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- PDB-3os9: Estrogen Receptor -

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基本情報

登録情報
データベース: PDB / ID: 3os9
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 / nuclear estrogen receptor activity / epithelial cell development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...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 / nuclear estrogen receptor activity / epithelial cell development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / positive regulation of DNA-binding transcription factor activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of DNA-binding transcription factor activity / negative regulation of miRNA transcription / nitric-oxide synthase regulator activity / ESR-mediated signaling / TBP-class protein binding / transcription coregulator binding / nuclear estrogen receptor binding / transcription corepressor binding / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / euchromatin / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / calmodulin binding / 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 / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / 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 / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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 / Double treble clef zinc finger, C4 type / 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-KN1 / 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: 2.303 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 1.22020年2月26日Group: Advisory / Derived calculations
カテゴリ: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
改定 1.32021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 1.42024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)120,53712
ポリマ－117,8624
非ポリマー2,6748
水3,909217
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)60,2686
ポリマ－58,9312
非ポリマー1,3374
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-33 kcal/mol
Surface area19040 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)60,2686
ポリマ－58,9312
非ポリマー1,3374
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-33 kcal/mol
Surface area18340 Å2
手法PISA
単位格子
Length a, b, c (Å)52.904, 59.058, 93.761
Angle α, β, γ (deg.)86.64, 74.64, 63.43
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 306:329 or resid 332:415 or resid 420:461 or resid 465:526 or resid 533:546)
211chain B and (resid 306:329 or resid 332:415 or resid 420:461 or resid 465:526 or resid 533:546)
112chain C and (resid 306:329 or resid 332:415 or resid 420:461 or resid 471:526 or resid 533:546)
212chain D and (resid 306:329 or resid 332:415 or resid 420:461 or resid 471:526 or resid 533:546)

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-KN1 / 4-[1-allyl-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol / WAY-169916


分子量: 334.293 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C17H13F3N2O2
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 217 / 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: 2.14 Å3/Da / 溶媒含有率: 42.48 %
