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- PDB-8hbm: Structural basis of the farnesoid X receptor/retinoid X receptor ... -

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基本情報

登録情報
データベース: PDB / ID: 8hbm
タイトルStructural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA
要素
  • Bile acid receptor
  • DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*AP*TP*GP*AP*CP*CP*TP*CP*G)-3')
  • DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*TP*TP*GP*AP*CP*CP*TP*CP*G)-3')
  • Retinoic acid receptor RXR-alpha
キーワードDNA BINDING PROTEIN/DNA / FXR / RXR / DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
機能・相同性
機能・相同性情報


regulation of urea metabolic process / 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 / positive regulation of transporter activity / negative regulation of very-low-density lipoprotein particle remodeling ...regulation of urea metabolic process / 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 / positive regulation of transporter activity / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of monocyte chemotactic protein-1 production / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / toll-like receptor 9 signaling pathway / Carnitine shuttle / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / bile acid metabolic process / retinoic acid binding / TGFBR3 expression / cell-cell junction assembly / bile acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / regulation of cholesterol metabolic process / Signaling by Retinoic Acid / DNA binding domain binding / cellular response to fatty acid / negative regulation of interleukin-2 production / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear steroid receptor activity / bile acid and bile salt transport / LBD domain binding / positive regulation of interleukin-17 production / intracellular glucose homeostasis / negative regulation of interleukin-6 production / negative regulation of type II interferon production / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor production / positive regulation of cholesterol efflux / negative regulation of tumor necrosis factor-mediated signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / fatty acid homeostasis / positive regulation of bone mineralization / positive regulation of insulin receptor signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / Notch signaling pathway / hormone-mediated signaling pathway / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian expression / peptide binding / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / negative regulation of inflammatory response / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / nervous system development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II
類似検索 - 分子機能
Bile acid receptor, ligand binding domain / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / Retinoid X receptor/HNF4 / : / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Bile acid receptor, ligand binding domain / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / Retinoid X receptor/HNF4 / : / : / 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
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Retinoic acid receptor RXR-alpha / 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: 3.3 Å
データ登録者Jiang, L. / Chen, Y.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)81974074 and 82172654 中国
引用ジャーナル: Comput Struct Biotechnol J / 年: 2023
タイトル: Structural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA.
著者: Jiang, L. / Liu, X. / Liang, X. / Dai, S. / Wei, H. / Guo, M. / Chen, Z. / Xiao, D. / Chen, Y.
履歴
登録2022年10月29日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02023年6月14日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年5月1日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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: Retinoic acid receptor RXR-alpha
B: Bile acid receptor
C: DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*AP*TP*GP*AP*CP*CP*TP*CP*G)-3')
D: DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*TP*TP*GP*AP*CP*CP*TP*CP*G)-3')
E: Retinoic acid receptor RXR-alpha
F: Bile acid receptor
G: DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*AP*TP*GP*AP*CP*CP*TP*CP*G)-3')
H: DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*TP*TP*GP*AP*CP*CP*TP*CP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,87216
