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- PDB-7w2c: The closed conformation of the sigma-1 receptor from Xenopus laev... -

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基本情報

登録情報
データベース: PDB / ID: 7w2c
タイトルThe closed conformation of the sigma-1 receptor from Xenopus laevis complexed with PRE084
要素Sigma non-opioid intracellular receptor 1
キーワードMEMBRANE PROTEIN / sigma receptor / membrane receptor / S1R / ligand entry
機能・相同性
機能・相同性情報


nuclear outer membrane / nuclear inner membrane / lipid transport / cytoplasmic vesicle / endoplasmic reticulum membrane / membrane
類似検索 - 分子機能
ERG2/sigma1 receptor-like / ERG2 and Sigma1 receptor like protein
類似検索 - ドメイン・相同性
: / Chem-E84 / Sigma non-opioid intracellular receptor 1
類似検索 - 構成要素
生物種Xenopus laevis (アフリカツメガエル)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.335 Å
データ登録者Meng, F. / Sun, Z. / Zhou, X.
資金援助 中国, 1件
組織認可番号
National Natural Science Foundation of China (NSFC)31770783 中国
引用ジャーナル: Nat Commun / : 2022
タイトル: An open-like conformation of the sigma-1 receptor reveals its ligand entry pathway.
著者: Meng, F. / Xiao, Y. / Ji, Y. / Sun, Z. / Zhou, X.
履歴
登録2021年11月23日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年3月16日Provider: repository / タイプ: Initial release
改定 1.12022年3月23日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
改定 1.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Sigma non-opioid intracellular receptor 1
C: Sigma non-opioid intracellular receptor 1
E: Sigma non-opioid intracellular receptor 1
B: Sigma non-opioid intracellular receptor 1
D: Sigma non-opioid intracellular receptor 1
F: Sigma non-opioid intracellular receptor 1
G: Sigma non-opioid intracellular receptor 1
H: Sigma non-opioid intracellular receptor 1
I: Sigma non-opioid intracellular receptor 1
J: Sigma non-opioid intracellular receptor 1
K: Sigma non-opioid intracellular receptor 1
L: Sigma non-opioid intracellular receptor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)310,87451
ポリマ-301,46012
非ポリマー9,41339
181
1
A: Sigma non-opioid intracellular receptor 1
C: Sigma non-opioid intracellular receptor 1
E: Sigma non-opioid intracellular receptor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,79113
ポリマ-75,3653
非ポリマー2,42610
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-60 kcal/mol
Surface area29290 Å2
手法PISA
2
B: Sigma non-opioid intracellular receptor 1
D: Sigma non-opioid intracellular receptor 1
F: Sigma non-opioid intracellular receptor 1
ヘテロ分子


  • 登録者・ソフトウェアが定義した集合体
  • 77.8 kDa, 3 ポリマー
分子量 (理論値)分子数
合計 (水以外)77,79113
ポリマ-75,3653
非ポリマー2,42610
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-63 kcal/mol
Surface area29240 Å2
手法PISA
3
G: Sigma non-opioid intracellular receptor 1
H: Sigma non-opioid intracellular receptor 1
I: Sigma non-opioid intracellular receptor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,49912
ポリマ-75,3653
非ポリマー2,1349
181
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-66 kcal/mol
Surface area29340 Å2
手法PISA
4
J: Sigma non-opioid intracellular receptor 1
K: Sigma non-opioid intracellular receptor 1
L: Sigma non-opioid intracellular receptor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,79113
ポリマ-75,3653
非ポリマー2,42610
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-64 kcal/mol
Surface area29160 Å2
手法PISA
単位格子
Length a, b, c (Å)87.155, 148.780, 172.756
Angle α, β, γ (deg.)90.000, 92.760, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 3 through 19 or resid 25 through 402 or resid 501))
21(chain B and (resid 3 through 19 or resid 25 through 402 or resid 501))
31(chain C and (resid 3 through 19 or resid 25 through 402 or resid 501))
41(chain D and (resid 3 through 19 or resid 25 through 402 or resid 501))
