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- PDB-3os8: Estrogen Receptor -

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基本情報

登録情報
データベース: PDB / ID: 3os8
タイトルEstrogen Receptor
要素(Estrogen receptor) x 2
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 / 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-KN0 / 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: 2.031 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_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: 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)119,5528
ポリマ－118,0154
非ポリマー1,5374
水4,810267
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)59,7764
ポリマ－59,0072
非ポリマー7692
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-16 kcal/mol
Surface area19360 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)59,7764
ポリマ－59,0072
非ポリマー7692
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-14 kcal/mol
Surface area19280 Å2
手法PISA
単位格子
Length a, b, c (Å)53.698, 58.569, 93.461
Angle α, β, γ (deg.)80.40, 74.85, 62.79
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 and (resid 306:415 or resid 420:461 or resid 465:547 )
211chain B and (resid 306:415 or resid 420:461 or resid 465:547 )
112chain C and (resid 306:415 or resid 420:461 or resid 465:547 )
212chain D and (resid 306:415 or resid 420:461 or resid 465:547 )

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: 29541.723 Da / 分子数: 2 / 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: 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: 2 / 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
#3: 化合物
ChemComp-KN0 / 4-[1-benzyl-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol


分子量: 384.351 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C21H15F3N2O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 267 / 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: 2.13 Å3/Da / 溶媒含有率: 42.38 %
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: 2.03→38.2 Å / Num. obs: 49173 / % possible obs: 88.8 %

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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: 1.6_289)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: 2.031→38.2 Å / SU ML: 0.26 / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
Rfactor反射数%反射Selection details
Rfree0.2276 2347 5.08 %RANDOM
Rwork0.186 ---
all0.1881 46210 --
obs0.1881 46210 73.36 %-
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: 60.433 Å2 / ksol: 0.36 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--3.0971 Å2-0.9846 Å2-0.394 Å2
2---7.2271 Å2-0.5572 Å2
3---10.3243 Å2
精密化ステップサイクル: LAST / 解像度: 2.031→38.2 Å
タンパク質核酸リガンド溶媒全体
原子数7399 0 112 267 7778
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0047705
X-RAY DIFFRACTIONf_angle_d0.8710449
X-RAY DIFFRACTIONf_dihedral_angle_d16.4652801
X-RAY DIFFRACTIONf_chiral_restr0.0611222
X-RAY DIFFRACTIONf_plane_restr0.0031293