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: 2.303→20 Å / Num. all: 39541 / Num. obs: 39541 / % possible obs: 91.42 % / 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: 2.303→20 Å / SU ML: 0.33 / σ(F): 1.96 / 位相誤差: 28.42 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2491 1975 5.01 %
Rwork0.2048 --
obs0.207 39460 91.42 %
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: 61.197 Å2 / ksol: 0.329 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-5.9713 Å2-2.9478 Å2-1.2047 Å2
2---15.025 Å24.1596 Å2
3---9.0536 Å2
精密化ステップサイクル: LAST / 解像度: 2.303→20 Å
タンパク質核酸リガンド溶媒全体
原子数6961 0 192 217 7370
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0027411
X-RAY DIFFRACTIONf_angle_d0.6710079
X-RAY DIFFRACTIONf_dihedral_angle_d13.7042636
X-RAY DIFFRACTIONf_chiral_restr0.0431168
X-RAY DIFFRACTIONf_plane_restr0.0021226
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1747X-RAY DIFFRACTIONPOSITIONAL
12B1747X-RAY DIFFRACTIONPOSITIONAL0.019
21C1598X-RAY DIFFRACTIONPOSITIONAL
22D1598X-RAY DIFFRACTIONPOSITIONAL0.006
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3026-2.36010.35171060.28891827X-RAY DIFFRACTION63
2.3601-2.42380.33851180.29542290X-RAY DIFFRACTION78
2.4238-2.4950.28821050.27452476X-RAY DIFFRACTION84
2.495-2.57540.30251650.25532601X-RAY DIFFRACTION89
2.5754-2.66720.28961410.23672665X-RAY DIFFRACTION92
2.6672-2.77370.2691500.24562742X-RAY DIFFRACTION94
2.7737-2.89960.27181470.22712792X-RAY DIFFRACTION95
2.8996-3.0520.28471300.22452851X-RAY DIFFRACTION97
3.052-3.24250.27361690.21512854X-RAY DIFFRACTION98
3.2425-3.49160.24971490.19842912X-RAY DIFFRACTION98
3.4916-3.84070.21611460.17442864X-RAY DIFFRACTION98
3.8407-4.39140.19481350.16532920X-RAY DIFFRACTION99
4.3914-5.51350.19961640.17152896X-RAY DIFFRACTION99
5.5135-20.03780.25741500.21122795X-RAY DIFFRACTION95
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)
11.80641.28671.03732.9678-1.97423.98770.04731.85920.2858-0.4787-0.265-1.1302-0.25350.00540.16280.27480.07390.10430.58060.11130.75069.774-20.0086-70.8569
21.9576-1.4195-1.49561.24660.56893.5281-0.7272-0.15590.1112-1.29650.1567-0.4041.10480.49230.4250.53230.0391-0.03030.25670.07880.5436-3.0137-35.9638-68.1811
33.6215-2.062-0.70942.8604-1.4242.56351.50851.0001-1.3328-0.8562-0.4624-1.56350.8292-0.9035-1.14031.5926-0.1896-0.05940.6574-0.15171.46-16.6547-48.7083-65.0602
40.7619-1.4662-0.38974.3831.21640.2822-0.44620.2073-1.0137-0.1895-0.02010.37761.3973-0.09930.29920.7475-0.16740.00320.5804-0.10820.5245-20.7083-40.5307-63.0851
50.9201-0.402-0.05721.2967-0.03610.3771-0.30490.26030.17820.4810.32890.0873-0.0633-0.03150.05990.28170.07670.03850.2776-0.03710.4331-3.1745-31.7553-59.9647
61.641.1639-0.27753.7796-1.21332.60450.3630.0201-0.2745-0.0586-0.1139-0.296-0.02360.0992-0.16380.31090.05260.00180.3534-0.01930.4163-4.8223-23.4896-61.5075
72.0235-0.76631.83368.5787-2.73532.3234-0.2201-0.38490.6364-1.85220.44220.64360.8615-0.39730.060.59690.0375-0.05970.3562-0.01430.6666-15.2215-36.1097-75.3926