ポリマ－68,3498
非ポリマー5238
水00
1
A: Retinoic acid receptor RXR-alpha
B: Bile acid receptor
C: DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*AP*TP*GP*AP*CP*CP*TP*CP*G)-3')
D: DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*TP*TP*GP*AP*CP*CP*TP*CP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)34,4368
ポリマ－34,1744
非ポリマー2624
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-28 kcal/mol
Surface area13350 Å2
手法PISA
2
E: Retinoic acid receptor RXR-alpha
F: Bile acid receptor
G: DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*AP*TP*GP*AP*CP*CP*TP*CP*G)-3')
H: DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*TP*TP*GP*AP*CP*CP*TP*CP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)34,4368
ポリマ－34,1744
非ポリマー2624
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-34 kcal/mol
Surface area13930 Å2
手法PISA
単位格子
Length a, b, c (Å)50.650, 60.016, 241.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 132 through 140 or (resid 141...
21(chain E and (resid 132 through 171 or resid 173 through 209))
12(chain B and (resid 124 or (resid 125 and (name...
22(chain F and (resid 124 through 147 or (resid 148...
13(chain C and (resid 2 through 9 or resid 11 through 18))
23(chain D and (resid 2 through 9 or resid 11 through 18))
33(chain G and (resid 2 through 9 or resid 11 through 18))
43(chain H and (resid 2 through 9 or resid 11 through 18))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSASPASP(chain A and (resid 132 through 140 or (resid 141...AA132 - 14011 - 19
121ARGARGARGARG(chain A and (resid 132 through 140 or (resid 141...AA14120
131THRTHRARGARG(chain A and (resid 132 through 140 or (resid 141...AA131 - 20910 - 88
141THRTHRARGARG(chain A and (resid 132 through 140 or (resid 141...AA131 - 20910 - 88
151THRTHRARGARG(chain A and (resid 132 through 140 or (resid 141...AA131 - 20910 - 88
161THRTHRARGARG(chain A and (resid 132 through 140 or (resid 141...AA131 - 20910 - 88
211LYSLYSCYSCYS(chain E and (resid 132 through 171 or resid 173 through 209))EE132 - 17111 - 50
221ASPASPARGARG(chain E and (resid 132 through 171 or resid 173 through 209))EE173 - 20952 - 88
112ASPASPASPASP(chain B and (resid 124 or (resid 125 and (name...BB12416
122GLUGLUGLUGLU(chain B and (resid 124 or (resid 125 and (name...BB12517
132ASPASPCYSCYS(chain B and (resid 124 or (resid 125 and (name...BB124 - 19616 - 88
142ASPASPCYSCYS(chain B and (resid 124 or (resid 125 and (name...BB124 - 19616 - 88
152ASPASPCYSCYS(chain B and (resid 124 or (resid 125 and (name...BB124 - 19616 - 88
162ASPASPCYSCYS(chain B and (resid 124 or (resid 125 and (name...BB124 - 19616 - 88
212ASPASPCYSCYS(chain F and (resid 124 through 147 or (resid 148...FF124 - 14716 - 39
222LYSLYSLYSLYS(chain F and (resid 124 through 147 or (resid 148...FF14840
232ASPASPCYSCYS(chain F and (resid 124 through 147 or (resid 148...FF124 - 19616 - 88
242ASPASPCYSCYS(chain F and (resid 124 through 147 or (resid 148...FF124 - 19616 - 88
252ASPASPCYSCYS(chain F and (resid 124 through 147 or (resid 148...FF124 - 19616 - 88
262ASPASPCYSCYS(chain F and (resid 124 through 147 or (resid 148...FF124 - 19616 - 88
113DCDCDADA(chain C and (resid 2 through 9 or resid 11 through 18))CC2 - 92 - 9
123DTDTDGDG(chain C and (resid 2 through 9 or resid 11 through 18))CC11 - 1811 - 18
213DCDCDADA(chain D and (resid 2 through 9 or resid 11 through 18))DD2 - 92 - 9
223DTDTDGDG(chain D and (resid 2 through 9 or resid 11 through 18))DD11 - 1811 - 18
313DCDCDADA(chain G and (resid 2 through 9 or resid 11 through 18))GG2 - 92 - 9
323DTDTDGDG(chain G and (resid 2 through 9 or resid 11 through 18))GG11 - 1811 - 18
413DCDCDADA(chain H and (resid 2 through 9 or resid 11 through 18))HH2 - 92 - 9
423DTDTDGDG(chain H and (resid 2 through 9 or resid 11 through 18))HH11 - 1811 - 18

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質 Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


分子量: 10733.482 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: RXRA, NR2B1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P19793
#2: 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: 12446.835 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: NR1H4, BAR, FXR, HRR1, RIP14 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q96RI1
#3: DNA鎖 DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*AP*TP*GP*AP*CP*CP*TP*CP*G)-3')