51(chain E and (resid 3 through 19 or resid 25 through 402 or resid 501))
61(chain F and (resid 3 through 19 or resid 25 through 402 or resid 501))
71(chain G and (resid 3 through 402 or resid 501))
81(chain H and (resid 3 through 19 or resid 25 through 402 or resid 501))
91(chain I and (resid 3 through 19 or resid 25 through 402 or resid 501))
101(chain J and (resid 3 through 19 or resid 25 through 402 or resid 501))
111(chain K and (resid 3 through 19 or resid 25 through 402 or resid 501))
121(chain L and (resid 3 through 19 or resid 25 through 402 or resid 501))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 19 or resid 25 through 402 or resid 501))A3 - 19
121(chain A and (resid 3 through 19 or resid 25 through 402 or resid 501))A25 - 402
131(chain A and (resid 3 through 19 or resid 25 through 402 or resid 501))A501
211(chain B and (resid 3 through 19 or resid 25 through 402 or resid 501))B3 - 19
221(chain B and (resid 3 through 19 or resid 25 through 402 or resid 501))B25 - 402
231(chain B and (resid 3 through 19 or resid 25 through 402 or resid 501))B501
311(chain C and (resid 3 through 19 or resid 25 through 402 or resid 501))C3 - 19
321(chain C and (resid 3 through 19 or resid 25 through 402 or resid 501))C25 - 402
331(chain C and (resid 3 through 19 or resid 25 through 402 or resid 501))C501
411(chain D and (resid 3 through 19 or resid 25 through 402 or resid 501))D3 - 19
421(chain D and (resid 3 through 19 or resid 25 through 402 or resid 501))D25 - 402
431(chain D and (resid 3 through 19 or resid 25 through 402 or resid 501))D501
511(chain E and (resid 3 through 19 or resid 25 through 402 or resid 501))E3 - 19
521(chain E and (resid 3 through 19 or resid 25 through 402 or resid 501))E25 - 402
531(chain E and (resid 3 through 19 or resid 25 through 402 or resid 501))E501
611(chain F and (resid 3 through 19 or resid 25 through 402 or resid 501))F3 - 19
621(chain F and (resid 3 through 19 or resid 25 through 402 or resid 501))F25 - 402
631(chain F and (resid 3 through 19 or resid 25 through 402 or resid 501))F501
711(chain G and (resid 3 through 402 or resid 501))G0
811(chain H and (resid 3 through 19 or resid 25 through 402 or resid 501))H3 - 19
821(chain H and (resid 3 through 19 or resid 25 through 402 or resid 501))H25 - 402
831(chain H and (resid 3 through 19 or resid 25 through 402 or resid 501))H501
911(chain I and (resid 3 through 19 or resid 25 through 402 or resid 501))I3 - 19
921(chain I and (resid 3 through 19 or resid 25 through 402 or resid 501))I25 - 402
931(chain I and (resid 3 through 19 or resid 25 through 402 or resid 501))I501
1011(chain J and (resid 3 through 19 or resid 25 through 402 or resid 501))J3 - 19
1021(chain J and (resid 3 through 19 or resid 25 through 402 or resid 501))J25 - 402
1031(chain J and (resid 3 through 19 or resid 25 through 402 or resid 501))J501
1111(chain K and (resid 3 through 19 or resid 25 through 402 or resid 501))K3 - 19
1121(chain K and (resid 3 through 19 or resid 25 through 402 or resid 501))K25 - 402
1131(chain K and (resid 3 through 19 or resid 25 through 402 or resid 501))K501
1211(chain L and (resid 3 through 19 or resid 25 through 402 or resid 501))L3 - 19
1221(chain L and (resid 3 through 19 or resid 25 through 402 or resid 501))L25 - 402
1231(chain L and (resid 3 through 19 or resid 25 through 402 or resid 501))L501

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要素

#1: タンパク質
Sigma non-opioid intracellular receptor 1 / Sigma 1-type opioid receptor / Sigma1-receptor / Sigma1R


分子量: 25121.682 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
遺伝子: sigmar1, oprs1 / 発現宿主: Komagataella pastoris (菌類) / 参照: UniProt: Q6DCU6
#2: 化合物...
