65610344
X-RAY DIFFRACTIONf_dihedral_angle_d17.9342772
X-RAY DIFFRACTIONf_chiral_restr0.0971212
X-RAY DIFFRACTIONf_plane_restr0.0061280
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1867X-RAY DIFFRACTIONPOSITIONAL
12B1867X-RAY DIFFRACTIONPOSITIONAL0.162
21C1747X-RAY DIFFRACTIONPOSITIONAL
22D1747X-RAY DIFFRACTIONPOSITIONAL0.133
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2965-2.35390.3236970.25581955X-RAY DIFFRACTION65
2.3539-2.41750.32081120.24992197X-RAY DIFFRACTION75
2.4175-2.48870.30971440.22632285X-RAY DIFFRACTION79
2.4887-2.5690.27051340.21962391X-RAY DIFFRACTION81
2.569-2.66080.27761410.20862437X-RAY DIFFRACTION82
2.6608-2.76730.24191140.21032512X-RAY DIFFRACTION86
2.7673-2.89320.24251220.20022573X-RAY DIFFRACTION88
2.8932-3.04560.21241640.19332645X-RAY DIFFRACTION91
3.0456-3.23640.24561250.18712768X-RAY DIFFRACTION93
3.2364-3.48610.261660.18262754X-RAY DIFFRACTION95
3.4861-3.83660.19181340.16792894X-RAY DIFFRACTION97
3.8366-4.39110.1831480.1542904X-RAY DIFFRACTION99
4.3911-5.52960.20231620.1682895X-RAY DIFFRACTION99
5.5296-38.15820.23791450.21112930X-RAY DIFFRACTION99
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)
10.0672-0.06540.01120.016-0.12930.1060.06120.0549-0.0785-0.1176-0.1053-0.36690.10810.25230.00020.14210.03870.01390.17420.01370.25815.1676-26.0594-69.4213
2-0.00070.0020.0081-0.00260.00340.0103-0.18160.1099-0.213-0.0425-0.2881-0.0427-0.1052-0.23620.00010.37120.054-0.10130.34690.06050.7935-18.356-47.8851-66.8561
3-0.0117-0.0070.04050.01540.00050.00180.05310.02120.2295-0.1240.05140.24740.14380.1281-0.00020.1273-0.0071-0.01760.13830.00630.2445-20.8472-39.5756-62.5984
40.1259-0.1211-0.01720.06610.03390.0324-0.04950.22-0.23310.15930.03780.0396-0.08360.1688-0.00170.10810.0083-0.00840.0950.01240.0991-2.1749-31.3815-60.4379
5-0.00250.0043-0.01160-0.00590.0003-0.1482-0.12440.06220.18510.2063-0.0267-0.0213-0.07060.00020.2568-0.0489-0.08740.31330.05390.2112.8204-19.3504-54.4104
60.23920.0398-0.08710.2871-0.33261.54110.3225-0.08740.21180.04580.28370.1035-0.0015-0.20110.45150.09720.0274-0.03980.02680.00170.0317-9.4709-25.6964-64.4193
70.00290.0039-0.0021-0.00270.0118-0.00170.0614-0.0372-0.0692-0.11310.03520.00860.0881-0.0327-0.00010.374-0.0034-0.150.1879-0.04180.2883-16.3183-34.1326-79.6252
80.0506-0.02820.00090.03420.02340.0198-0.0953-0.06680.0618-0.1777-0.04710.04980.09090.3635-0.03890.18080.1815-0.0181-0.7014-0.15420.2061-17.999-37.9675-72.9019
9-0.00380.0036-0.0072-0.00240.02390.00260.0399-0.14470.1006-0.0853-0.16990.19450.10140.0136-00.4178-0.0902-0.11650.3093-0.00610.7466-28.3191-33.5439-68.5822
10-0.0010.00520.02130.013-0.00710.0112-0.24530.0722-0.0006-0.14840.2064-0.0166-0.0383-0.219200.17290.0121-0.04980.16720.01020.1851-21.6782-26.2517-73.4191
110.001-0.0008-0.00210.00220.0037-0.0012-0.076-0.06040.006-0.1766-0.0475-0.06130.10070.0671-0.00010.2219-0.08930.00470.3148-0.03350.231-13.2777-22.8851-81.8432
