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- PDB-5q0j: Ligand binding to FARNESOID-X-RECEPTOR -

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基本情報

登録情報
データベース: PDB / ID: 5q0j
タイトルLigand binding to FARNESOID-X-RECEPTOR
要素
  • Bile acid receptor
  • COACTIVATOR PEPTIDE SRC-1 HD3
キーワードTRANSCRIPTION / D3R / FXR / Docking
機能・相同性
機能・相同性情報


regulation of urea metabolic process / nuclear receptor-mediated bile acid signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / : / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...regulation of urea metabolic process / nuclear receptor-mediated bile acid signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / : / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to organonitrogen compound / toll-like receptor 9 signaling pathway / intracellular receptor signaling pathway / negative regulation of monocyte chemotactic protein-1 production / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / bile acid binding / cell-cell junction assembly / positive regulation of female receptivity / bile acid signaling pathway / cellular response to fatty acid / negative regulation of interleukin-2 production / regulation of cholesterol metabolic process / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of interleukin-17 production / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / cellular response to Thyroglobulin triiodothyronine / negative regulation of tumor necrosis factor-mediated signaling pathway / estrous cycle / Synthesis of bile acids and bile salts / fatty acid homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / positive regulation of insulin receptor signaling pathway / response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / Notch signaling pathway / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / cholesterol homeostasis / hippocampus development / nuclear receptor binding / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity
類似検索 - 分子機能
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / 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 ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / 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 / PAS domain superfamily / 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-9KV / Nuclear receptor coactivator / Nuclear receptor coactivator 1 / Bile acid 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 Å
Model detailsStructures re-refined for D3R docking challenge
データ登録者Rudolph, M.G. / Benz, J. / Burger, D. / Thoma, R. / Ruf, A. / Joseph, C. / Kuhn, B. / Shao, C. / Yang, H. / Burley, S.K.
引用ジャーナル: J. Comput. Aided Mol. Des. / 年: 2018
タイトル: D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
著者: Gaieb, Z. / Liu, S. / Gathiaka, S. / Chiu, M. / Yang, H. / Shao, C. / Feher, V.A. / Walters, W.P. / Kuhn, B. / Rudolph, M.G. / Burley, S.K. / Gilson, M.K. / Amaro, R.E.
履歴
登録2017年5月31日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年7月5日Provider: repository / タイプ: Initial release
改定 1.12017年7月19日Group: Database references / Structure summary / カテゴリ: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
改定 1.22017年12月20日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32018年1月31日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.42018年2月21日Group: Structure summary / カテゴリ: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
改定 1.52021年2月10日Group: Database references / Structure summary / カテゴリ: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _citation.country / _citation_author.identifier_ORCID
改定 1.62021年11月17日Group: Database references / Structure summary / カテゴリ: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description