ChemComp-AU / GOLD ION


分子量: 196.967 Da / 分子数: 24 / 由来タイプ: 合成 / : Au
#3: 化合物
ChemComp-E84 / 2-morpholin-4-ylethyl 1-phenylcyclohexane-1-carboxylate / PRE-084 / PRE-084


分子量: 317.423 Da / 分子数: 12 / 由来タイプ: 合成 / : C19H27NO3 / タイプ: SUBJECT OF INVESTIGATION / コメント: 抗うつ薬, アゴニスト*YM
#4: 糖 ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / オクチルβ-D-グルコピラノシド


タイプ: D-saccharide / 分子量: 292.369 Da / 分子数: 3 / 由来タイプ: 合成 / : C14H28O6 / コメント: 可溶化剤*YM
識別子タイププログラム
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかY

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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: 3.71 Å3/Da / 溶媒含有率: 66.86 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.2
詳細: 0.1M NaCl, 0.1M Na+-citrate pH 5.2, 28% PEG 400, 10mM KAu(CN)2, 0.4mM PRE084 soaking

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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: BL19U1 / 波長: 0.97918 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2020年4月25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: 0.97918 Å / 相対比: 1
反射解像度: 3.335→47.992 Å / Num. obs: 59588 / % possible obs: 92.8 % / 冗長度: 6.6 % / Biso Wilson estimate: 92.62 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.061 / Rrim(I) all: 0.159 / Net I/σ(I): 11.2 / Num. measured all: 395021
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.335-3.3926.70.8592135132090.780.360.9322.4100
9.033-47.9925.70.0721868032520.9920.0320.07922.598.6

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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
XDSBUILT 20200417データ削減
Aimless0.7.4データスケーリング
PHASER位相決定
PHENIX1.13_2998精密化
PDB_EXTRACT3.27データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 5HK1
解像度: 3.335→46.961 Å / SU ML: 0.38 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 27.08 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2592 2938 4.94 %
Rwork0.2294 56507 -
obs0.2309 59445 92.57 %
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: 172.51 Å2 / Biso mean: 91.8681 Å2 / Biso min: 41.13 Å2
精密化ステップサイクル: final / 解像度: 3.335→46.961 Å
タンパク質核酸リガンド溶媒全体
原子数20472 0 360 1 20833
Biso mean--89.49 58.3 -
残基数----2590
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsタイプ
11A11965X-RAY DIFFRACTION7.691TORSIONAL
12B11965X-RAY DIFFRACTION7.691TORSIONAL
13C11965X-RAY DIFFRACTION7.691TORSIONAL
14D11965X-RAY DIFFRACTION7.691TORSIONAL
15E11965X-RAY DIFFRACTION7.691TORSIONAL
16F11965X-RAY DIFFRACTION7.691TORSIONAL
17G11965X-RAY DIFFRACTION7.691TORSIONAL
18H11965X-RAY DIFFRACTION7.691TORSIONAL
19I11965X-RAY DIFFRACTION7.691TORSIONAL
110J11965X-RAY DIFFRACTION7.691TORSIONAL
111K11965X-RAY DIFFRACTION7.691TORSIONAL
112L11965X-RAY DIFFRACTION7.691TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.335-3.38960.2961520.28882902100