120.40790.33940.02470.4505-0.06220.4513-0.19150.09750.0511-0.1453-0.171-0.3099-0.16820.1673-0.02980.08430.0190.04180.0915-0.00450.1286-4.0485-20.948-71.8795
130.14880.0776-0.00260.0622-0.0314-0.08650.0194-0.02720.07630.10570.01220.0752-0.01070.00310.00140.7390.5327-0.00060.60920.08490.3458-7.0319-11.1218-55.2799
14-0.01330.0058-0.00480.0121-0.0052-0.00260.00020.024-0.0064-0.0352-0.03080.0247-0.0836-0.0551-00.8839-0.1337-0.23570.7394-0.02811.10060.7778-7.2361-47.9169
150.0034-0.0012-0.00370.00370.00050.0036-0.1157-0.14150.04770.0036-0.05530.02590.04210.08650.00010.381-0.08450.05430.27940.05190.55632.369-8.473-54.3052
160.01960.0039-0.0308-0.0009-0.01590.01320.0968-0.02990.18950.05640.1923-0.006-0.2350.19220.00030.27220.0704-0.12430.32970.0170.25463.2294-11.1036-61.1854
170.21430.23030.24230.38550.01060.33410.0580.0759-0.1242-0.14370.08-0.06560.13130.28880.20040.0065-0.01850.07930.06320.05720.0016-1.9356-12.8142-78.4352
180.0024-0.02280.07460.0823-0.0407-0.0019-0.11870.25870.12860.39740.00010.07440.20450.1201-0.0436-1.0399-0.7881-0.3852-0.4961-0.263-0.0549-18.3422-19.772-66.0845
190.0008-0.0145-0.031-0.00780.00210.00230.27320.0955-0.10210.187-0.010.1359-0.0121-0.2408-0.00010.46070.0366-0.0380.175-0.00110.3169-22.6865-28.5556-54.9864
20-0.010.01430.02850.0339-0.07550.12280.0452-0.39840.1226-0.0613-0.02980.14690.0924-0.1943-0.02120.2741-0.10040.09940.01110.1226-0.0061-5.8982-29.0007-49.7878
210.0041-0.00170.0054-0.0024-0.00480.0018-0.1218-0.0082-0.0205-0.03980.0138-0.0115-0.0654-0.0465-00.3040.11480.01780.18530.01470.393511.9118-26.3626-21.8152
22-0.12150.1979-0.1965-0.12870.01080.1933-0.2237-0.0650.27360.25160.0828-0.1842-0.21360.3445-0.00450.0925-0.0339-0.03710.1305-0.01830.14372.196-12.2584-19.1809
23-0.00890.0041-0.01030.00570.00050.0111-0.01390.17720.2492-0.0142-0.2280.0370.13570.1002-0.00010.31140.0529-0.13350.5382-0.0810.6399-18.54965.6909-22.6127
24-0.00480.005-0.01460.0386-0.03550.01650.0051-0.04120.07710.1551-0.30140.2774-0.06530.03580.00020.111-0.0156-0.02790.1333-0.08340.2187-21.1189-3.0157-26.5284
250.01060.10110.00030.01750.01290.295-0.1424-0.02240.1742-0.1790.01060.03560.02790.1197-0.02580.0715-0.02820.01730.08620.01330.1509-2.0612-11.0995-28.6808
26-0.01460.00550.02810.0102-0.00460.0085-0.16170.132-0.2657-0.19580.01680.16-0.02950.0018-00.23170.02670.08640.26350.01770.2552.9122-23.1087-34.7492
270.0773-0.066-0.08450.1569-0.15680.3613-0.013-0.05340.05310.10540.11910.2667-0.03670.07090.2610.1424-0.00780.03290.10080.00940.0187-9.3353-16.7902-24.6781
28-0.0068-0.0186-0.00660.0152-0.0043-0.00650.012-0.24730.10140.1356-0.0135-0.04140.014-0.046500.1868-0.04270.02930.1055-0.03610.1175-15.6173-5.5085-13.7488
29-0.0009-0.00410.0019-0.001-0.0009-0.0048-0.00210.0435-0.0142-0.05810.0705-0.0495-0.08030.119600.76950.31530.52430.66950.16890.7081-26.479-6.192-14.5254
300.0010.00250.00820.0016-0.0025-0.0025-0.14120.0962-0.1123-0.0651-0.12280.0960.0842-0.0132-0.00030.32340.1208-0.1440.3728-0.17960.8171-28.8699-11.3414-22.7826