86.6869-0.46020.27131.0231-0.37552.12310.07780.748-0.0114-1.16390.2487-0.34540.964-0.1502-0.19930.7342-0.1924-0.19310.5983-0.03230.5642-24.1682-35.5496-74.8603
94.34252.71312.28274.938-1.22774.1368-0.253-1.78570.30010.2974-0.7772-1.0693-0.353-2.35120.62521.0738-0.0056-0.19350.95-0.4031.3032-27.9702-34.697-67.3818
101.64440.97940.64633.4578-2.14912.2278-0.01290.23380.0696-0.69090.40550.6520.2836-0.5228-0.37790.3796-0.0087-0.12050.4139-0.0160.5994-19.2956-24.772-75.2023
115.97460.40251.52122.0887-0.79561.2512-0.82141.56520.0251-1.21540.39380.03260.96550.64680.2930.9632-0.06980.15270.3795-0.01890.4111-4.5733-22.5415-80.8757
120.88380.65320.00750.525-0.24120.8218-0.06610.3054-0.0343-0.0983-0.3859-0.4827-0.0894-0.08980.3370.32420.05130.01190.3938-0.05910.4329-3.7409-19.4019-67.6042
130.4104-0.76021.06831.533-1.94352.71831.8696-1.07881.35281.06440.04411.36550.6904-0.0618-1.28471.51150.24980.2531.42550.30590.7311-5.9656-10.1796-54.5091
141.9127-1.57992.10735.8252-4.89495.33530.20731.23850.9141.6393-1.0455-0.73650.56510.71221.01321.7087-0.07720.00420.7558-0.17760.77243.4081-7.5584-50.6241
159.74656.4953-6.20935.2531-3.94413.96260.8835-0.46272.9511-0.20640.62090.5895-2.4030.8199-0.31940.75830.0259-0.20140.678-0.14540.74422.9654-9.6181-59.6676
161.8993-0.5591-1.17454.4585-0.99231.69050.08270.23910.1616-0.7091-0.0332-0.47630.11470.1735-0.04840.42890.02270.08760.45380.00270.3237-1.275-12.2629-78.1915
174.19161.0124-3.30135.14793.55136.6004-0.69120.3825-0.33580.65390.11680.6890.8067-0.1380.17820.41270.0356-0.01390.33710.01940.5104-18.1202-19.1594-65.1471
183.95223.5769-3.1377.76950.38155.24610.66650.69870.61310.9771-0.5081-0.08720.8604-2.2111-0.09260.9679-0.19420.18970.61570.10371.1946-23.9478-26.5307-55.7327
193.6703-3.17522.37863.93210.15685.89112.4077-1.77251.4068-0.3413-0.7601-1.24811.6271-0.0904-1.24621.2607-0.3920.22580.56380.00360.6349-9.0312-27.1966-48.8534
207.6971-0.72890.89361.04960.66740.9079-0.341-1.68290.6748-1.98510.33160.550.226-0.1118-0.07141.0117-0.11690.00840.5808-0.00950.3952-0.4134-29.3495-50.1722
210.23620.2611-0.95563.0637-2.68864.5872-0.05380.31690.6657-0.1447-1.347-1.31250.36080.43160.99340.37860.04210.03390.69420.05440.686710.0022-22.4619-18.3449
221.50921.80390.24272.13440.86592.8505-0.1701-0.30430.43960.5886-0.1368-0.8334-0.8780.67090.22450.6124-0.104-0.05430.41430.04840.6293-2.9174-6.4077-20.57
234.04442.65311.2191.79180.7530.46250.8608-1.640.71190.9119-0.7466-0.3380.6265-0.12750.15011.381-0.4657-0.21652.28440.61561.2962-16.67635.9766-23.7001
242.52081.3559-0.79483.646-1.85030.9379-0.7021-1.29331.1674-0.71691.56430.15660.72460.6513-0.34591.06970.0130.02550.658-0.26330.9672-25.78060.6251-23.5449
258.12764.68040.56126.92890.69141.9695-0.3796-1.39881.1504-0.9035-0.281.36680.94480.38950.83640.58420.096-0.02340.7915-0.19510.6356-20.7845-3.4272-26.735
264.39961.7987-0.52491.81451.36362.93410.14990.7557-0.7593-0.45930.0382-0.2596-0.067-0.3994-0.22150.5693-0.0632-0.02310.3744-0.00710.4083-8.9546-6.377-28.9233
271.5027-0.44221.35432.4686-0.76271.3450.20420.02820.0507-0.0478-0.1422-0.0750.17470.0623-0.0530.311-0.00530.02380.3412-0.01190.3946-3.9326-18.1253-27.4439