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1833X-RAY DIFFRACTIONPOSITIONAL
12B1833X-RAY DIFFRACTIONPOSITIONAL0.025
21C1758X-RAY DIFFRACTIONPOSITIONAL
22D1758X-RAY DIFFRACTIONPOSITIONAL0.022
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0305-2.0720.3453310.2624627X-RAY DIFFRACTION18
2.072-2.1170.2896370.25981013X-RAY DIFFRACTION29
2.117-2.16630.3418720.24161347X-RAY DIFFRACTION38
2.1663-2.22040.2416840.24291694X-RAY DIFFRACTION48
2.2204-2.28050.29741160.22451958X-RAY DIFFRACTION56
2.2805-2.34760.25591010.22652275X-RAY DIFFRACTION64
2.3476-2.42330.28131440.23012536X-RAY DIFFRACTION73
2.4233-2.50990.22751340.21592761X-RAY DIFFRACTION79
2.5099-2.61040.3071760.21532942X-RAY DIFFRACTION84
2.6104-2.72920.23671570.20753114X-RAY DIFFRACTION88
2.7292-2.8730.24921740.19823163X-RAY DIFFRACTION90
2.873-3.05290.2221990.1873291X-RAY DIFFRACTION94
3.0529-3.28850.21241740.18963340X-RAY DIFFRACTION95
3.2885-3.61920.23441880.17133413X-RAY DIFFRACTION97
3.6192-4.14240.18281930.15043451X-RAY DIFFRACTION98
4.1424-5.21690.19231840.15493448X-RAY DIFFRACTION99
5.2169-38.28160.22131830.18283490X-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)
10.1408-0.1101-0.08970.02410.00510.09380.108-0.06870.15590.0333-0.44890.28030.2351-0.8165-0.00020.3582-0.02270.01240.5257-0.06530.4813-9.587329.2641-20.2526
20.07630.0058-0.36430.10810.12780.063-0.12020.5773-0.92980.3885-0.26330.84560.3233-0.2481-0.00020.3875-0.07440.0040.34060.02980.45080.888314.4608-20.765
30.0320.07880.14350.15440.0970.1397-0.27830.4246-1.45662.0379-0.06390.9710.9521-0.0847-0.0030.46340.03590.01930.4904-0.01490.72821.53870.1861-22.802
40.12670.1507-0.18420.0777-0.25940.0548-0.5151-0.00230.2805-0.17910.1406-0.47060.07940.0802-0.00020.29340.0196-0.05050.33810.02470.402521.05998.7381-28.2225
50.178-0.3214-0.11960.1328-0.60610.6819-0.0228-0.02-0.1235-0.36210.05490.07510.2722-0.358600.2686-0.0365-0.02330.2695-0.00560.26922.735116.9305-29.321
60.0569-0.6825-0.01290.61680.64790.26780.1076-0.0096-0.01920.0194-0.0218-0.08990.0673-0.1226-0.00010.2613-0.0356-0.03430.24890.02020.24697.7323.3418-28.3283
70.0107-0.08030.00240.09490.0538-0.0405-0.11360.188-0.09650.54990.241-0.30370.2954-0.02940.00010.4862-0.0307-0.06860.27790.03850.307417.01210.3752-14.5513
8-0.0004-0.0733-0.07070.0385-0.02360.07020.231-0.3332-1.7585-0.5459-0.313-1.31980.31010.37380.00160.83050.0843-0.07820.4077-0.10530.677328.18111.4279-17.5532
90.02690.0081-0.03580.0521-0.06620.03810.48090.4482-0.03220.1335-1.1468-1.48180.08290.34850.00010.41470.0499-0.00020.63330.00910.780230.235619.222-22.9338
100.0856-0.08690.01980.15350.11320.0179-0.2031-0.5063-0.06690.68020.3425-0.53540.03710.4300.32150.022-0.13440.31670.01290.421521.542421.1506-15.6595
11-0.0002-0.0106-0.08760.05230.03730.03660.1161-0.0268-0.89030.2276-0.76050.720.9361.1653-0.00040.51170.0767-0.01750.4586-0.00020.436814.474324.4523-8.0115
120.8046-0.2491.17230.82040.84910.9409-0.04310.05210.03080.0260.14050.3011-0.2956-0.0793-0.00010.2673-0.03360.03590.2497-0.00330.26575.597327.5059-19.442
