[日本語] English
- PDB-7w2d: The closed conformation of the sigma-1 receptor from Xenopus laev... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7w2d
タイトルThe closed conformation of the sigma-1 receptor from Xenopus laevis complexed with S1RA
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 / endoplasmic reticulum / 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-88E / : / 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: 3.471 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

-
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

-
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)310,23648
ポリマ-301,46012
非ポリマー8,77636
00
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


  • 登録者・ソフトウェアが定義した集合体
  • 77.6 kDa, 3 ポリマー
分子量 (理論値)分子数
合計 (水以外)77,55912
ポリマ-75,3653
非ポリマー2,1949
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-64 kcal/mol
Surface area28650 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
  • 77.6 kDa, 3 ポリマー
分子量 (理論値)分子数
合計 (水以外)77,55912
ポリマ-75,3653
非ポリマー2,1949
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-67 kcal/mol
Surface area28460 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)77,55912
ポリマ-75,3653
非ポリマー2,1949
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-66 kcal/mol
Surface area28050 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)77,55912
ポリマ-75,3653
非ポリマー2,1949
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-64 kcal/mol
Surface area28650 Å2
手法PISA
単位格子
Length a, b, c (Å)86.299, 147.888, 171.395
Angle α, β, γ (deg.)90.000, 91.670, 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 5 through 19 or resid 31 through 501))
21(chain B and (resid 5 through 19 or resid 31 through 501))
31(chain C and (resid 5 through 19 or resid 31 through 501))
41(chain D and (resid 5 through 19 or resid 31 through 501))
51(chain E and (resid 5 through 19 or resid 31 through 501))
61(chain F and (resid 5 through 19 or resid 31 through 501))
71(chain G and resid 5 through 501)
81(chain H and (resid 5 through 19 or resid 31 through 501))
91(chain I and (resid 5 through 19 or resid 31 through 501))
101(chain J and (resid 5 through 19 or resid 31 through 501))
111(chain K and (resid 5 through 19 or resid 31 through 501))
121(chain L and (resid 5 through 19 or resid 31 through 501))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 19 or resid 31 through 501))A5 - 19
121(chain A and (resid 5 through 19 or resid 31 through 501))A31 - 501
211(chain B and (resid 5 through 19 or resid 31 through 501))B5 - 19
221(chain B and (resid 5 through 19 or resid 31 through 501))B31 - 501
311(chain C and (resid 5 through 19 or resid 31 through 501))C5 - 19
321(chain C and (resid 5 through 19 or resid 31 through 501))C31 - 501
411(chain D and (resid 5 through 19 or resid 31 through 501))D5 - 19
421(chain D and (resid 5 through 19 or resid 31 through 501))D31 - 501
511(chain E and (resid 5 through 19 or resid 31 through 501))E5 - 19
521(chain E and (resid 5 through 19 or resid 31 through 501))E31 - 501
611(chain F and (resid 5 through 19 or resid 31 through 501))F5 - 19
621(chain F and (resid 5 through 19 or resid 31 through 501))F31 - 501
711(chain G and resid 5 through 501)G5 - 501
811(chain H and (resid 5 through 19 or resid 31 through 501))H5 - 19
821(chain H and (resid 5 through 19 or resid 31 through 501))H31 - 501
911(chain I and (resid 5 through 19 or resid 31 through 501))I5 - 19
921(chain I and (resid 5 through 19 or resid 31 through 501))I31 - 501
1011(chain J and (resid 5 through 19 or resid 31 through 501))J5 - 19
1021(chain J and (resid 5 through 19 or resid 31 through 501))J31 - 501
1111(chain K and (resid 5 through 19 or resid 31 through 501))K5 - 19
1121(chain K and (resid 5 through 19 or resid 31 through 501))K31 - 501
1211(chain L and (resid 5 through 19 or resid 31 through 501))L5 - 19
1221(chain L and (resid 5 through 19 or resid 31 through 501))L31 - 501

-
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-88E / 4-[2-(5-methyl-1-naphthalen-2-yl-pyrazol-3-yl)oxyethyl]morpholine / S1RA


分子量: 337.416 Da / 分子数: 12 / 由来タイプ: 合成 / : C20H23N3O2 / タイプ: SUBJECT OF INVESTIGATION / コメント: アンタゴニスト*YM
研究の焦点であるリガンドがあるかY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.63 Å3/Da / 溶媒含有率: 66.08 %
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, 26% PEG 400, 10mM KAu(CN)2, 0.4mM S1RA soaking

-
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: BL18U1 / 波長: 0.97915 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年5月8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: 3.471→48.269 Å / Num. obs: 53754 / % possible obs: 96.5 % / 冗長度: 3.4 % / Biso Wilson estimate: 100.23 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.094 / Rrim(I) all: 0.175 / Net I/σ(I): 6.7 / Num. measured all: 184286
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
3.471-3.533.30.786908527550.6520.5130.9421.799.9
9.399-48.2693.10.072854627830.9860.0490.08716.197