3.3896-3.44810.3143900.2953177084
3.4481-3.51070.2841120.2818266494
3.5107-3.57820.29851700.25532848100
3.5782-3.65130.25481500.2446266895
3.6513-3.73060.2625980.2467165692
3.7306-3.81740.24631400.22622917100
3.8174-3.91280.277880.2434174691
3.9128-4.01850.27931250.2424253294
4.0185-4.13670.2421360.22512918100
4.1367-4.27010.25251340.21482870100
4.2701-4.42260.2151360.21032946100
4.4226-4.59960.23121560.20252877100
4.5996-4.80870.23291590.19812896100
4.8087-5.0620.23931630.20512881100
5.062-5.37870.27791600.22112910100
5.3787-5.79330.31621530.24282906100
5.7933-6.3750.29551270.25692945100
6.375-7.29450.24181580.23522909100
7.2945-9.17910.23381720.20362901100
9.1791-46.9610.27631590.2459284595
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1473-1.22460.01442.28120.39480.102-0.7306-0.1352-0.43190.10230.27260.0140.525-0.6092-0.16360.2547-0.3730.11580.68590.0450.5368-24.554-48.868724.2949
20.031-0.1409-0.18931.3060.32761.3020.0823-0.2471-0.31920.3276-0.05760.2978-0.0259-0.079-0.00010.6401-0.0085-0.05210.62580.09090.71-2.3899-49.493654.085
31.05010.10830.28890.8399-0.11250.98260.25260.3012-0.2045-0.1048-0.22260.2-0.11-0.0347-0.00010.4601-0.01860.0690.51790.00760.6443-0.9604-46.323241.7079
40.1969-0.00050.03240.64930.0710.00940.328-0.2715-0.4440.1325-0.12260.1589-0.57380.2051-0.00020.65350.05630.02690.7470.01840.675-5.0415-29.471246.8236
50.3478-0.054-0.3910.4747-0.10740.4838-0.4560.2940.2760.04270.1271-0.1456-0.0060.2754-0.00110.4694-0.02530.06040.44210.01180.4343-5.0945-40.488440.6428
61.5385-0.61360.79840.91880.31890.9962-0.14330.2364-0.40740.01870.1311-0.3509-0.0696-0.14970.00010.36080.03320.0230.4264-0.15020.5103-0.3482-53.805433.0252
71.93180.5575-0.78520.3077-0.61791.30230.12392.572-0.02470.47280.4578-1.1799-0.39260.11260.03830.90230.1359-0.00780.9489-0.10181.19112.3516-57.2447.4915
83.5477-0.06730.23282.2997-0.27561.12750.04520.0462-0.1582-0.1510.0249-0.0448-0.04040.1796-00.4675-0.06410.07130.61020.05430.512827.1648-30.825321.9822
91.1136-0.4281-0.4730.4715-0.18460.59610.0947-0.2982-0.53950.4575-0.0535-0.22310.0942-0.041-00.4269-0.00230.05720.67780.08290.696521.7419-37.855435.5368
100.123-0.0750.09640.22620.20540.4672-0.0743-0.01650.1405-0.0575-0.07170.0565-0.12990.3211-0.00080.3396-0.0150.08150.61140.04340.372418.5012-32.93717.3009
110.8521-0.51050.09430.61210.29860.38210.3186-0.0423-0.0443-0.7484-0.57881.31820.1686-0.401-0.02541.44350.00670.02160.56760.0750.6145-5.9996-22.0035-1.699
121.3308-0.4045-0.41870.93290.22620.30590.2470.16970.2438-0.28830.02790.1211-0.7080.30320.00010.7536-0.05030.07040.61220.10330.832-6.7661-2.56726.3914
130.72540.373-0.95310.4794-0.87721.75310.02220.1546-0.14790.0110.00450.3767-0.0578-0.207900.49670.02070.07880.4863-0.0320.5579-12.4223-13.060430.3643