130.03050.00180.0043-0.0161-0.0462-0.01650.1738-0.71210.7708-1.2115-0.7155-0.3195-0.93260.64320.00021.6178-0.2233-0.07730.94210.16541.06384.701738.9914-40.1858
140.0764-0.08510.0104-0.01870.010.007-0.22870.07970.11910.8479-0.1341-0.89220.5597-1.11590.0010.59930.13150.03830.5784-0.10560.6014-0.853638.2772-37.8788
150.0930.1157-0.5131.24211.44780.6624-0.0691-0.02240.28740.0456-0.08670.3351-0.2156-0.2035-0.00010.2676-0.01770.03060.3713-0.02110.3368-0.653435.3306-14.4745
160.1131-0.1775-0.2814-0.3306-0.0976-0.0118-0.062-0.02220.10480.18430.0490.04410.03960.099100.22250.0055-0.02390.2376-0.04450.256713.282931.7044-16.6465
170.0539-0.1072-0.1380.02440.03660.01010.119-0.1812-0.0677-0.7491-0.02830.0635-1.04070.5370.00010.3462-0.00270.01930.21050.01610.20722.62822.9434-31.1366
180.00730.012-0.01560.00740.04870.0191-0.6548-0.1935-0.1851-0.75420.15950.459-0.18120.8866-0.00071.28440.2776-0.10840.405-0.02181.09823.037314.8256-37.7451
190.0258-0.0354-0.083-0.0134-0.0230.08820.64431.2769-0.8718-0.453-0.34080.26340.05270.23710.00010.38480.0772-0.00660.3707-0.03760.2810.29619.6433-40.6174
200.06680.0450.0190.1482-0.02450.014-0.63661.4005-0.78660.4904-0.9990.70090.72520.2246-0.0020.6508-0.03340.04060.5151-0.12970.48641.579617.0409-40.5091
210.13850.0238-0.07350.034-0.1809-0.02450.11530.3714-0.1953-0.2114-0.06251.11430.1975-0.34850.00040.334-0.01480.03550.3951-0.00430.4071-9.61423.0609-70.4294
22-0.17440.19420.16320.1170.10970.1225-0.2559-0.29130.922-0.56250.14920.9305-0.4321-0.2312-0.00020.35230.035-0.01620.32710.00310.44730.813137.9022-69.9735
230.0315-0.0412-0.10290.12090.13830.0733-0.18-0.5091.3295-1.4546-0.16980.19460.1125-0.0797-0.00030.26410.0164-0.02520.44640.0530.625121.162852.1131-67.6292
240.1099-0.02260.12510.2626-0.44740.3226-0.1443-0.1216-0.41240.0976-0.5612-0.57030.00410.1431-0.00030.2690.00860.00090.3330.10060.387521.483843.6301-62.4978
250.16710.2915-0.2310.1172-0.05890.3830.0889-0.20060.22830.276-0.0881-0.0433-0.1965-0.331900.24990.02950.00080.2520.00180.24052.688935.4549-61.415
26-0.40771.0188-0.66950.4693-0.4495-0.10750.00730.10720.156-0.11470.12210.07780.0568-0.2061-0.00010.259500.03720.25840.00920.22957.702229.0569-62.4036
270.23570.2379-0.1460.2293-0.08230.0005-0.115-0.07160.2764-0.44960.1294-0.0113-0.30380.18560.00010.4441-0.017-0.00230.27730.04650.318316.909442.0225-76.2325
280.0874-0.03340.08090.008-0.09860.08140.3838-0.3192-0.12610.3797-0.6196-1.3125-0.0766-0.053800.7018-0.14460.00580.45490.02150.726628.974938.7258-71.0007
290.26870.1457-0.3130.163-0.13830.1031-0.13980.4843-0.2441-0.45530.2064-0.10710.00940.36650.00010.2837-0.00760.08270.2767-0.00510.315422.440431.4403-74.555
300.1893-0.04220.17180.0343-0.04250.0396-0.291-0.3926-0.393-0.5658-0.46940.11980.09820.00620.00020.3926-0.05130.01170.38310.03750.411913.782627.2799-82.8319