281.5657-0.8632-1.43356.7215-2.77753.3472-0.05710.03530.29692.61650.3850.4098-1.6584-0.1879-0.13890.77060.01590.05390.3387-0.1010.5335-16.2472-5.9663-13.4449
292.4076-1.75131.34671.2175-0.88030.86611.20911.9612-1.3130.03180.11631.1148-0.1171-1.0951-0.91230.56220.14770.28010.83590.0061.4326-27.6126-8.5942-16.9629
302.0305-2.1063.4292.0362-7.9882.0061-1.3039-2.25252.7020.24742.02230.39921.5962-3.1932-0.71910.1557-0.16590.11070.72720.20151.0217-25.1014-14.8245-19.5376
313.1582-1.22791.6432.7254-1.30331.336-0.386-0.98620.41720.70820.35670.3122-1.2784-0.3792-0.07840.62570.0344-0.01160.4457-0.00760.4039-15.5068-19.3901-10.2844
323.4186-1.4829-2.57320.65960.94632.4376-0.93580.1096-0.57911.642-0.64360.38941.8093-0.50961.04420.8283-0.0882-0.02510.3825-0.10280.629-2.8602-19.1681-10.7047
331.8569-0.08060.49381.3852-2.29326.7666-0.4009-0.08030.3163-0.1611-0.61920.17081.0487-0.30340.74420.3694-0.05990.0370.3146-0.11230.521-4.1236-24.6514-24.0364
342.3145-2.027-0.94381.67550.54732.28230.41030.3188-2.3309-0.5966-0.75410.36492.03740.21520.00071.1803-0.1473-0.04690.72720.21111.0252-1.3821-32.9817-35.2855
357.804-7.59631.13139.901-3.60072.71990.9413-0.6082-2.1923-0.2609-0.0566-0.09242.17362.5356-0.45260.596-0.02750.05270.5818-0.09210.58663.3046-32.7891-28.8479
360.20930.7051.49532.20342.62645.60.2130.0001-0.140.6815-0.0172-0.57040.92331.4229-0.19650.4764-0.0668-0.04480.5533-0.02160.43593.7734-28.4485-12.8884
371.86130.62971.32090.45710.3921-0.0052-0.1446-0.3760.08230.42140.01630.10840.3314-0.15080.14060.49570.05240.03430.40590.02130.3406-8.547-29.5195-11.8275
385.9012-2.80974.6944.4195-1.1914.07330.0692-0.46360.012-2.7973-0.26882.2497-1.1648-2.27950.01720.446-0.0515-0.27790.38770.01141.0614-21.0201-20.8207-28.443
394.578-1.9773.79899.7285-0.40755.85650.492-1.3961-1.933-1.695-1.53720.3264-0.147-1.9840.67340.85030.1173-0.28380.4950.19711.3126-23.2915-15.2114-34.0104
404.2779-0.0321.12854.1418-2.81032.44151.27571.60070.6074-1.5496-0.19221.07250.685-0.2899-0.71390.89730.21490.010.38230.04630.3686-4.5518-14.0446-39.2186
413.21810.15931.77760.99020.49494.278-1.19091.08810.44670.27180.4591-0.0489-0.20231.64310.40831.0266-0.0267-0.04590.31380.05260.1074-15.88232.3603-88.018
421.4545-0.1914-0.46391.9060.38450.35440.4010.07360.374-2.2871-0.38390.08010.07520.3913-0.0421.0053-0.00930.07260.34030.02020.2496-15.00937.9793-79.8331
432.5489-0.2064-0.39193.22583.10143.22580.42940.29760.1346-0.8315-0.26020.3172-2.73120.2339-0.1070.61540.09350.04370.38450.06320.5686-24.469810.4521-65.4319
441.5343-0.475-0.55281.17120.18021.16671.38030.33250.2554-0.0634-0.75640.6260.80321.6385-0.35350.6419-0.1450.25680.73570.12650.7324-31.68024.4812-50.1211
450.3271-0.12940.58011.90371.14960.98620.0216-0.2801-0.8510.0258-0.35970.88780.1379-0.34610.18130.25150.07870.09860.3920.02490.6974-31.01873.2694-62.9238
467.69323.6847-1.41918.6858-1.10945.3948-1.00540.93681.5981-1.64641.40550.8131-3.9679-0.92890.24670.83060.1499-0.17090.4821-0.01730.316-26.83044.3255-75.8441
470.64090.5328-0.42350.8003-0.48870.635-0.1245-0.0797-0.419-0.53330.1687-0.07620.1843-0.313-0.03350.49290.0023-0.16790.4635-0.04420.5851-28.2149-5.5779-79.6534