310.1295-0.0402-0.04590.0782-0.0010.0045-0.0863-0.31580.18720.24720.1666-0.0227-0.0418-0.22170.03850.06680.02450.05210.04130.00760.1206-21.1263-16.1066-15.3811
320.00160.0045-0.00050.00860.004-0.0003-0.1027-0.0109-0.03870.08860.01740.12780.0217-0.084300.23970.021-0.02130.1948-0.04290.1809-13.0836-19.6452-7.2445
330.07240.0401-0.08720.23110.01670.51790.12120.15570.24290.1954-0.2388-0.38680.56810.0253-0.13040.103-0.0559-0.03050.0385-0.02810.0286-4.2388-22.6543-18.6561
34-0.0024-0.0016-0.00120.00270.00610.00440.0389-0.0166-0.0129-0.08550.03360.09370.01050.04350.00020.93990.0361-0.08970.8873-0.36090.9926-4.9131-33.4781-39.026
350.0045-0.00180.0080.0031-0.0010.0025-0.12710.01040.03520.0519-0.19730.0148-0.06410.0118-00.65120.0909-0.02920.3285-0.05650.44793.0759-34.2441-38.0685
360.0053-0.00260.00390.0080.0031-0.01080.29980.0366-0.30340.03090.07920.05270.09560.315400.20750.01710.05060.1593-0.02530.33682.7469-32.2839-29.1674
370.15470.0788-0.03310.5852-0.15950.07520.04720.00090.02450.3255-0.00880.0036-0.0870.01010.01360.06690.0306-0.01830.1081-0.01310.0682-2.7753-29.1543-11.302
38-0.0477-0.03630.070.02590.02020.1165-0.3109-0.03050.1271-0.3015-0.2625-0.0268-0.0511-0.1436-0.02740.0996-0.02750.05930.0356-0.1081-0.0683-18.3182-22.0513-24.519
390.0068-0.00670.0151-0.0049-0.0029-0.00070.07840.06140.1687-0.2022-0.1070.0582-0.0846-0.2565-00.41530.0186-0.09830.13670.0870.4291-22.3479-13.8906-34.1559
400.0073-0.01050.00440.0055-0.03390.01190.08750.33440.0863-0.0976-0.01610.1783-0.0689-0.07570.00010.320.0228-0.01750.23270.02540.0902-4.9894-13.7068-39.5926
41-0.00280.0732-0.01620.1314-0.0899-0.0058-0.30290.0068-0.0028-0.21860.0438-0.0797-0.08320.0269-0.07070.19330.0768-0.3412-0.09850.5106-1.218-15.91374.5365-83.5861
420.0165-0.0047-0.01690.02580.02050.0234-0.01070.09460.1887-0.2486-0.05890.2505-0.2402-0.01620.00040.14610.0382-0.0050.15410.0270.3009-25.06979.1367-65.3369
43-0.004-0.00150.0032-0.005-0.00150.020.1013-0.03870.05240.1294-0.040.0872-0.1373-0.153800.33050.00080.10740.41060.03550.5788-31.95640.9055-52.5015
440.05270.06820.0315-0.00260.01290.00530.0415-0.04190.0109-0.1032-0.17420.4804-0.18340.0571-0.00550.16660.0317-0.01910.144-0.00860.0546-29.86822.5496-68.968
450.233-0.13-0.05350.0774-0.11060.0605-0.05710.0135-0.09380.15880.03390.39340.14-0.0028-0.2463-0.0024-0.0097-0.07370.0661-0.00320.0299-24.5034-4.4139-70.9573
460.01030.0138-0.00270.002-0.0019-0.0052-0.05650.02740.12760.1864-0.042-0.0313-0.08120.0747-00.2386-0.0062-0.09970.33830.0020.2172-13.79395.1856-52.7665
470-0.11850.02360.0811-0.05510.060.0628-0.25160.14880.23880.1329-0.0827-0.0011-0.16280.02820.15440.13660.02640.203-0.03970.1325-22.07285.8087-51.862
48-0.00780.0027-0.00430.01630.002-0.00030.1017-0.0364-0.04290.06040.1810.0440.0821-0.146600.77420.27760.09230.92370.08460.405-19.8459-3.4615-44.2773
490.02940.0008-0.0084-0.0050.0120.0027-0.1488-0.2458-0.1135-0.0865-0.2002-0.03380.04150.04820.00010.4070.0346-0.04290.24140.01840.0955-19.7834-8.0661-50.2039