分子量: 5501.567 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#4: DNA鎖 DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*TP*TP*GP*AP*CP*CP*TP*CP*G)-3')


分子量: 5492.553 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#5: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn
研究の焦点であるリガンドがあるかN

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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: 2.69 Å3/Da / 溶媒含有率: 54.25 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 100mM BTP pH 6.7, 10mM MgCl2, 50mM MgSO4, 50mM Li2SO4, 5mM DTT, 16% PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL17U1 / 波長: 0.97915 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年10月13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: 0.97915 Å / 相対比: 1
反射解像度: 3.3→50 Å / Num. obs: 11689 / % possible obs: 97.53 % / 冗長度: 19.99 % / CC1/2: 0.9336 / Net I/σ(I): 7.8
反射 シェル解像度: 3.3→3.4 Å / Num. unique obs: 1131 / CC1/2: 0.9729 / % possible all: 91.12

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
PDB_EXTRACT3.27データ抽出
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
開始モデル: 1R0N

1r0n


解像度: 3.3→49.57 Å / SU ML: 0.52 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 36.34 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3008 1141 9.94 %
Rwork0.2478 10335 -
obs0.2529 11476 97.54 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 273.21 Å2 / Biso mean: 124.797 Å2 / Biso min: 42.23 Å2
精密化ステップサイクル: final / 解像度: 3.3→49.57 Å
タンパク質核酸リガンド溶媒全体
原子数2155 1470 8 0 3633
Biso mean--131.14 --
残基数----373
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A440X-RAY DIFFRACTION8.234TORSIONAL
12E440X-RAY DIFFRACTION8.234TORSIONAL
21B424X-RAY DIFFRACTION8.234TORSIONAL
22F424X-RAY DIFFRACTION8.234TORSIONAL
31C616X-RAY DIFFRACTION8.234TORSIONAL
32D616X-RAY DIFFRACTION8.234TORSIONAL
33G616X-RAY DIFFRACTION8.234TORSIONAL
34H616X-RAY DIFFRACTION8.234TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.450.43321240.36481191131592
3.45-3.630.37791410.31081254139597
3.63-3.860.40721380.32071246138497
3.86-4.160.30591430.28971284142798
4.16-4.570.28731440.23011300144499
4.58-5.240.26431460.23521310145699
5.24-6.590.30691490.22091335148499
6.6-49.570.25511560.20761415157199
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)
18.2816-0.4935-0.456.33550.3692.0225-0.2266-1.37190.6545-0.00880.74450.0136-1.0444-0.0332-0.03290.45350.08250.08130.5678-0.04940.624-18.9059-19.4011-2.5982
23.6135-0.95931.59218.4849-3.09914.7420.73960.1565-0.6543-1.1438-1.03060.24671.89580.51990.21040.7205-0.009-0.10910.5266-0.09130.749-20.5225-31.404-1.5704
38.244-0.2541-0.23297.6589-0.53191.4380.5332-0.0002-0.255-0.4464-0.42210.63230.9453-0.13590.05541.7777-0.18210.22341.03920.16691.3262-27.5516-38.2959.5845
42.00932.37937.37430.66951.69215.1872-0.3188-0.36341.57610.3743-1.39951.3928-0.1815-0.51641.40790.6038-0.24420.0991.23950.01241.4396-34.1582-27.446316.0158
57.8514-3.2031-0.07622.3775-2.25516.2896-0.3376-2.65180.27511.4191-0.91821.3922-1.6715-0.13160.97320.75340.078-0.02720.8614-0.34520.8804-24.1543-21.66710.6728
62.29550.58270.2632.33460.45723.9101-0.003-0.5607-0.37240.379-0.24360.99351.3052-1.90580.18080.78-0.2198-0.04310.6633-0.060.8982-28.6014-30.16212.177