483.0722-2.11-0.17572.868-0.0142.1506-0.1686-0.105-0.12690.41560.5208-0.2131-0.28580.2906-0.23780.35850.06420.0390.3430.01670.2794-19.66652.3001-58.755
494.02590.2195-1.93920.29480.24611.29320.7323-1.17150.5296-0.6065-0.69820.2888-2.2282-0.3521-0.13441.2830.0014-0.1620.75430.03710.3694-19.001-1.9843-45.4712
503.3042.8938-1.64984.033-1.75932.26030.3819-0.1621-0.66770.959-0.2675-0.53950.033-0.2787-0.17750.5122-0.0082-0.00380.39180.10650.4252-13.6379-4.4556-54.4386
515.3341-0.3216-2.78360.11450.07571.4663-0.1502-1.08530.4816-0.50990.40880.21160.36210.6945-0.00350.6734-0.092-0.030.55010.06410.3332-5.28782.0085-61.1194
522.34180.238-0.53041.33980.14350.38350.63370.3626-0.24110.4101-0.2599-0.035-0.3115-0.1634-0.23780.4976-0.0544-0.06630.2958-0.03710.2593-15.5602-1.2146-72.0767
534.2627-0.25173.33921.54860.53062.9421-1.39910.09220.20620.11830.1548-0.56131.4130.32370.7980.95130.02350.31960.84930.01091.2197-24.9631-17.3966-78.8578
540.74160.1221-0.64560.16810.20331.4217-0.7014-0.12920.3443-0.5540.7333-0.28481.22310.1448-0.00820.9518-0.134-0.23770.4906-0.07710.8909-26.4013-14.5079-87.3745
554.71620.8593-0.40527.1388-3.25664.9923-0.51260.6860.1569-2.50530.5963-0.16762.35621.2887-0.16820.7103-0.0142-0.07170.41460.02020.4072-17.2673-8.2492-83.9116
562.9719-2.97731.48043.8605-0.34523.3274-0.16790.240.5277-0.2347-0.01-0.6338-0.36050.54730.16140.3627-0.08760.06730.4091-0.00260.377-3.3847-1.5224-74.844
571.182-0.1895-0.70613.59841.40410.7833-0.03180.0419-0.4140.9175-0.0380.3949-0.10970.2346-0.04840.3540.04850.01830.33850.05030.3961-17.6203-11.2472-61.042
582.5976-1.0665-2.17312.52973.09124.1242-1.5488-0.9927-2.25510.6153-0.79430.69850.5432-0.30131.55671.6333-0.3047-0.1170.71180.35751.4971-28.3895-13.5553-56.4042
594.0063-1.75791.43837.8427-1.96211.04860.6514-0.29651.843-1.8488-0.30341.70621.23040.1363-0.31051.1647-0.18570.20051.0024-0.23421.8511-36.1982-8.9514-66.0729
600.4980.3534-0.24270.5767-0.98512.8710.1359-0.60640.9235-1.05931.06490.9944-0.1825-2.5705-0.92790.45030.0991-0.28170.9209-0.25351.4602-37.2135-1.8084-74.5776
612.39181.63970.36493.04820.64690.32590.3775-1.3520.22220.3594-0.9052-1.3454-0.12510.58210.49821.2945-0.13780.09990.58070.03880.2197-14.7255-46.0312-1.5862
620.9101-0.55680.79790.4722-0.53550.6830.10020.0458-0.8021-0.12470.29450.9874-0.2507-1.2523-0.47290.9168-0.07590.02160.36350.02810.2179-15.8675-50.0682-9.2687
632.57470.42760.19081.21040.38050.9795-0.4050.57320.48550.431-0.31541.0344-0.01480.54290.49950.4161-0.0735-0.08290.35010.08580.7777-25.0528-52.7348-24.0704
643.4222-1.493.77894.9322-0.27254.5597-0.3434-1.5752-0.1765-0.5780.72582.0668-0.8259-1.145-0.3720.4478-0.0372-0.22640.33470.13070.8796-31.4874-44.7075-34.8549
650.2818-0.0202-0.00280.20370.19321.881-0.68-0.07570.55960.0219-0.82890.94590.23280.2821.08760.3942-0.1472-0.04810.3939-0.01951.1637-30.8745-45.8632-22.6946
662.4308-1.2645-2.13911.13462.67178.0217-0.59750.0856-0.92371.5550.43960.45093.5853-0.07140.83010.6161-0.09930.29910.4258-0.0230.5439-26.8293-46.5821-12.8861