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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: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,7766
ポリマ－57,7804
非ポリマー9952
水4,017223
1
A: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,3883
ポリマ－28,8902
非ポリマー4981
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area11970 Å2
手法PISA
2
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,3883
ポリマ－28,8902
非ポリマー4981
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area11850 Å2
手法PISA
単位格子
Length a, b, c (Å)71.865, 84.076, 188.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain B and resid 746 through 755)
21chain D
12(chain A and (resid 248 through 331 or resid 333...
22(chain C and (resid 248 through 331 or resid 333...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and resid 746 through 755)B746 - 755
211chain DD746 - 755
112(chain A and (resid 248 through 331 or resid 333...A248 - 331
122(chain A and (resid 248 through 331 or resid 333...A333 - 352
132(chain A and (resid 248 through 331 or resid 333...A354 - 357
142(chain A and (resid 248 through 331 or resid 333...A359 - 374
152(chain A and (resid 248 through 331 or resid 333...A376 - 395
162(chain A and (resid 248 through 331 or resid 333...A397 - 404
172(chain A and (resid 248 through 331 or resid 333...A406 - 412
182(chain A and (resid 248 through 331 or resid 333...A414 - 425
192(chain A and (resid 248 through 331 or resid 333...A427 - 435
1102(chain A and (resid 248 through 331 or resid 333...A437 - 442
1112(chain A and (resid 248 through 331 or resid 333...A444 - 452
1122(chain A and (resid 248 through 331 or resid 333...A455 - 458
1132(chain A and (resid 248 through 331 or resid 333...A460 - 476
212(chain C and (resid 248 through 331 or resid 333...C248 - 331
222(chain C and (resid 248 through 331 or resid 333...C333 - 352
232(chain C and (resid 248 through 331 or resid 333...C354 - 357
242(chain C and (resid 248 through 331 or resid 333...C359 - 374
252(chain C and (resid 248 through 331 or resid 333...C376 - 395
262(chain C and (resid 248 through 331 or resid 333...C397 - 404
272(chain C and (resid 248 through 331 or resid 333...C406 - 412
282(chain C and (resid 248 through 331 or resid 333...C414 - 425
292(chain C and (resid 248 through 331 or resid 333...C427 - 435
2102(chain C and (resid 248 through 331 or resid 333...C437 - 442
2112(chain C and (resid 248 through 331 or resid 333...C444 - 452
2122(chain C and (resid 248 through 331 or resid 333...C455 - 458
2132(chain C and (resid 248 through 331 or resid 333...C460 - 476

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 Bile acid receptor / Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H ...Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H member 4 / Retinoid X receptor-interacting protein 14 / RXR-interacting protein 14


分子量: 27100.191 Da / 分子数: 2 / 断片: UNP residues 258-486 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NR1H4, BAR, FXR, HRR1, RIP14 / プラスミド: PET28A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q96RI1
#2: タンパク質・ペプチド COACTIVATOR PEPTIDE SRC-1 HD3


分子量: 1790.026 Da / 分子数: 2 / 断片: UNP residues 744-757 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: A8K1V4, UniProt: Q15788*PLUS
#3: 化合物 ChemComp-9KV / (2S)-N,2-dicyclohexyl-2-[2-(5-phenylthiophen-2-yl)-1H-benzimidazol-1-yl]acetamide


分子量: 497.694 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C31H35N3OS
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 223 / 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: 2.52 Å3/Da / 溶媒含有率: 51.13 %
結晶化温度: 298 K / 手法: 蒸発脱水法, ハンギングドロップ法 / pH: 6.5
詳細: 0.2 M Na Chloride, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350

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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: SLS / ビームライン: X10SA / 波長: 1 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2006年9月27日
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: 1 Å / 相対比: 1
反射解像度: 2→38.4 Å / Num. all: 39139 / Num. obs: 38634 / % possible obs: 98.7 % / 冗長度: 0.99 % / Net I/σ(I): 13.46
反射 シェル解像度: 2→2.1 Å / 冗長度: 1 % / Num. possible: 5247 / Num. unique obs: 5241 / Net I/σ(I) obs: 2.24 / % possible all: 99.9