-
位相決定

位相決定手法: 分子置換

-
解析

ソフトウェア
名称バージョン分類
XDSBUILT 20210323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: 3.471→48.269 Å / SU ML: 0.44 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 27.93 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2665 2702 5.04 %
Rwork0.2394 50957 -
obs0.2407 53659 96.32 %
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: 204.42 Å2 / Biso mean: 104.5118 Å2 / Biso min: 55.62 Å2
精密化ステップサイクル: final / 解像度: 3.471→48.269 Å
タンパク質核酸リガンド溶媒全体
原子数20269 0 324 0 20593
Biso mean--92.28 --
残基数----2565
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsタイプ
11A11558X-RAY DIFFRACTION7.044TORSIONAL
12B11558X-RAY DIFFRACTION7.044TORSIONAL
13C11558X-RAY DIFFRACTION7.044TORSIONAL
14D11558X-RAY DIFFRACTION7.044TORSIONAL
15E11558X-RAY DIFFRACTION7.044TORSIONAL
16F11558X-RAY DIFFRACTION7.044TORSIONAL
17G11558X-RAY DIFFRACTION7.044TORSIONAL
18H11558X-RAY DIFFRACTION7.044TORSIONAL
19I11558X-RAY DIFFRACTION7.044TORSIONAL
110J11558X-RAY DIFFRACTION7.044TORSIONAL
111K11558X-RAY DIFFRACTION7.044TORSIONAL
112L11558X-RAY DIFFRACTION7.044TORSIONAL
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 (%)
3.471-3.53370.33881450.30642760100
3.5337-3.60170.28631420.30112778100
3.6017-3.67510.30421300.2831219181
3.6751-3.7550.3161500.27692783100
3.755-3.84230.34351270.26922762100
3.8423-3.93840.3084700.2698166959
3.9384-4.04480.28351590.25392734100
4.0448-4.16380.23521450.23292761100
4.1638-4.29810.24431550.22532796100
4.2981-4.45160.24551450.20792748100
4.4516-4.62970.2221130.21172823100
4.6297-4.84020.26721480.20862743100
4.8402-5.09520.25151280.22662827100
5.0952-5.4140.25591740.24492761100
5.414-5.83140.30771770.27632727100
5.8314-6.4170.27321760.24542758100
6.417-7.34270.25811340.23632807100
7.3427-9.24040.23141380.1951280999
9.2404-48.2690.26281460.2502272095
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)
11.186-1.29350.71442.215-0.16030.679-0.0328-0.7368-0.10270.57150.0025-1.03540.2101-0.02040.15310.5066-0.27960.26070.69140.02860.6183-28.9449-48.2815.3697
26.19-0.30791.57773.99860.89554.98460.1357-2.1437-0.47540.86280.03460.2585-0.1601-0.2654-0.15620.75180.04120.05111.06580.06680.9009-11.7416-48.217545.6098
34.0951.717-0.00697.2097-0.13864.02430.6609-0.91030.16830.5284-0.917-0.5777-0.50341.4845-0.01060.8864-0.129-0.01080.88750.21460.8544-1.7866-52.565646.4837
42.24951.06130.32813.5572-0.7552.14840.4649-0.0563-0.22440.6388-0.83520.07080.21930.45290.29370.49470.09150.04390.6184-0.030.8462-3.7787-49.9833.8267
53.2516-0.31970.91581.4174-0.31012.50680.6367-0.103-2.169-0.04230.15870.26030.2207-0.1592-0.84260.78870.0154-0.03440.64930.09591.3311-8.5453-35.932929.6825
61.3966-0.36580.32771.527-1.12571.97760.4224-0.20390.15810.7035-0.70060.2329-0.2995-0.06530.10380.50180.03080.15230.8046-0.12581.0152-10.3862-31.510339.1714
72.16150.5099-0.63130.169-0.46093.0955-0.4649-0.44060.20740.3064-0.0593-0.00750.0019-0.19510.50450.60280.0652-0.03040.7356-0.12180.7006-8.1432-39.872531.2867
84.11520.45051.09244.30330.50923.62090.0688-0.2901-1.21610.1138-0.3088-0.7251.06680.21190.19180.67720.0927-0.00420.5476-0.08560.8089-5.4618-57.933427.5468
91.6311.37160.16771.2894-0.31041.03190.21.534-1.97980.26160.8175-1.1231-0.4370.6382-0.71711.33080.1086-0.10771.1167-0.28221.840610.1944-54.19890.77
105.26072.07720.98413.8816-0.10253.2984-0.02660.1824-0.1259-0.1626-0.1241-0.42310.11180.27760.15570.73440.0614-0.03380.71350.07360.970122.505-28.313316.5271
112.04040.3897-0.67332.4667-1.00461.2311-0.2876-0.5324-0.10310.31040.1459-0.21010.20710.30670.08960.70680.1563-0.0010.727-0.02810.946516.9895-36.259129.5005