140.45220.68710.34641.01430.51280.25220.33150.1123-0.1747-0.0784-0.1919-0.3535-0.385-0.0076-00.64780.01180.01140.62180.07950.63713.5559-16.153727.6805
150.4779-0.6025-0.06132.01360.01871.89420.19720.66160.80030.5011-0.5103-0.441-0.3272-0.5209-0.29520.8738-0.3260.18710.77340.15020.724614.059-13.756829.5203
160.2254-0.09070.05210.3515-0.14740.07120.0124-0.31190.03810.65740.4234-0.73110.45960.09990.00010.642-0.11830.05720.6756-0.11650.70864.7479-10.421824.4919
170.1692-0.2158-0.26181.22320.73150.56220.19840.17-0.18390.1427-0.1872-0.0028-0.04870.31620.00010.5391-0.0125-0.03440.5791-0.0820.6313-3.0969-21.344525.7259
180.8220.2097-1.04130.0913-0.19231.4009-0.484-0.14070.26310.03110.1341-0.5402-0.3821-0.2368-0.01020.4423-0.019-0.08130.5973-0.03820.6332-19.4262-18.587321.631
193.5361.7066-0.67712.965-0.82780.2486-0.26780.15910.1474-0.25210.5873-0.11430.25820.3460.94490.2410.43320.04380.5733-0.17110.478668.4434-47.946970.1476
200.63260.834-0.25311.2636-0.16370.2710.5640.6735-0.6765-0.9419-0.11970.07910.21620.1715-0.00040.79550.1263-0.02340.86070.00140.667951.8163-47.453339.8402
210.09490.092-0.19370.1657-0.3020.55840.07720.7874-0.4444-0.8736-0.15090.8789-0.3441-0.5009-0.00040.80380.0144-0.08580.9692-0.29870.890641.8305-52.10639.0614
221.1865-0.0524-0.4650.71610.2871.0130.162-0.01470.0990.2516-0.2084-0.09130.05970.1003-0.00010.3430.04370.02230.5164-0.00390.569646.602-41.954351.1564
231.24080.4593-0.78541.67190.09820.57260.1760.40210.0084-0.1011-0.23020.13230.3386-0.0648-0.00020.6273-0.05530.060.61240.06630.508149.9882-37.843449.7389
241.05921.21151.36061.38011.54891.7389-0.7092-0.8490.6426-0.72380.0198-0.2224-0.3147-0.9099-0.34670.5270.1927-0.07030.45590.08870.444440.3543-39.885767.3761
251.02050.56640.11150.8204-0.52390.6633-0.0299-0.0366-0.15140.05020.0679-0.03880.4834-0.12720.00010.55470.0210.01770.59270.08790.598945.8959-57.298758.0058
260.2802-0.5974-0.47171.1661.12851.1521-0.0099-0.8499-0.5405-0.57780.57321.0231-0.03450.07640.00041.0059-0.0473-0.1380.85390.23451.145530.6358-55.679385.5985
272.5342-0.8831-0.46983.1675-0.72271.5011-0.1333-0.1370.15560.35440.02290.14280.027-0.1608-00.5055-0.01850.02960.6088-0.07610.550615.1908-26.885469.6393
281.3798-0.6826-0.48630.31820.3871.4392-0.1988-0.09290.0407-0.07320.05380.1041-0.1494-0.0727-0.00010.39310.04120.03540.49020.04240.580324.9094-32.637166.7615
290.69840.3378-0.08950.238-0.20170.22330.40280.2433-0.43980.9302-0.8665-1.1285-0.35990.70.00071.63130.09-0.30460.924-0.17511.07449.2742-19.597594.0523
302.03330.1247-0.76680.9975-0.6352.82220.19740.03080.46150.2514-0.1515-0.3028-0.350.0108-00.5782-0.03120.01510.512-0.0270.877654.3684-10.346463.4797
311.4061-0.4475-0.72530.62310.51030.49770.1457-0.22260.3128-0.23330.13680.1798-0.4402-0.350200.6624-0.02230.03410.6150.0440.875540.4073-11.508962.6107