50-0.0441-0.0220.0721-0.04080.03990.00950.1372-0.1827-0.1848-0.2014-0.2083-0.05910.02510.16570.02290.12010.0111-0.04990.12650.04090.0975-11.4885-3.7998-56.8616
510.17760.0493-00.2068-0.13030.27580.02350.13720.3437-0.1418-0.2861-0.3966-0.14040.1607-0.21750.0663-0.0644-0.1728-0.0519-0.2441-0.3717-13.471-1.3512-69.8595
520.00680.00090.00550.0132-0.00010.0033-0.11330.10490.0065-0.02530.0234-0.04180.1561-0.0406-00.68870.0353-0.10150.5253-0.15730.7949-25.3638-18.7405-79.6182
530.01040.00080.00040.00380.0020.0048-0.1861-0.13450.003-0.08070.13510.12460.00090.107900.3923-0.08220.05530.22530.01510.171-27.0629-16.2806-88.6554
54-0.00420.00170.0096-0.0024-0.0043-0.0053-0.03950.0152-0.0085-0.0987-0.23080.11070.04230.0935-0.00010.36170.0705-0.07490.2194-0.08380.0982-22.0656-11.5255-84.9295
550.2359-0.36260.28970.67550.17460.2631-0.10410.07230.04220.03430.0617-0.2993-0.4079-0.0255-0.0397-0.071-0.05970.03390.07470.01080.1205-6.17-3.6552-75.6184
56-0.05620.02280.0190.01290.0315-0.02520.0111-0.23330.02410.21960.26570.14350.087-0.29470.03780.0635-0.0022-0.01380.1247-0.01390.0569-18.999-12.0281-61.996
570.0075-0.0038-0.01330.0042-0.0124-0.00340.0382-0.0479-0.2415-0.003-0.1442-0.0287-0.0689-0.2618-00.21140.02590.10510.33350.03630.2354-27.5976-14.3351-55.8782
58-0.0003-0.00310.0021-0.0082-0.0032-0.00010.0626-0.0251-0.0799-0.01360.09240.08-0.02940.07880.00010.47730.25270.02041.12910.16180.5056-35.0467-11.4791-55.1545
59-0.0059-0.00770.00020.00170.0066-0.0008-0.2471-0.1779-0.11090.1641-0.15470.16570.1547-0.0243-0.00030.3444-0.0949-0.00780.30150.06230.3584-36.6058-9.0446-69.5101
60-0.0028-0.00660.00190.00110.0036-0.001-0.0298-0.1621-0.0897-0.09210.01880.11060.0399-0.184600.33050.1616-0.14610.4028-0.0860.5406-38.3323-2.8712-75.2724
61-0.0204-0.01610.00130.0811-0.03220.00880.17030.10690.01260.1721-0.10910.2064-0.0313-0.06-0.02830.1563-0.01230.04120.05420.02350.0466-15.8302-46.9271-5.4394
620.02290.0476-0.0099-0.01860.01040.0070.1710.0881-0.23410.2645-0.0850.40510.12590.04350.00050.1257-0.0960.00850.15340.03080.3038-25.0173-51.5255-23.6817
63-0.0045-0.00540.00620.0037-0.00150.00220.09790.0197-0.02150.01870.02550.06150.0495-0.02500.45630.059-0.16480.53180.02280.3273-31.8594-43.27-36.529
640.024-0.0008-0.02490.10020.04630.1476-0.3152-0.01870.05220.1448-0.39290.63350.2457-0.0841-0.09850.0891-0.01090.11350.14270.0031-0.0922-29.7878-44.8612-20.1449
650.03020.0304-0.01770.01110.01360.023-0.0478-0.0350.4686-0.1989-0.11760.2709-0.20650.1189-0.00020.07670.01220.0720.1863-0.03280.1304-28.3188-35.5448-8.9131
660.08640.0483-0.06370.1810.00050.0527-0.43680.05230.3643-0.22160.11510.2394-0.3886-0.3412-0.0381-1.7593-0.29510.7750.04830.1065-0.2422-21.3061-39.799-25.1676
670.0106-0.0096-0.0024-0.00630.01020.00210.01430.0176-0.0348-0.1060.09130.0365-0.0750.09-0.00020.2528-0.08980.0750.3896-0.07440.096-13.7231-47.668-36.2634
680.01590.1389-0.0494-0.0145-0.00450.06410.10160.2412-0.3809-0.34220.2462-0.0208-0.207-0.18250.01660.2784-0.0855-0.01180.1543-0.06840.1476-22.0071-48.24-37.1611