310.0766-0.0338-0.05590.05330.10510.02860.1708-0.11580.3487-0.32790.1905-0.43570.457-0.2455-0.00030.39740.0755-0.03990.27080.0370.31873.885928.8042-78.9866
320.03210.0849-0.44230.26460.2350.5217-0.1459-0.23810.17580.00320.0670.07910.3879-0.09310.00010.25290.01620.01120.2901-0.02960.30696.162122.2979-65.0408
330.0196-0.03110.0129-0.0367-0.01170.0312-0.4190.1864-0.0860.7009-0.08560.02780.27450.418-0.00021.16060.34430.26160.71870.14750.53274.628113.2819-50.6513
34-0.0345-0.05360.0779-0.0093-0.18760.24570.0390.3015-0.68710.1180.1814-0.23550.8255-1.216700.5138-0.11530.0590.41370.04830.4762-1.23114.3589-57.1136
35-0.0593-0.18090.1016-0.0933-0.27420.1315-0.1271-0.04360.0506-0.2102-0.16220.06350.2254-0.56740.00030.2571-0.0024-0.01390.31350.00590.3214-2.050518.9173-74.8574
360.2770.15550.07420.145-0.11540.39590.2082-0.1106-0.18590.04280.08960.211-0.0750.1225-0.00040.29880.0375-0.05390.28480.02020.20592.756215.922-85.3321
370.2131-0.16270.12980.2334-0.16610.04720.0414-0.135-0.385-0.29120.1721-0.4013-0.39410.1350.00020.2648-0.01180.00830.2337-0.01910.26712.870820.4028-73.3857
380.46720.2903-0.54270.2596-0.37210.45280.1737-0.07130.15130.1368-0.2693-0.3690.02580.2102-00.2981-0.0401-0.05410.2176-0.00220.349623.003830.7323-59.2448
390.1255-0.09790.07980.1096-0.0366-0.004-0.0668-1.3966-0.16-0.0474-0.384-0.5533-0.1570.27640.00010.5307-0.0899-0.0230.428-0.00910.344711.747833.7151-50.8169
40-0.0178-0.05780.03240.0554-0.0162-0.0263-0.1215-1.24110.9205-0.7051-0.32710.3717-0.3598-0.3197-0.00070.67190.03490.06120.455-0.14970.44091.219135.0202-50.6206
41-0.04020.22730.12790.40780.16490.51230.0285-0.10660.24880.2349-0.0261-0.0982-0.45050.06030.00010.36920.0206-0.00440.3071-0.04670.311220.274553.6496-12.556
42-0.0464-0.013-0.06020.0640.14150.10350.1101-0.2541-0.3325-0.38560.0515-0.3952-0.27750.4473-00.5305-0.08390.13030.5187-0.0130.460532.968549.2264-37.4767
43-0.0149-0.04690.1291-0.1335-0.17930.2486-0.0415-0.0087-0.12710.1273-0.263-0.77130.15120.3983-0.00020.2974-0.01840.02330.31420.02010.317832.563649.6667-24.741
440.56450.41870.22830.13110.24230.8942-0.07130.029-0.2009-0.0232-0.07810.3577-0.1570.3767-00.3314-0.0115-0.01420.35910.01120.247929.288644.392-10.4614
450.0316-0.0149-0.2853-0.29270.20220.83670.03620.0745-0.08820.0339-0.0262-0.0718-0.07950.178100.2362-0.0318-0.01980.2811-0.02020.285123.329543.8403-24.8496
460.0847-0.09920.01890.1185-0.06190.0253-0.154-1.10030.0292-0.30960.002-0.1481-0.7816-0.2911-0.00010.4503-0.0491-0.07570.62280.01210.287114.974652.566-37.1556
470.12570.0752-0.1454-0.00840.1230.133-0.40520.33820.3253-0.74680.53210.0498-0.01490.381500.4546-0.1085-0.01510.2940.02570.321822.090651.2373-39.8089
480.07410.0123-0.00030.0953-0.0228-0.03590.36890.2893-0.4590.0983-0.1182-0.28311.15670.92850.00091.3620.01330.28571.25750.04860.488424.591742.6291-45.2274
490.0770.00260.0102-0.0078-0.08410.109-0.52570.3047-1.0402-0.1650.54810.5495-0.2796-0.6809-0.00050.5919-0.07210.03760.3749-0.0870.283121.036839.2332-39.6358