76.19930.8547-1.84445.36720.02875.92050.0686-0.1331-2.691-1.35440.4762-0.54451.5619-0.7348-0.52771.6122-0.2181-0.34480.8360.17241.0106-18.029-43.4988-5.7177
83.3455-1.31012.98132.2124-0.33983.04440.4576-0.33840.15811.09630.83171.34531.62440.1575-1.18820.73560.02930.08271.3726-0.34061.0593-18.9541-15.674925.9087
95.6617-1.1766-0.5542.3563-0.63233.97411.4901-1.13740.65750.2657-0.8945-0.34450.1389-0.2046-0.3940.9633-0.23650.05311.0986-0.01380.6559-8.8191-21.905424.484
103.2981.7512-1.90062.82920.92692.9566-0.2447-0.6372-0.13490.20270.305-0.21440.66720.61020.18430.94940.0826-0.10550.5631-0.10170.8249-2.3916-14.755311.2908
113.93960.62561.47652.62270.4836.86960.9494-0.60350.57080.6187-0.49930.52340.3467-1.4009-0.35380.5774-0.09510.01570.7324-0.16370.7352-6.0667-16.856418.0516
127.0936-3.66111.64415.3325-3.11562.08150.54580.41920.4642-0.1956-0.382-1.3569-0.7881.624-0.5631.0118-0.01860.01490.9579-0.06091.0006-14.2932-30.9125-12.0208
132.95791.0661.05324.04971.89035.37480.6036-0.1721-1.14940.4542-0.32330.25731.27420.0566-0.37490.91060.09350.00040.85430.0451.0402-10.0291-33.480412.3109
145.1663-2.59790.20252.7742-2.52624.01790.6729-0.9566-0.56241.41871.16730.43910.5880.4249-1.60841.91670.0901-0.22491.84030.43241.2008-10.4551-37.612635.4504
153.59372.30722.68066.4861-1.07193.5667-0.35060.99441.46041.24160.91660.78771.2775-0.6829-0.42732.0052-0.32660.0381.92530.25990.9219-11.3912-28.60934.8858
162.4223-0.91240.57532.6457-0.11374.07240.79810.3322-0.82550.0467-0.093-0.36850.92110.4789-0.7360.992-0.0576-0.14020.7721-0.00431.0108-9.1754-34.02285.0726
172.3989-1.02-1.37044.9797-0.16631.78960.97380.56280.9990.47670.29061.4237-0.359-0.81360.48512.04161.94950.74453.0396-0.25870.8345.83477.276164.5354
184.80180.7277-1.02940.6252-2.25128.98430.04590.54370.36880.58470.7424-0.824-0.5089-1.8516-0.44062.15480.6274-0.16570.9062-0.22191.107817.32248.094358.2328
191.45271.6455-0.23923.75661.75652.3002-0.56980.611-0.37090.09020.40180.50371.25050.3438-0.22082.12450.0627-0.30791.3322-0.06571.451914.8217.893947.4849
207.6311-2.8704-7.05982.23763.50277.12791.47510.92572.3446-0.19481.5508-0.5921-2.9839-1.2933-0.00022.58861.2964-0.1462.1758-0.64380.988.280413.942752.5449
211.89830.76632.79498.0631-0.41188.83590.4965-0.29720.7126-2.3295-0.12241.5421-1.7803-2.54250.6042.58170.2752-0.16172.4882-1.06180.876318.856111.967665.5255
222.1955-0.1976-0.51140.1192-0.22750.76370.36610.11410.13720.10240.70920.41160.39170.18190.5540.97821.7332-0.60784.1568-0.25821.4575-0.27463.504137.6321
235.644-1.63162.0063.7209-0.8456.67331.03160.1868-0.37-0.8638-0.18440.00030.8501-0.5928-0.90651.1905-0.1174-0.06492.35140.18570.9945.7645-4.099434.3482
243.9551-0.3681-2.67681.93191.18673.8252-0.2939-1.9399-0.96490.474-1.05072.7245-0.6741-0.79481.08691.0442-0.1722-0.07382.50820.08751.21830.8525-9.312248.1471
253.31751.25162.8523.20862.63073.2985-1.2615-0.206-0.7771-0.32250.96040.45291.973-0.99760.47781.4547-0.8339-0.09691.9490.15471.13180.8031-10.801538.2333
264.7536-3.2845-4.4552.39782.71787.06490.2973-3.2393-0.1344-0.66570.10141.0155-0.941-1.2775-0.56581.95610.61110.10032.4372-0.18391.285714.25511.642172.5586