321.0175-0.2991-1.11120.39940.25711.1896-0.47990.2905-0.0798-0.61690.40820.08960.03610.1247-0.01210.37650.0158-0.13270.64010.08670.672758.103-21.069471.2858
330.52840.1875-0.20770.0564-0.07890.08230.19140.5061-0.8631-0.57960.32310.0570.4697-0.99950.00040.87620.0922-0.03541.3403-0.15971.040911.274137.782998.3949
341.1890.61370.26670.6190.32360.8792-0.0675-0.2942-0.2551-0.0753-0.32521.5472-0.6196-0.6014-0.06541.43020.322-0.130.9077-0.01040.9069-5.583136.455760.2492
351.68180.0292-1.14480.4660.37791.1267-0.12591.2948-0.0710.4206-0.3625-0.15860.2784-0.2177-0.15351.2160.3635-0.39550.7823-0.11520.83510.322540.252547.9572
360.2450.2653-0.30250.3095-0.34840.38640.3094-0.72230.0739-0.2672-0.42170.0605-0.1650.2052-0.06541.20750.1868-0.19720.6469-0.14440.66867.906138.285658.4276
370.50970.3386-0.09350.2519-0.01770.0521-0.23580.367-0.03210.1512-0.1909-0.1707-0.1364-0.3512-01.08450.2583-0.0590.7696-0.12540.75864.963326.014462.1995
380.29270.06360.23620.40360.00470.1856-0.1282-0.6383-0.6424-0.0925-0.4777-0.30830.2031-0.4095-0.00050.83760.1554-0.1410.8386-0.01710.71782.519714.28861.8502
390.39670.499-0.02880.69670.01650.0213-0.26650.3656-0.28610.04820.04170.14790.07740.025-0.00011.00490.2183-0.11350.705-0.07680.76293.046326.38661.4196
400.2957-0.2015-0.3040.14090.06360.6494-0.14460.42530.08510.29420.1906-0.188-0.28320.4028-0.00331.090.1129-0.10830.5341-0.13320.598313.763941.794164.9233
411.7534-0.55390.29050.1831-0.19160.71741.1083-1.5155-0.1338-0.5956-0.7607-1.0174-0.8321.05370.01461.4935-0.13760.29151.04620.16371.082641.758844.687671.3099
421.88620.2484-1.67161.5248-0.42391.487-0.018-0.16670.10640.3847-0.139-0.4274-0.0181-0.160500.73440.0141-0.00850.73390.05010.727142.697117.471650.4157
430.677-0.2889-0.6230.5059-0.05990.7660.1212-0.10930.0271-0.1506-0.22510.0215-0.3527-0.0099-00.9411-0.0297-0.10760.61520.0920.59333.737923.055955.8378
440.54990.3674-0.4860.4315-0.06640.68980.0520.1254-0.66211.470.07660.4130.045-0.0089-0.00751.12640.2125-0.29210.75590.00780.904836.228910.249692.0964
450.92550.6722-0.51981.0814-0.27780.30870.3590.11180.0426-0.0614-0.1691-0.14650.41440.30640.00030.83140.1573-0.10760.61030.00840.85414.7061-9.427674.1988
460.8906-0.16131.1590.60320.0861.90670.0622-0.3061-0.11490.0562-0.2190.0307-0.34930.1412-00.60740.10780.0370.6026-0.0490.717110.23312.40574.465
471.4395-1.0044-0.19291.7535-0.94251.08690.12220.1853-0.0977-0.2082-0.1386-0.00810.05160.2146-00.69150.0574-0.08830.6898-0.10890.690620.77952.19466.0616
480.48340.49060.88130.5480.94011.6272-0.1270.00710.2190.0497-0.2052-0.0144-0.3084-0.2213-00.84350.0777-0.0250.6657-0.12270.48911.475810.710783.2776
491.87620.69360.65340.22870.18730.2802-0.24690.2077-0.4261.04390.80620.91290.4251-0.15850.06731.46590.19730.14570.6890.1680.7196-5.170544.38467.1119
