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- PDB-5kra: 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: 5kra
タイトルCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with DDT and DDE
要素
  • Estrogen receptor
  • NCOA2
キーワードTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
機能・相同性
機能・相同性情報


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / estrogen receptor signaling pathway / cellular response to estrogen stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / regulation of cellular response to insulin stimulus / 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 / Recycling of bile acids and salts / negative regulation of miRNA transcription / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / RORA activates gene expression / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / Regulation of lipid metabolism by PPARalpha / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / PPARA activates gene expression / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / euchromatin / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / negative regulation of DNA-binding transcription factor activity / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / nuclear receptor activity / 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 / Circadian Clock / regulation of inflammatory response / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / HATs acetylate histones / 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
類似検索 - 分子機能
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / : / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / 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-6WS / Chem-6WT / Estrogen receptor / Nuclear receptor coactivator 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.401 Å
データ登録者Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
引用ジャーナル: Cell Chem Biol / 年: 2017
タイトル: Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
著者: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / ...著者: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
履歴
登録2016年7月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年2月15日Provider: repository / タイプ: Initial release
改定 1.12024年3月6日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: NCOA2
D: NCOA2
E: Estrogen receptor
F: Estrogen receptor
G: NCOA2
H: NCOA2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)125,21112
ポリマ－123,8668
非ポリマー1,3454
水5,332296
1
A: Estrogen receptor
B: Estrogen receptor
C: NCOA2
D: NCOA2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,6056
ポリマ－61,9334
非ポリマー6732
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-29 kcal/mol
Surface area19760 Å2
手法PISA
2
E: Estrogen receptor
F: Estrogen receptor
G: NCOA2
H: NCOA2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,6056
ポリマ－61,9334
非ポリマー6732
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-29 kcal/mol
Surface area19790 Å2
手法PISA
単位格子
Length a, b, c (Å)58.580, 82.960, 104.970
Angle α, β, γ (deg.)90.00, 101.12, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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


分子量: 29299.535 Da / 分子数: 4 / 断片: ligand-binding domain / 変異: Y537S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ESR1, ESR, NR3A1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P03372
#2: タンパク質・ペプチド
NCOA2


分子量: 1666.943 Da / 分子数: 4 / 断片: Nuclear receptor-interacting peptide / 由来タイプ: 合成 / 詳細: This sequence occurs naturally in humans / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q15596*PLUS
#3: 化合物 ChemComp-6WS / 1-[2,2-bis(chloranyl)-1-(4-chlorophenyl)ethenyl]-4-chloranyl-benzene / 2,2-ビス(4-クロロフェニル)-1,1-ジクロロエチレン


分子量: 318.025 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C14H8Cl4
#4: 化合物 ChemComp-6WT / 1-chloranyl-4-[2,2,2-tris(chloranyl)-1-(4-chlorophenyl)ethyl]benzene / DDT


分子量: 354.486 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C14H9Cl5
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 296 / 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: 2.03 Å3/Da / 溶媒含有率: 39.3 % / Mosaicity: 0.638 °
結晶化温度: 294 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.3 / 詳細: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SSRL / ビームライン: BL11-1 / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2011年12月14日
放射モノクロメーター: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.4→50 Å / Num. obs: 37877 / % possible obs: 98 % / 冗長度: 3.4 % / Biso Wilson estimate: 26.49 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Χ2: 0.54 / Net I/av σ(I): 12.79 / Net I/σ(I): 4.5 / Num. measured all: 128694
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.443.40.4780.972195.6
2.44-2.493.40.4420.869196.4
2.49-2.533.40.4230.859197.7
2.53-2.593.40.3580.923198.2
2.59-2.643.40.3030.959197.1
2.64-2.73.30.2770.958197.7
2.7-2.773.10.2450.956197.3
2.77-2.8530.2140.953194.5
2.85-2.933.50.1780.979199.5
2.93-3.023.60.1440.983199.5
3.02-3.133.60.1260.99199.8
3.13-3.263.50.1040.992199.5
3.26-3.413.50.080.996199.2
3.41-3.583.50.070.996198.1
3.58-3.813.40.0550.997197.4
3.81-4.13.10.0460.998196.6
4.1-4.523.50.0450.998198.4
4.52-5.173.60.0420.997199.9
5.17-6.513.40.0480.998199.6
6.51-503.30.0320.999197.2