273.7885-2.19480.20823.36510.44837.3887-0.36570.177-1.0947-0.03850.77641.00540.17390.3797-0.58591.7379-0.2707-0.0151.5213-0.18461.224819.3206-6.139656.2865
281.5486-1.0389-0.37860.83490.33273.54530.75480.8022-0.51-0.31220.0477-0.65090.0598-0.1565-0.53851.5706-0.0451-0.05021.9268-0.22271.258117.1629-0.00734.4431
297.76632.7792-1.40743.71190.7847.4572-0.11240.39330.04071.5727-0.2292-0.19571.18770.03640.25881.8262-0.34520.04781.45740.09041.156912.194-1.56425.6543
306.1867-1.2708-1.18682.814-0.65284.89330.3699-1.3093-0.8846-0.41890.4624-0.43840.26571.0328-0.82391.4562-0.0149-0.14471.2996-0.18231.088921.211-2.082541.6553
310.6198-0.33850.87893.3525-2.72498.5986-0.4743-0.8043-0.31360.17661.4675-0.8382-1.0034-2.3878-0.71311.7020.0231-0.02512.3364-0.18631.121415.4478-3.970764.2976
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 131 through 143 )A131 - 143
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 165 )A144 - 165
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 170 )A166 - 170
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 175 )A171 - 175
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 187 )A176 - 187
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 204 )A188 - 204
7X-RAY DIFFRACTION7chain 'A' and (resid 205 through 209 )A205 - 209
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 128 )B124 - 128
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 157 )B129 - 157
10X-RAY DIFFRACTION10chain 'B' and (resid 158 through 172 )B158 - 172
11X-RAY DIFFRACTION11chain 'B' and (resid 173 through 196 )B173 - 196
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 5 )C1 - 5
13X-RAY DIFFRACTION13chain 'C' and (resid 6 through 15 )C6 - 15
14X-RAY DIFFRACTION14chain 'C' and (resid 16 through 18 )C16 - 18
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 5 )D1 - 5
16X-RAY DIFFRACTION16chain 'D' and (resid 6 through 18 )D6 - 18
17X-RAY DIFFRACTION17chain 'E' and (resid 132 through 152 )E132 - 152
18X-RAY DIFFRACTION18chain 'E' and (resid 153 through 165 )E153 - 165
19X-RAY DIFFRACTION19chain 'E' and (resid 166 through 175 )E166 - 175
20X-RAY DIFFRACTION20chain 'E' and (resid 176 through 197 )E176 - 197
21X-RAY DIFFRACTION21chain 'E' and (resid 198 through 209 )E198 - 209
22X-RAY DIFFRACTION22chain 'F' and (resid 124 through 133 )F124 - 133
23X-RAY DIFFRACTION23chain 'F' and (resid 134 through 155 )F134 - 155
24X-RAY DIFFRACTION24chain 'F' and (resid 156 through 179 )F156 - 179
25X-RAY DIFFRACTION25chain 'F' and (resid 180 through 196 )F180 - 196
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 5 )G1 - 5
27X-RAY DIFFRACTION27chain 'G' and (resid 6 through 10 )G6 - 10
28X-RAY DIFFRACTION28chain 'G' and (resid 11 through 18 )G11 - 18
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 5 )H1 - 5
30X-RAY DIFFRACTION30chain 'H' and (resid 6 through 10 )H6 - 10
31X-RAY DIFFRACTION31chain 'H' and (resid 11 through 18 )H11 - 18

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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://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