501.14920.1796-0.47950.6676-0.08511.7580.0509-0.24330.15470.03-0.01450.3754-0.0666-0.051400.8250.00950.04070.64750.00380.6549-3.179214.220529.7256
511.74511.3314-0.18441.0005-0.29081.16420.16640.00020.14790.2064-0.143-0.2014-0.16780.276-00.8787-0.0406-0.02310.54450.06050.53724.804520.5423.8748
522.76561.1192-1.88041.4922-1.82642.36520.774-0.5027-0.9911-1.5266-1.0303-0.0510.60680.0452-0.4321.8634-0.0954-0.59190.6416-0.19080.94731.11668.4711-12.7981
531.2994-0.3219-0.62961.8323-0.64271.5908-0.42060.3770.049-0.02270.23180.00180.10190.7184-0.01410.62940.14260.17160.77080.01260.565328.8756-2.54882.1366
540.58340.3726-0.57840.89550.10530.8577-0.11-0.2137-0.25830.52630.0667-0.14160.30710.1255-00.7031-0.0172-0.01670.81740.07260.781617.95931.733514.9717
551.07030.02020.2990.353-0.64841.2222-0.2470.17370.023-0.02730.1450.02110.16290.6607-00.86050.10710.07080.97840.10630.589123.76797.7719-2.7933
561.56112.3850.64456.6649-0.11790.6578-0.0909-1.5911.5639-0.59760.10350.44670.47850.51640.40751.08390.16480.21391.5613-0.40450.731129.50537.6656-11.3012
571.27160.3745-0.41641.13770.02380.45060.12040.3032-0.41310.660.011-0.448-0.55330.01220.00491.1468-0.4201-0.19680.86240.13720.769835.330338.179222.6074
580.7433-0.1882-0.89011.71780.41061.0515-0.1070.0684-0.25020.2202-0.0009-0.3117-0.21960.8665-00.775-0.2383-0.03231.03090.1260.57632.280525.771515.5311
590.6432-0.5358-0.44970.4380.37650.40240.1353-0.68610.04810.6109-0.2522-0.9163-0.5759-0.0379-0.00021.1833-0.1918-0.11140.91430.2480.864725.523245.672414.3552
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 29 )A3 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 65 )A30 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 127 )A66 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 151 )A128 - 151
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 182 )A152 - 182
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 217 )A183 - 217
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 27 )C1 - 27
8X-RAY DIFFRACTION8chain 'C' and (resid 28 through 118 )C28 - 118
9X-RAY DIFFRACTION9chain 'C' and (resid 119 through 156 )C119 - 156
10X-RAY DIFFRACTION10chain 'C' and (resid 157 through 217 )C157 - 217
11X-RAY DIFFRACTION11chain 'E' and (resid 3 through 27 )E3 - 27
12X-RAY DIFFRACTION12chain 'E' and (resid 28 through 50 )E28 - 50
13X-RAY DIFFRACTION13chain 'E' and (resid 51 through 106 )E51 - 106
14X-RAY DIFFRACTION14chain 'E' and (resid 107 through 134 )E107 - 134
15X-RAY DIFFRACTION15chain 'E' and (resid 135 through 144 )E135 - 144
16X-RAY DIFFRACTION16chain 'E' and (resid 145 through 156 )E145 - 156
17X-RAY DIFFRACTION17chain 'E' and (resid 157 through 192 )E157 - 192
18X-RAY DIFFRACTION18chain 'E' and (resid 193 through 217 )E193 - 217
19X-RAY DIFFRACTION19chain 'B' and (resid 3 through 29 )B3 - 29
20X-RAY DIFFRACTION20chain 'B' and (resid 30 through 50 )B30 - 50