671.41021.1942-0.04072.2968-1.70141.23540.26470.07140.59320.1868-0.03740.82650.0109-0.1034-0.18640.2961-0.06430.10370.3638-0.06130.6171-24.6399-38.6759-17.4252
684.39753.62740.80667.4253.35962.08841.38581.2334-1.32240.22571.759-0.3425-0.880.096-1.54380.8099-0.04870.01940.7036-0.17240.673-11.6254-48.981-34.8263
692.1621-0.54321.85321.56611.55835.2066-0.35330.3382-1.4003-0.50270.64260.1357-0.954-0.3064-0.1270.5373-0.1249-0.07150.3830.02180.4547-21.6926-49.5369-36.0197
704.69543.33293.22643.00610.74656.4746-0.09551.0656-0.0482-0.91720.87250.32581.51441.8111-0.81671.361-0.1796-0.03920.81740.00690.5763-18.3401-40.834-43.7757
710.80950.9058-0.32731.7616-0.13020.5297-0.39881.105-0.325-0.64820.44620.3656-0.80690.097-0.07570.5999-0.0250.01390.45110.09810.2895-13.1177-38.3988-33.4822
722.8213.4068-1.94884.8458-0.06218.3492-1.03550.8092-1.6918-0.4296-0.0884-0.6965-0.9156-0.51710.88810.56160.0750.01940.50910.00960.477-5.1889-45.8031-25.9023
733.5518-2.0546-0.27365.86051.330.63310.3152-0.72940.30070.05240.1702-0.21140.2538-0.0331-0.37720.59250.00830.14460.3483-0.05850.3084-16.5697-40.1867-15.9926
742.891-2.505-0.57773.51461.75741.2415-1.38-0.5103-0.25911.25610.06911.54910.13040.7661.03291.0117-0.2748-0.01441.08750.09861.5228-23.664-27.6555-6.3257
750.5194-0.0625-0.75364.170.04071.9099-0.1827-1.7183-0.2579-0.1116-0.97531.16910.42450.35660.76010.920.10830.25580.3687-0.06520.7654-19.6075-31.9886-4.286
765.9963-3.5691-1.98896.35142.11750.88970.0748-0.82511.06210.91990.1693-0.80150.20960.3135-0.11420.48460.0214-0.01610.3180.00280.3027-6.145-42.3946-9.3242
770.1770.0799-0.03881.1887-0.33971.85750.22910.8424-0.5055-0.064-0.40090.25040.15070.74790.26710.27910.0205-0.05030.38250.01640.336-2.6921-37.3836-17.4875
783.50193.46161.62156.96761.46653.8807-0.0379-0.15751.2135-0.8462-0.34151.25140.27730.63950.35550.3825-0.0436-0.0190.3670.09320.4793-18.4262-31.003-27.7944
794.30662.20283.68516.06914.66148.3673-2.5319-1.321-0.3429-0.7477-1.37511.5648-1.3225-2.71552.11260.75950.2397-0.21360.83230.33981.4539-33.355-31.2083-25.2918
803.74480.1693-2.09212.0306-0.42471.2149-0.6427-0.31512.79071.529-0.04810.4280.6696-1.09170.40410.7617-0.14450.29940.8784-0.58051.7627-36.8254-39.0516-16.2001
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 307:320
2X-RAY DIFFRACTION2chain A and resid 321:329
3X-RAY DIFFRACTION3chain A and resid 330:334
4X-RAY DIFFRACTION4chain A and resid 335:350
5X-RAY DIFFRACTION5chain A and resid 351:362
6X-RAY DIFFRACTION6chain A and resid 363:396
7X-RAY DIFFRACTION7chain A and resid 397:408
8X-RAY DIFFRACTION8chain A and resid 409:413
9X-RAY DIFFRACTION9chain A and resid 414:420
10X-RAY DIFFRACTION10chain A and resid 421:437
11X-RAY DIFFRACTION11chain A and resid 438:443
12X-RAY DIFFRACTION12chain A and resid 444:457
13X-RAY DIFFRACTION13chain A and resid 458:464
14X-RAY DIFFRACTION14chain A and resid 465:471
15X-RAY DIFFRACTION15chain A and resid 472:477
16X-RAY DIFFRACTION16chain A and resid 478:511
17X-RAY DIFFRACTION17chain A and resid 512:522
18X-RAY DIFFRACTION18chain A and resid 523:533