50-0.0479-0.07020.1534-0.02140.12170.0878-0.26670.9361-0.17440.10420.18230.5990.266-0.6147-0.00110.2743-0.0318-0.06330.33140.02090.279612.952343.0205-33.8662
510.01810.0899-0.00610.14750.027-0.0243-0.23790.52521.5341-0.22560.02860.0789-0.39720.01840.00080.3597-0.0152-0.05450.40490.02860.30466.943248.5716-28.5812
520.03360.05720.10320.0863-0.120.1286-0.1512-0.0012-0.10170.2520.05280.3995-0.2723-0.28790.00020.35320.0159-0.04210.27160.02540.253713.77350.1401-19.4485
530.2301-0.2357-0.32930.0652-0.12370.2153-0.1041-0.0242-0.2717-0.36540.27310.030.0657-0.317900.2261-0.041-0.01880.22110.01910.19622.415236.1828-14.5492
540.0265-0.02420.0147-0.0042-0.02170.0501-0.4299-0.1579-0.62870.0054-0.738-0.18520.19550.49010.00120.59630.14460.04930.41560.08670.508529.684928.3508-3.2236
550.1323-0.10790.14640.1079-0.08030.1071-0.5967-0.11631.49160.84470.12170.2599-0.0081-0.7514-0.00090.36490.0016-0.00770.3420.01670.20725.092132.9258-3.3307
560.76760.3786-0.4510.2018-0.3380.0325-0.0018-0.0780.1670.297-0.05190.0995-0.1987-0.1535-0.00010.28440.03080.00560.3095-0.03110.3157.697844.8202-10.6085
570.08860.39390.0448-0.09160.86710.0557-0.06390.11140.389-0.09910.02430.1235-0.1026-0.0944-00.22540.01760.0110.2820.02340.286711.419638.9248-23.4397
580.198-0.02470.1680.25860.07520.19420.2878-0.4081-1.2143-0.4178-0.4131-0.6935-0.23410.3268-0.00010.365-0.00510.10020.3817-0.05880.466728.864733.4274-33.9288
590.19360.1448-0.10120.08320.2380.07290.05090.0703-0.39740.020.3263-0.6740.57870.12050.00160.34810.04810.03060.60770.0360.524637.58937.6508-24.7861
600.07160.14530.04240.0931-0.08780.0955-0.53180.68980.2310.91260.6465-1.0982-0.39071.73180.00140.3908-0.1447-0.10760.6266-0.14620.746239.587644.4984-14.5798
610.2234-0.23470.13610.25090.08520.12680.3554-0.32630.2134-0.072-0.32730.1343-0.23040.3228-0.00020.46220.0198-0.01110.3001-0.09330.289917.16251.9854-87.4197
620.31360.22790.08820.1302-0.3101-0.06460.14930.2167-0.2619-0.1259-0.0191-0.2480.8250.30710.00030.38670.04030.01310.3208-0.04420.395723.3464-3.5691-71.209
630.06380.15250.03270.0960.07930.0090.23280.29250.27120.8263-0.3954-0.5316-0.31920.44290.00060.5266-0.0469-0.15630.4759-0.02050.543732.77932.6768-52.0415
640.0494-0.2579-0.36130.0857-0.04450.1371-0.00710.11530.3043-0.0038-0.23-0.11350.08730.2412-0.00020.2766-0.0029-0.02080.2787-0.01360.324332.91313.3388-64.0309
651.35530.13180.66940.38440.12320.852-0.1077-0.00930.1886-0.10620.1026-0.09860.05470.2608-00.23320.02380.04780.24580.01380.23527.019.202-73.7107
66-0.0116-0.0178-0.01560.1022-0.0399-0.0113-0.2665-0.2534-0.68090.55220.1334-1.07640.45560.17780.00050.37770.08180.0220.36390.02950.273615.7198-1.0333-58.4541
67-0.01310.03160.1868-0.01740.18970.2634-0.1152-0.181-0.57430.24420.46230.10090.18330.18330.00030.39680.08160.02220.39440.02940.292921.2253-0.032-52.5257
680.06320.0264-0.04540.0211-0.02170.04490.486-0.45731.20080.53390.99110.4539-1.41430.73970.0010.87640.3409-0.02220.9213-0.01690.353121.75598.3029-44.7592