69-0.0023-0.00240.00370.0023-0.00070.0091-0.04430.03650.0426-0.07950.04560.0403-0.1376-0.184100.7862-0.265-0.08351.15860.05890.539-19.7181-39.0019-44.7715
70-0.01130.0111-0.00220.00770.01350.00840.01460.06330.0590.0589-0.1215-0.08410.17890.0265-0.00020.3852-0.08010.11270.1765-0.01690.2394-19.6672-34.392-38.8621
71-0.0145-0.0357-0.1645-0.03130.1141-0.0770.01460.3816-0.02530.0047-0.0441-0.07870.15370.13960.0064-0.0513-0.03320.48660.06870.021-1.2936-10.8166-39.5207-32.1237
720.11370.0427-0.02360.3838-0.27510.28320.0291-0.25840.1306-0.0353-0.0299-0.37820.0298-0.0022-0.03570.08370.00180.0398-0.02330.02960.0165-13.7676-40.8022-18.3819
730.00280.00020.00580.00390.0033-0.00080.0189-0.1498-0.11720.01310.23-0.0439-0.0201-0.005900.8702-0.16470.15670.88370.44441.162-24.3663-25.4675-8.051
740.0008-0.00430.00650.0072-0.00650.0151-0.02190.06070.04090.0060.0580.09660.11890.220300.3657-0.06680.13540.115-0.0090.3951-21.3797-30.9126-3.5126
750.12550.06680.10720.1516-0.0220.01020.0687-0.0087-0.14480.05290.0038-0.0873-0.08660.0520.02810.0910.0251-0.01810.13630.00620.0913-5.3789-39.2096-14.0214
76-0.03320.01490.013-0.03710.00860.02220.07690.06880.0418-0.1630.09890.22210.0233-0.12920.0623-1.2067-1.2462-0.1129-1.1305-0.4046-0.7111-18.8142-30.3889-27.0739
770.0004-0.00610.00420.0071-0.00550.00560.00880.11890.1946-0.0104-0.1313-0.0501-0.0857-0.08190.00030.2042-0.0459-0.14510.18730.03990.4807-26.0171-28.747-33.017
780.00670.00070.0085-0.00690.00790.00350.0969-0.0724-0.0698-0.0049-0.03040.11190.17630.047900.3048-0.2231-0.13251.0158-0.11310.6518-34.1725-29.4118-34.0983
790.0042-0.00460.00080.0025-0.01370.0086-0.00550.0930.1516-0.0111-0.08380.1136-0.09590.07920.00030.1637-0.01280.0810.26660.01060.4121-36.646-33.5103-18.7572
800.00680.0079-0.0017-0.007-0.0170.0045-0.00940.01940.02050.24140.2192-0.0537-0.0185-0.06460.00030.1104-0.09830.15780.5511-0.20830.5756-38.089-40.8298-13.449
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 306:328)
2X-RAY DIFFRACTION2(chain A and resid 329:335)
3X-RAY DIFFRACTION3(chain A and resid 336:350)
4X-RAY DIFFRACTION4(chain A and resid 351:364)
5X-RAY DIFFRACTION5(chain A and resid 365:374)
6X-RAY DIFFRACTION6(chain A and resid 375:396)
7X-RAY DIFFRACTION7(chain A and resid 397:402)
8X-RAY DIFFRACTION8(chain A and resid 403:412)
9X-RAY DIFFRACTION9(chain A and resid 413:421)
10X-RAY DIFFRACTION10(chain A and resid 422:433)
11X-RAY DIFFRACTION11(chain A and resid 434:437)
12X-RAY DIFFRACTION12(chain A and resid 438:457)
13X-RAY DIFFRACTION13(chain A and resid 458:462)
14X-RAY DIFFRACTION14(chain A and resid 463:468)
15X-RAY DIFFRACTION15(chain A and resid 469:473)
16X-RAY DIFFRACTION16(chain A and resid 474:478)
17X-RAY DIFFRACTION17(chain A and resid 479:512)
18X-RAY DIFFRACTION18(chain A and resid 513:521)
19X-RAY DIFFRACTION19(chain A and resid 522:532)
20X-RAY DIFFRACTION20(chain A and resid 533:546)
21X-RAY DIFFRACTION21(chain B and resid 306:312)
22X-RAY DIFFRACTION22(chain B and resid 313:329)
23X-RAY DIFFRACTION23(chain B and resid 330:335)