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
PHENIX精密化
HKL-2000データスケーリング
PDB_EXTRACT3.23データ抽出
HKL-2000データ削減
精密化構造決定の手法: 分子置換 / 解像度: 2→35.729 Å / SU ML: 0.28 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 26.29 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2471 1922 4.99 %
Rwork0.1945 36578 -
obs0.1972 38500 98.51 %
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
原子変位パラメータBiso max: 128.66 Å2 / Biso mean: 46.0839 Å2 / Biso min: 17.11 Å2
精密化ステップサイクル: final / 解像度: 2→35.729 Å
タンパク質核酸リガンド溶媒全体
原子数3949 0 83 223 4255
Biso mean--33.55 49.5 -
残基数----481
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.014231
X-RAY DIFFRACTIONf_angle_d1.3245739
X-RAY DIFFRACTIONf_chiral_restr0.062635
X-RAY DIFFRACTIONf_plane_restr0.009733
X-RAY DIFFRACTIONf_dihedral_angle_d10.0853543
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11B78X-RAY DIFFRACTION10.7TORSIONAL
12D78X-RAY DIFFRACTION10.7TORSIONAL
21A1962X-RAY DIFFRACTION10.7TORSIONAL
22C1962X-RAY DIFFRACTION10.7TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.32461410.273726442785100
2.05-2.10540.31861400.263525822722100
2.1054-2.16740.28271360.245325852721100
2.1674-2.23730.4051230.34852421254492
2.2373-2.31730.41741170.32672339245688
2.3173-2.410.26031370.215626442781100
2.41-2.51970.25921270.20726332760100
2.5197-2.65250.26541410.226262767100
2.6525-2.81860.26411420.202126302772100
2.8186-3.03620.25871310.205626552786100
3.0362-3.34150.2691250.196826672792100
3.3415-3.82450.25121430.181426772820100
3.8245-4.81660.20181660.149726762842100
4.8166-35.73510.19981530.165727992952100
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)
10.7406-0.5149-0.26320.5650.51880.7667-0.0996-0.1943-0.2657-0.1395-0.03280.55140.5077-0.4938-0.16190.251-0.1778-0.06530.34630.01850.373-2.547115.1356-16.4717
20.50740.0599-0.34240.1344-0.08130.23180.1045-0.36570.10220.3341-0.1380.14570.3377-0.32450.00150.2445-0.08170.02630.2866-0.06630.276110.289917.48545.7683
30.12320.04680.02940.3727-0.53890.8092-0.0317-0.07610.0168-0.1114-0.1711-0.07980.14780.064300.2381-0.00570.01980.19550.0030.284713.811113.8799-9.9826
4-0.0009-0.00050.00580.5352-0.46070.43820.00230.11410.22190.3003-0.2643-0.0702-0.4901-0.31-0.05060.3580.10290.00060.4228-0.14960.41168.90932.44847.5425
50.1217-0.0603-0.07580.07810.08650.09550.2122-0.18250.19920.12840.06570.0994-0.40230.14140.00470.3436-0.08-0.0670.27880.05090.454115.599533.1139-2.8838
60.25580.32660.13420.5041-0.02190.34-0.14050.34650.4239-0.07460.0787-0.24740.13910.1239-0.00070.22120.02030.01360.2506-0.00170.261112.09718.4535-14.9687
70.2797-0.0480.14660.1819-0.18550.371-0.20860.05840.4328-0.56120.02820.06870.0526-0.01250.0030.3691-0.0121-0.05120.27120.00540.39386.091122.8649-22.5603
80.071-0.1005-0.04010.13550.11910.1191-0.2303-0.02830.4450.0318-0.1563-0.2318-0.24540.2226-0.00570.3235-0.0279-0.06060.36120.02870.507918.735626.3252-9.4614
90.0456-0.09160.0040.25140.03930.1313-0.0721-0.28080.3624-0.2861-0.0757-0.23450.2816-0.13540.00460.3347-0.036-0.08510.3144-0.03880.442725.454219.496810.267
100.0366-0.01460.03440.02140.01180.08560.25630.01120.06830.0886-0.024-0.26020.27920.53450.00260.3320.00380.05860.27440.0560.460423.807911.67840.3523