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_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
精密化構造決定の手法: 分子置換 / 解像度: 2.401→40.576 Å / SU ML: 0.27 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 30.69 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2485 1718 5.24 %
Rwork0.2038 --
obs0.2062 32802 84.76 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.401→40.576 Å
タンパク質核酸リガンド溶媒全体
原子数7576 0 74 296 7946
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0057801
X-RAY DIFFRACTIONf_angle_d0.97510546
X-RAY DIFFRACTIONf_dihedral_angle_d17.4252878
X-RAY DIFFRACTIONf_chiral_restr0.1521257
X-RAY DIFFRACTIONf_plane_restr0.0031305
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4008-2.47140.2601480.2325940X-RAY DIFFRACTION31
2.4714-2.55120.2974970.23981905X-RAY DIFFRACTION62
2.5512-2.64230.29371360.2322473X-RAY DIFFRACTION82
2.6423-2.74810.29941500.23242654X-RAY DIFFRACTION87
2.7481-2.87310.28561470.23822645X-RAY DIFFRACTION87
2.8731-3.02460.25431550.23292823X-RAY DIFFRACTION93
3.0246-3.2140.27341620.23132910X-RAY DIFFRACTION95
3.214-3.4620.26631590.21642928X-RAY DIFFRACTION96
3.462-3.81020.2281600.18392890X-RAY DIFFRACTION95
3.8102-4.3610.24241630.16612910X-RAY DIFFRACTION95
4.361-5.49220.2021700.17373052X-RAY DIFFRACTION99
5.4922-40.58190.22531710.20282954X-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)
14.5024-1.95712.01413.8996-0.89134.06410.06490.03610.1031-0.1079-0.1911-0.46310.10050.44730.16310.17880.01630.04190.203-0.00370.1818-1.2719-17.0414-13.9218
24.7542-0.9890.81734.59410.72223.28650.0473-0.0508-0.3024-0.2875-0.20050.17040.00210.07380.16660.10770.00860.01660.18420.06670.2193-7.1089-19.227-13.1909
34.9776-0.51630.87366.7247-2.10624.51190.186-0.3949-1.479-0.0051-0.04310.09581.19060.1999-0.10810.32460.02510.00650.23170.05940.7501-12.6005-33.8732-15.036
43.2175-0.19691.53692.2504-0.69696.18010.0193-0.12910.01360.1478-0.06250.073-0.0413-0.09210.00820.12210.00430.04050.14030.00740.2093-14.2715-16.7776-16.4751
53.81330.6428-0.78330.7518-1.12996.8020.03570.0926-0.156-0.00260.21940.30480.0986-0.3035-0.17250.29850.0823-0.05610.25380.02130.3528-44.4963-17.8416-17.1123
65.3177-0.7784-1.69674.73131.07874.41440.0102-0.346-0.52330.1216-0.08820.22590.1722-0.19610.0830.1341-0.0031-0.00930.22930.03850.2896-38.8587-21.6393-12.4046
76.69410.30815.80580.05290.2135.3204-0.0142-1.39090.70180.74540.2824-0.30080.17330.7008-0.29380.6354-0.0430.05440.9123-0.31030.5798-38.7468-8.67030.2786
83.5235-0.0897-0.73612.60010.91924.10960.0396-0.27580.32090.00790.1568-0.1197-0.27670.0824-0.18670.1730.01510.01270.2511-0.02830.3381-30.7202-14.8951-17.2269
93.9344-0.1236-0.25192.9852-0.76473.13780.02890.05-0.3332-0.0928-0.06980.0350.0307-0.07770.05040.10230.0326-0.00930.15410.02930.2229-27.4345-18.9665-21.0786
102.6114-1.9894-0.86995.99121.91567.91460.9152-0.8144-0.81990.39821.5118-0.4216-0.08251.0513-0.55030.58570.29930.13370.3711.07620.7289-35.9014-30.5017-1.1328
111.68151.3273.02243.61893.04575.47040.1146-0.47280.740.0434-0.4836-0.393-1.23060.6420.01010.47720.0744-0.23240.5256-0.39960.6035-2.1103-6.6613-0.9756
122.1504-3.9820.70167.4329-0.47819.44640.1442-0.0688-2.6311-0.2368-0.44830.32731.4021-1.76380.18230.4503-0.14230.09730.42830.12261.1317-43.0283-37.3189-13.7531
134.70360.98531.07494.67711.10274.3207-0.4619-0.31460.66050.22980.37180.252-1.7549-0.1335-0.09290.4186-0.02620.10210.5221-0.20210.3405-14.8782-47.2416-24.191
144.2712-0.5227-0.08667.66012.73476.13310.34610.3461-0.5597-0.89390.1973-0.25220.1173-0.3471-0.3330.2549-0.0105-0.04070.2452-0.02040.2326-22.4346-67.4561-41.0611
154.89011.80460.93464.8879-2.05793.53420.01420.03250.04120.20750.01190.3859-0.1775-0.1163-0.00080.13950.03570.01020.12660.00830.2216-13.8727-59.8766-40.7041
160.2322-0.49570.56913.186-0.97192.37720.00940.3577-0.6734-0.58740.1665-0.18420.79310.6532-0.30210.4363-0.0451-0.11540.2696-0.05931.0578-13.4751-78.6526-43.8484
175.3478-2.2-2.62167.553.97712.0469-0.1925-0.0383-1.29080.12230.05250.18020.60250.31050.10290.15250.0213-0.01710.18950.00630.6674-5.6328-73.2698-34.9235