24X-RAY DIFFRACTION24(chain B and resid 336:350)
25X-RAY DIFFRACTION25(chain B and resid 351:364)
26X-RAY DIFFRACTION26(chain B and resid 365:374)
27X-RAY DIFFRACTION27(chain B and resid 375:396)
28X-RAY DIFFRACTION28(chain B and resid 397:410)
29X-RAY DIFFRACTION29(chain B and resid 411:415)
30X-RAY DIFFRACTION30(chain B and resid 416:421)
31X-RAY DIFFRACTION31(chain B and resid 422:433)
32X-RAY DIFFRACTION32(chain B and resid 434:437)
33X-RAY DIFFRACTION33(chain B and resid 438:459)
34X-RAY DIFFRACTION34(chain B and resid 460:465)
35X-RAY DIFFRACTION35(chain B and resid 466:471)
36X-RAY DIFFRACTION36(chain B and resid 472:478)
37X-RAY DIFFRACTION37(chain B and resid 479:513)
38X-RAY DIFFRACTION38(chain B and resid 514:521)
39X-RAY DIFFRACTION39(chain B and resid 522:533)
40X-RAY DIFFRACTION40(chain B and resid 534:546)
41X-RAY DIFFRACTION41(chain C and resid 305:320)
42X-RAY DIFFRACTION42(chain C and resid 321:329)
43X-RAY DIFFRACTION43(chain C and resid 330:348)
44X-RAY DIFFRACTION44(chain C and resid 349:363)
45X-RAY DIFFRACTION45(chain C and resid 364:396)
46X-RAY DIFFRACTION46(chain C and resid 397:402)
47X-RAY DIFFRACTION47(chain C and resid 403:411)
48X-RAY DIFFRACTION48(chain C and resid 412:420)
49X-RAY DIFFRACTION49(chain C and resid 421:425)
50X-RAY DIFFRACTION50(chain C and resid 426:435)
51X-RAY DIFFRACTION51(chain C and resid 436:458)
52X-RAY DIFFRACTION52(chain C and resid 459:464)
53X-RAY DIFFRACTION53(chain C and resid 465:470)
54X-RAY DIFFRACTION54(chain C and resid 471:475)
55X-RAY DIFFRACTION55(chain C and resid 476:513)
56X-RAY DIFFRACTION56(chain C and resid 514:519)
57X-RAY DIFFRACTION57(chain C and resid 520:527)
58X-RAY DIFFRACTION58(chain C and resid 528:533)
59X-RAY DIFFRACTION59(chain C and resid 534:540)
60X-RAY DIFFRACTION60(chain C and resid 541:546)
61X-RAY DIFFRACTION61(chain D and resid 305:320)
62X-RAY DIFFRACTION62(chain D and resid 321:329)
63X-RAY DIFFRACTION63(chain D and resid 330:348)
64X-RAY DIFFRACTION64(chain D and resid 349:363)
65X-RAY DIFFRACTION65(chain D and resid 364:378)
66X-RAY DIFFRACTION66(chain D and resid 379:396)
67X-RAY DIFFRACTION67(chain D and resid 397:402)
68X-RAY DIFFRACTION68(chain D and resid 403:411)
69X-RAY DIFFRACTION69(chain D and resid 412:420)
70X-RAY DIFFRACTION70(chain D and resid 421:425)
71X-RAY DIFFRACTION71(chain D and resid 426:436)
72X-RAY DIFFRACTION72(chain D and resid 437:458)
73X-RAY DIFFRACTION73(chain D and resid 459:469)
74X-RAY DIFFRACTION74(chain D and resid 470:476)
75X-RAY DIFFRACTION75(chain D and resid 477:513)
76X-RAY DIFFRACTION76(chain D and resid 514:519)
77X-RAY DIFFRACTION77(chain D and resid 520:525)
78X-RAY DIFFRACTION78(chain D and resid 526:533)
79X-RAY DIFFRACTION79(chain D and resid 534:541)
80X-RAY DIFFRACTION80(chain D and resid 542:547)

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万見について

-
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://pdbjlc1.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