110.0373-0.11440.13660.3641-0.38280.54580.35890.1209-0.2602-0.0281-0.2425-0.53130.80040.1632-0.00030.3723-0.0523-0.00780.22630.03150.337619.041.3756-5.5741
120.06610.02820.03290.2019-0.0220.1358-0.05040.0204-0.14060.10390.2051-0.03780.06590.3683-0.00020.4670.1810.02210.3632-0.02720.352830.767339.661927.0667
130.27120.1719-0.17620.3364-0.13740.3621-0.3188-0.7591-0.23510.70860.1024-0.18360.31180.5528-0.00480.48650.18820.08120.50080.06720.249419.193751.227646.965
140.0417-0.02170.02550.20080.25340.6115-0.2401-0.1072-0.00080.22070.135-0.10160.07320.228800.2930.09360.02510.37110.00640.28427.162355.897533.192
150.03470.0679-0.08530.1329-0.15660.1672-0.1018-0.0933-0.1259-0.0316-0.1382-0.02850.3716-0.0501-2.16230.29490.14260.57910.2234-0.09120.00854.953147.505843.9073
160.43340.1930.40450.43620.08480.4962-0.135-0.05540.2240.0960.04870.00950.1876-0.2347-00.2630.04930.05020.3437-0.00570.255917.385853.579629.7431
170.2113-0.1310.05870.1539-0.10930.3754-0.25590.3622-0.0087-0.54620.16190.18350.06310.1004-0.00180.34140.03990.04210.3237-0.0120.307624.319446.845318.6787
180.1852-0.0712-0.07150.06840.00780.0704-0.0504-0.03420.0925-0.1574-0.03160.0857-0.1966-0.1426-0.0010.34920.09980.02570.3440.01240.279814.148458.609729.5255
190.0861-0.10740.10050.2398-0.19220.1546-0.1091-0.13270.41410.7343-0.26620.2683-0.27920.1002-0.02440.45540.09830.04190.6121-0.08280.445312.284265.338149.9745
200.2108-0.1771-0.08010.19670.05660.06820.5258-0.00010.2098-0.59230.5662-0.1309-0.27390.36550.00490.49950.0279-0.01970.7144-0.03020.358823.955665.87243.5728
211.84760.3204-0.44180.5179-0.42160.3683-0.0231-0.04710.425-0.08260.03780.0743-0.61170.29970.05860.43910.0426-0.14530.7652-0.02680.349337.10261.702341.2231
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 247 through 266 )A247 - 266
2X-RAY DIFFRACTION2chain 'A' and (resid 267 through 307 )A267 - 307
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 341 )A308 - 341
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 362 )A342 - 362
5X-RAY DIFFRACTION5chain 'A' and (resid 363 through 379 )A363 - 379
6X-RAY DIFFRACTION6chain 'A' and (resid 380 through 404 )A380 - 404
7X-RAY DIFFRACTION7chain 'A' and (resid 405 through 432 )A405 - 432
8X-RAY DIFFRACTION8chain 'A' and (resid 433 through 456 )A433 - 456
9X-RAY DIFFRACTION9chain 'A' and (resid 457 through 466 )A457 - 466
10X-RAY DIFFRACTION10chain 'A' and (resid 467 through 476 )A467 - 476
11X-RAY DIFFRACTION11chain 'B' and (resid 745 through 755 )B745 - 755
12X-RAY DIFFRACTION12chain 'C' and (resid 247 through 266 )C247 - 266
13X-RAY DIFFRACTION13chain 'C' and (resid 267 through 307 )C267 - 307
14X-RAY DIFFRACTION14chain 'C' and (resid 308 through 341 )C308 - 341
15X-RAY DIFFRACTION15chain 'C' and (resid 342 through 362 )C342 - 362
16X-RAY DIFFRACTION16chain 'C' and (resid 363 through 404 )C363 - 404
17X-RAY DIFFRACTION17chain 'C' and (resid 405 through 432 )C405 - 432
18X-RAY DIFFRACTION18chain 'C' and (resid 433 through 456 )C433 - 456
19X-RAY DIFFRACTION19chain 'C' and (resid 457 through 466 )C457 - 466
20X-RAY DIFFRACTION20chain 'C' and (resid 467 through 476 )C467 - 476
21X-RAY DIFFRACTION21chain 'D' and (resid 746 through 755 )D746 - 755

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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