690.04440.0632-0.02050.0413-0.05990.0296-0.45050.42211.08350.1834-0.40760.4497-0.62250.3847-0.0010.5867-0.0052-0.03620.4426-0.01270.337722.35814.7567-50.2432
700.0504-0.1993-0.1020.06110.41750.10720.2277-0.43680.35950.3223-0.13710.61260.2333-0.3586-0.00030.33970.00560.04680.2901-0.02420.216113.88579.3043-56.213
710.0682-0.0470.03020.1332-0.10120.08720.57020.5003-0.6256-0.4915-0.11210.74760.68740.0162-0.00050.2516-0.07460.09180.291-0.03920.26027.04213.7608-62.2661
720.1010.0279-0.15030.0285-0.10690.25860.05980.0706-0.2358-0.1840.08110.4550.2257-0.05710.00010.37120.01930.03030.270.02020.340313.90072.2898-71.3892
730.1346-0.1266-0.06110.0345-0.0075-0.05850.2115-0.01690.840.5519-0.4327-0.3030.009-0.1665-0.00030.23070.01670.01580.2190.01620.23921.360213.5851-75.3606
740.0246-0.03720.05320.0198-0.08680.0826-0.71920.4242-0.59-0.17122.2249-1.1394-1.28-0.33290.00120.81110.1960.23411.3023-0.23341.400125.783422.176-81.8895
750.10640.11490.00710.09410.04490.11170.66521.04430.997-1.2672-0.1264-1.98480.0646-0.41410.0030.59270.11980.31470.41110.07450.825922.909417.012-86.243
760.9126-0.10730.47720.3964-0.3084-0.17370.25830.2894-0.0006-0.3153-0.07980.22110.1654-0.069500.24870.0026-0.01960.2618-0.0340.30095.74826.4606-79.4219
77-0.16380.02540.03470.00340.4301-0.19450.0407-0.1249-0.03660.0269-0.08210.0220.0908-0.0606-00.2322-0.0024-0.00980.27130.01490.292111.981113.5871-67.1405
780.07440.0266-0.0060.2046-0.02990.242-0.4218-0.31011.4811-0.0571-0.28030.0543-0.39250.43960.00080.33020.0371-0.07620.492-0.04640.424930.095319.0684-56.1326
790.20650.2095-0.00130.16630.0748-0.03240.0332-0.3734-0.18030.04970.2907-0.7142-0.17970.80870.00110.319-0.02070.00340.4399-0.01710.606737.934914.6183-67.8448
800.1121-0.1133-0.02070.02940.04720.1327-0.57230.05490.9028-1.79720.7721-1.06310.42480.98550.00330.40880.13710.15880.6285-0.0740.604939.55386.7236-76.4779
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 306:316)
2X-RAY DIFFRACTION2(chain A and resid 317:328)
3X-RAY DIFFRACTION3(chain A and resid 329:337)
4X-RAY DIFFRACTION4(chain A and resid 338:350)
5X-RAY DIFFRACTION5(chain A and resid 351:366)
6X-RAY DIFFRACTION6(chain A and resid 367:396)
7X-RAY DIFFRACTION7(chain A and resid 397:410)
8X-RAY DIFFRACTION8(chain A and resid 411:417)
9X-RAY DIFFRACTION9(chain A and resid 418:423)
10X-RAY DIFFRACTION10(chain A and resid 424:433)
11X-RAY DIFFRACTION11(chain A and resid 434:437)
12X-RAY DIFFRACTION12(chain A and resid 438:459)
13X-RAY DIFFRACTION13(chain A and resid 460:466)
14X-RAY DIFFRACTION14(chain A and resid 467:472)
15X-RAY DIFFRACTION15(chain A and resid 473:501)
16X-RAY DIFFRACTION16(chain A and resid 502:517)
17X-RAY DIFFRACTION17(chain A and resid 518:526)
18X-RAY DIFFRACTION18(chain A and resid 527:533)
19X-RAY DIFFRACTION19(chain A and resid 534:540)
20X-RAY DIFFRACTION20(chain A and resid 541:546)
21X-RAY DIFFRACTION21(chain B and resid 306:316)
22X-RAY DIFFRACTION22(chain B and resid 317:328)