185.11850.10381.81662.2746-0.44534.94140.1088-0.6120.50710.1972-0.02480.2331-0.64550.1060.09990.24920.01370.05570.2354-0.10440.2363-5.623-53.5861-27.2536
194.8527-0.15952.23191.7981-0.14765.21060.08590.5424-0.4151-0.348-0.07690.07060.43030.4921-0.13910.2028-0.02360.02710.1302-0.00810.2613-4.2284-62.4661-42.1482
204.5859-0.1282-0.26144.3261-2.05388.28130.0345-0.1264-0.25340.1559-0.302-0.0888-0.13150.61740.28430.09040.0248-0.0010.2002-0.06050.16325.3427-59.481-34.3392
213.86541.1472-1.77842.836-0.09214.9645-0.05790.1351-0.5394-0.23720.108-0.21750.30710.436-0.03760.16740.01390.0350.1776-0.02120.289123.6538-63.613-44.1599
224.30451.04-0.86432.92150.24533.36030.1405-0.2259-0.4860.1304-0.18490.03440.3970.06530.03990.14780.03890.03960.16370.05190.277715.8809-67.1567-35.5249
237.8081-0.2495-1.06616.7356-0.33531.9437-0.07181.25910.8694-0.69970.14350.4335-0.3716-0.0384-0.01730.2935-0.0558-0.00350.35560.1680.364720.1943-47.9371-47.2702
244.50930.0452-0.47714.7733-1.3556.58030.2496-0.07490.61810.1402-0.00050.4105-0.7110.1527-0.14210.1326-0.05340.08440.17620.00390.322212.717-53.1353-35.6847
254.66675.2461-0.95186.9751-0.11881.7952-0.1977-0.3149-1.01290.9037-0.44260.54490.0141-0.35730.71430.4062-0.03790.0540.37810.00981.04264.5511-75.5342-30.7543
264.4698-0.0173-0.73375.3011.86175.7430.0409-0.7293-0.37420.9549-0.00660.34220.46020.5328-0.09190.20760.01460.03380.45720.05650.228210.026-62.2771-20.1899
274.04040.1188-1.12653.97753.06277.35920.08980.2403-0.02-0.2809-0.14950.2456-0.2283-0.15720.01030.10920.0222-0.01920.16790.06820.22387.237-57.9796-38.7431
289.38926.4091-5.5229.8046-7.41695.80650.12991.37580.07140.11690.78230.6434-0.356-0.8124-0.72720.46760.0593-0.00620.4775-0.18430.427316.0599-71.0264-51.4422
294.0393-0.647-1.49047.50327.10932.02490.62611.01080.4047-0.9926-0.73250.2166-1.943-0.97390.15510.4430.0516-0.15110.51060.14630.4359-17.2728-47.0774-49.9545
303.408-1.0310.51052.02786.12639.4220.93630.0472-2.12020.19221.0475-1.28660.43941.0099-1.63160.45180.1028-0.01660.3518-0.00010.722123.0414-78.8661-39.9708
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 363 )
2X-RAY DIFFRACTION2chain 'A' and (resid 364 through 410 )
3X-RAY DIFFRACTION3chain 'A' and (resid 411 through 437 )
4X-RAY DIFFRACTION4chain 'A' and (resid 438 through 548 )
5X-RAY DIFFRACTION5chain 'B' and (resid 305 through 338 )
6X-RAY DIFFRACTION6chain 'B' and (resid 339 through 405 )
7X-RAY DIFFRACTION7chain 'B' and (resid 406 through 421 )
8X-RAY DIFFRACTION8chain 'B' and (resid 422 through 465 )
9X-RAY DIFFRACTION9chain 'B' and (resid 466 through 531 )
10X-RAY DIFFRACTION10chain 'B' and (resid 532 through 549 )
11X-RAY DIFFRACTION11chain 'C' and (resid 687 through 696 )
12X-RAY DIFFRACTION12chain 'D' and (resid 688 through 696 )
13X-RAY DIFFRACTION13chain 'E' and (resid 305 through 321 )
14X-RAY DIFFRACTION14chain 'E' and (resid 322 through 338 )
15X-RAY DIFFRACTION15chain 'E' and (resid 339 through 405 )
16X-RAY DIFFRACTION16chain 'E' and (resid 406 through 420 )
17X-RAY DIFFRACTION17chain 'E' and (resid 421 through 437 )
18X-RAY DIFFRACTION18chain 'E' and (resid 438 through 496 )
19X-RAY DIFFRACTION19chain 'E' and (resid 497 through 548 )
20X-RAY DIFFRACTION20chain 'F' and (resid 305 through 338 )
21X-RAY DIFFRACTION21chain 'F' and (resid 339 through 363 )
22X-RAY DIFFRACTION22chain 'F' and (resid 364 through 395 )
23X-RAY DIFFRACTION23chain 'F' and (resid 396 through 420 )
24X-RAY DIFFRACTION24chain 'F' and (resid 421 through 455 )
25X-RAY DIFFRACTION25chain 'F' and (resid 456 through 470 )
26X-RAY DIFFRACTION26chain 'F' and (resid 471 through 496 )
27X-RAY DIFFRACTION27chain 'F' and (resid 497 through 531 )
28X-RAY DIFFRACTION28chain 'F' and (resid 532 through 549 )
29X-RAY DIFFRACTION29chain 'G' and (resid 687 through 696 )
30X-RAY DIFFRACTION30chain 'H' and (resid 687 through 696 )

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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