19X-RAY DIFFRACTION19chain A and resid 534:539
20X-RAY DIFFRACTION20chain A and resid 540:546
21X-RAY DIFFRACTION21chain B and resid 306:320
22X-RAY DIFFRACTION22chain B and resid 321:329
23X-RAY DIFFRACTION23chain B and resid 330:334
24X-RAY DIFFRACTION24chain B and resid 335:340
25X-RAY DIFFRACTION25chain B and resid 341:346
26X-RAY DIFFRACTION26chain B and resid 347:356
27X-RAY DIFFRACTION27chain B and resid 357:396
28X-RAY DIFFRACTION28chain B and resid 397:411
29X-RAY DIFFRACTION29chain B and resid 412:420
30X-RAY DIFFRACTION30chain B and resid 421:426
31X-RAY DIFFRACTION31chain B and resid 427:438
32X-RAY DIFFRACTION32chain B and resid 439:446
33X-RAY DIFFRACTION33chain B and resid 447:458
34X-RAY DIFFRACTION34chain B and resid 459:471
35X-RAY DIFFRACTION35chain B and resid 472:478
36X-RAY DIFFRACTION36chain B and resid 479:493
37X-RAY DIFFRACTION37chain B and resid 494:517
38X-RAY DIFFRACTION38chain B and resid 518:523
39X-RAY DIFFRACTION39chain B and resid 524:533
40X-RAY DIFFRACTION40chain B and resid 534:546
41X-RAY DIFFRACTION41chain C and resid 305:312
42X-RAY DIFFRACTION42chain C and resid 313:320
43X-RAY DIFFRACTION43chain C and resid 321:329
44X-RAY DIFFRACTION44chain C and resid 330:345
45X-RAY DIFFRACTION45chain C and resid 346:358
46X-RAY DIFFRACTION46chain C and resid 359:363
47X-RAY DIFFRACTION47chain C and resid 364:379
48X-RAY DIFFRACTION48chain C and resid 380:410
49X-RAY DIFFRACTION49chain C and resid 411:422
50X-RAY DIFFRACTION50chain C and resid 423:434
51X-RAY DIFFRACTION51chain C and resid 435:439
52X-RAY DIFFRACTION52chain C and resid 440:458
53X-RAY DIFFRACTION53chain C and resid 459:464
54X-RAY DIFFRACTION54chain C and resid 465:472
55X-RAY DIFFRACTION55chain C and resid 473:480
56X-RAY DIFFRACTION56chain C and resid 481:511
57X-RAY DIFFRACTION57chain C and resid 512:521
58X-RAY DIFFRACTION58chain C and resid 522:526
59X-RAY DIFFRACTION59chain C and resid 527:539
60X-RAY DIFFRACTION60chain C and resid 540:546
61X-RAY DIFFRACTION61chain D and resid 306:313
62X-RAY DIFFRACTION62chain D and resid 314:320
63X-RAY DIFFRACTION63chain D and resid 321:330
64X-RAY DIFFRACTION64chain D and resid 341:350
65X-RAY DIFFRACTION65chain D and resid 351:358
66X-RAY DIFFRACTION66chain D and resid 359:363
67X-RAY DIFFRACTION67chain D and resid 364:395
68X-RAY DIFFRACTION68chain D and resid 396:401
69X-RAY DIFFRACTION69chain D and resid 402:410
70X-RAY DIFFRACTION70chain D and resid 411:422
71X-RAY DIFFRACTION71chain D and resid 423:435
72X-RAY DIFFRACTION72chain D and resid 436:441
73X-RAY DIFFRACTION73chain D and resid 442:458
74X-RAY DIFFRACTION74chain D and resid 459:471
75X-RAY DIFFRACTION75chain D and resid 472:476
76X-RAY DIFFRACTION76chain D and resid 477:497
77X-RAY DIFFRACTION77chain D and resid 498:511
78X-RAY DIFFRACTION78chain D and resid 512:522
79X-RAY DIFFRACTION79chain D and resid 523:538
80X-RAY DIFFRACTION80chain D and resid 539:544

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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://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