21X-RAY DIFFRACTION21chain 'B' and (resid 51 through 65 )B51 - 65
22X-RAY DIFFRACTION22chain 'B' and (resid 66 through 140 )B66 - 140
23X-RAY DIFFRACTION23chain 'B' and (resid 141 through 182 )B141 - 182
24X-RAY DIFFRACTION24chain 'B' and (resid 183 through 192 )B183 - 192
25X-RAY DIFFRACTION25chain 'B' and (resid 193 through 217 )B193 - 217
26X-RAY DIFFRACTION26chain 'D' and (resid -1 through 27 )D-1 - 27
27X-RAY DIFFRACTION27chain 'D' and (resid 28 through 106 )D28 - 106
28X-RAY DIFFRACTION28chain 'D' and (resid 107 through 217 )D107 - 217
29X-RAY DIFFRACTION29chain 'F' and (resid 3 through 27 )F3 - 27
30X-RAY DIFFRACTION30chain 'F' and (resid 28 through 118 )F28 - 118
31X-RAY DIFFRACTION31chain 'F' and (resid 119 through 173 )F119 - 173
32X-RAY DIFFRACTION32chain 'F' and (resid 174 through 217 )F174 - 217
33X-RAY DIFFRACTION33chain 'G' and (resid -1 through 18 )G-1 - 18
34X-RAY DIFFRACTION34chain 'G' and (resid 19 through 50 )G19 - 50
35X-RAY DIFFRACTION35chain 'G' and (resid 51 through 65 )G51 - 65
36X-RAY DIFFRACTION36chain 'G' and (resid 66 through 106 )G66 - 106
37X-RAY DIFFRACTION37chain 'G' and (resid 107 through 127 )G107 - 127
38X-RAY DIFFRACTION38chain 'G' and (resid 128 through 140 )G128 - 140
39X-RAY DIFFRACTION39chain 'G' and (resid 141 through 182 )G141 - 182
40X-RAY DIFFRACTION40chain 'G' and (resid 183 through 217 )G183 - 217
41X-RAY DIFFRACTION41chain 'H' and (resid 3 through 27 )H3 - 27
42X-RAY DIFFRACTION42chain 'H' and (resid 28 through 95 )H28 - 95
43X-RAY DIFFRACTION43chain 'H' and (resid 96 through 217 )H96 - 217
44X-RAY DIFFRACTION44chain 'I' and (resid 3 through 27 )I3 - 27
45X-RAY DIFFRACTION45chain 'I' and (resid 28 through 50 )I28 - 50
46X-RAY DIFFRACTION46chain 'I' and (resid 51 through 118 )I51 - 118
47X-RAY DIFFRACTION47chain 'I' and (resid 119 through 182 )I119 - 182
48X-RAY DIFFRACTION48chain 'I' and (resid 183 through 217 )I183 - 217
49X-RAY DIFFRACTION49chain 'J' and (resid -2 through 27 )J-2 - 27
50X-RAY DIFFRACTION50chain 'J' and (resid 28 through 95 )J28 - 95
51X-RAY DIFFRACTION51chain 'J' and (resid 96 through 217 )J96 - 217
52X-RAY DIFFRACTION52chain 'K' and (resid 3 through 27 )K3 - 27
53X-RAY DIFFRACTION53chain 'K' and (resid 28 through 105 )K28 - 105
54X-RAY DIFFRACTION54chain 'K' and (resid 106 through 165 )K106 - 165
55X-RAY DIFFRACTION55chain 'K' and (resid 166 through 217 )K166 - 217
56X-RAY DIFFRACTION56chain 'L' and (resid 3 through 27 )L3 - 27
57X-RAY DIFFRACTION57chain 'L' and (resid 28 through 95 )L28 - 95
58X-RAY DIFFRACTION58chain 'L' and (resid 96 through 192 )L96 - 192
59X-RAY DIFFRACTION59chain 'L' and (resid 193 through 217 )L193 - 217

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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