23X-RAY DIFFRACTION23(chain B and resid 329:337)
24X-RAY DIFFRACTION24(chain B and resid 338:350)
25X-RAY DIFFRACTION25(chain B and resid 351:366)
26X-RAY DIFFRACTION26(chain B and resid 367:396)
27X-RAY DIFFRACTION27(chain B and resid 397:410)
28X-RAY DIFFRACTION28(chain B and resid 411:421)
29X-RAY DIFFRACTION29(chain B and resid 422:433)
30X-RAY DIFFRACTION30(chain B and resid 434:438)
31X-RAY DIFFRACTION31(chain B and resid 439:446)
32X-RAY DIFFRACTION32(chain B and resid 447:459)
33X-RAY DIFFRACTION33(chain B and resid 460:466)
34X-RAY DIFFRACTION34(chain B and resid 467:477)
35X-RAY DIFFRACTION35(chain B and resid 478:491)
36X-RAY DIFFRACTION36(chain B and resid 492:503)
37X-RAY DIFFRACTION37(chain B and resid 504:515)
38X-RAY DIFFRACTION38(chain B and resid 516:531)
39X-RAY DIFFRACTION39(chain B and resid 532:540)
40X-RAY DIFFRACTION40(chain B and resid 541:546)
41X-RAY DIFFRACTION41(chain C and resid 305:328)
42X-RAY DIFFRACTION42(chain C and resid 329:348)
43X-RAY DIFFRACTION43(chain C and resid 349:358)
44X-RAY DIFFRACTION44(chain C and resid 359:376)
45X-RAY DIFFRACTION45(chain C and resid 377:396)
46X-RAY DIFFRACTION46(chain C and resid 397:402)
47X-RAY DIFFRACTION47(chain C and resid 403:413)
48X-RAY DIFFRACTION48(chain C and resid 414:420)
49X-RAY DIFFRACTION49(chain C and resid 421:425)
50X-RAY DIFFRACTION50(chain C and resid 426:434)
51X-RAY DIFFRACTION51(chain C and resid 435:439)
52X-RAY DIFFRACTION52(chain C and resid 440:449)
53X-RAY DIFFRACTION53(chain C and resid 450:461)
54X-RAY DIFFRACTION54(chain C and resid 462:467)
55X-RAY DIFFRACTION55(chain C and resid 468:473)
56X-RAY DIFFRACTION56(chain C and resid 474:501)
57X-RAY DIFFRACTION57(chain C and resid 502:517)
58X-RAY DIFFRACTION58(chain C and resid 518:529)
59X-RAY DIFFRACTION59(chain C and resid 530:540)
60X-RAY DIFFRACTION60(chain C and resid 541:546)
61X-RAY DIFFRACTION61(chain D and resid 305:315)
62X-RAY DIFFRACTION62(chain D and resid 316:328)
63X-RAY DIFFRACTION63(chain D and resid 329:345)
64X-RAY DIFFRACTION64(chain D and resid 346:358)
65X-RAY DIFFRACTION65(chain D and resid 359:393)
66X-RAY DIFFRACTION66(chain D and resid 394:398)
67X-RAY DIFFRACTION67(chain D and resid 399:411)
68X-RAY DIFFRACTION68(chain D and resid 412:418)
69X-RAY DIFFRACTION69(chain D and resid 419:424)
70X-RAY DIFFRACTION70(chain D and resid 425:434)
71X-RAY DIFFRACTION71(chain D and resid 435:439)
72X-RAY DIFFRACTION72(chain D and resid 440:449)
73X-RAY DIFFRACTION73(chain D and resid 450:458)
74X-RAY DIFFRACTION74(chain D and resid 459:469)
75X-RAY DIFFRACTION75(chain D and resid 470:476)
76X-RAY DIFFRACTION76(chain D and resid 477:501)
77X-RAY DIFFRACTION77(chain D and resid 502:518)
78X-RAY DIFFRACTION78(chain D and resid 519:530)
79X-RAY DIFFRACTION79(chain D and resid 531:541)
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://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