120.8410.70510.31832.70381.34762.5146-0.5206-0.08630.0388-0.28060.29040.0176-0.27280.33810.24240.6996-0.0185-0.03690.82390.01410.671114.23-30.549711.3409
130.1696-0.6336-0.59163.69183.55313.33780.17540.0823-0.261-0.1457-1.08820.61820.83380.73660.6382.67030.2375-0.4871.40350.12891.3019-9.8387-20.5294-8.4477
142.58930.7308-0.9743.4399-0.10533.1747-0.23740.21150.92420.24510.5375-0.0968-0.646-0.7048-0.06770.88610.1139-0.07320.90350.02141.4233-17.5369-7.82623.4062
152.0395-0.43491.20761.7327-0.18341.4066-0.15130.33590.16950.05650.10970.1126-0.1480.02820.01680.67920.1131-0.06280.6789-0.06120.8773-9.0657-16.617419.3024
164.13323.09494.3242.26953.06664.6739-1.65441.1040.5178-0.0376-0.65261.59990.7231.53570.8430.51670.210.12180.68370.0110.828664.5516-49.476160.859
176.7613-1.94682.60664.2957-1.14244.03840.56130.8181-0.5298-0.4764-0.5868-0.6843-0.10440.9224-0.14510.7735-0.0248-0.020.64940.00670.845746.159-48.294331.3121
185.4523-2.95051.58857.3072-1.354.9463-0.59560.4296-0.0284-0.89330.2906-0.2617-0.9063-0.77620.21980.6714-0.09310.11850.7995-0.23890.9536.2793-52.919630.7541
193.83180.86261.54261.50060.73492.74290.1944-0.5823-0.45530.086-0.4922-0.01540.4947-0.43080.23160.58770.00820.02140.66130.05430.742738.9897-51.009243.3599
201.2353-0.07210.66512.38531.76453.48430.29980.1292-0.3413-0.1106-0.11510.30810.0228-0.0059-0.12250.57390.02420.09190.69240.05920.783744.2927-33.59841.5775
210.961.3927-0.04573.42180.46033.1096-0.66280.360.13480.22730.30420.5216-1.2980.2270.33760.70490.0194-0.10210.75090.05390.593744.091-38.648339.851
221.44640.3472-0.15373.29420.73711.9838-0.0969-0.2337-0.2253-0.3781-0.05860.17030.0155-0.13340.14030.7285-0.0041-0.04880.70120.20260.711541.4193-53.147652.0172
233.9276-3.43010.37873.02440.40763.5141.0209-2.9052-2.44231.3081-0.14461.6305-0.37130.4322-0.21861.163-0.0440.0322.20260.54141.672227.4791-57.418677.4376
243.84822.35740.55913.68310.80372.880.1827-0.3359-0.33680.1908-0.54620.4003-0.115-0.44740.31690.55380.0946-0.00180.8214-0.19340.774213.235-31.455163.602
253.75050.15020.822.9788-0.19031.1922-0.0651-0.2087-0.9608-0.566-0.09850.54340.0821-0.10190.15180.67660.0186-0.06580.7845-0.09030.963718.2005-38.490649.8597
262.0621-0.38841.21031.1141-0.76932.32630.058-0.41430.0033-0.0419-0.29160.3744-0.2361-1.23830.23810.65960.06370.02330.9805-0.07440.665221.8324-33.589668.0874
271.98231.0873-0.69022.0137-1.832.04490.5697-0.2322-0.66611.31810.2026-0.99071.0262-1.304-0.97942.47390.0319-0.31741.36750.08031.099546.7884-23.611186.8155
283.53881.093-0.50583.6457-0.19393.65260.0853-0.2437-0.00550.11930.0092-0.4427-0.09310.4065-0.02390.6323-0.00740.19180.5473-0.00110.667251.0579-11.099156.1024
292.40871.1973-0.35583.582-0.33081.4460.0535-0.30470.1526-0.0565-0.14690.7307-1.0278-0.64640.17760.79820.1628-0.03760.795-0.03110.667135.8846-15.339957.2678
302.5010.026-0.37661.2648-0.21275.3191-0.02670.3689-0.04550.1064-0.02880.0447-0.61190.30040.14070.57120.021-0.0780.69050.15770.671154.0531-23.532263.3793
312.4146-1.73930.64112.7469-0.36532.9691.5393-0.8871-1.79610.7221-0.8843-0.24790.27820.0541-0.29871.0915-0.38990.11240.78320.29851.010432.902438.28170.0311
323.0408-1.2939-0.24371.52531.43241.8030.3592-0.00090.5187-0.2072-0.295-0.2789-0.41940.1677-0.08051.4732-0.4733-0.14030.99910.07720.941536.358436.897533.1282
33-0.0545-0.7367-0.15523.37840.4035-0.0427-0.01380.1138-0.2881-0.04510.03860.0348-0.35490.1589-0.05931.2407-0.2742-0.11670.86130.20320.844933.069529.574823.9341
341.41430.98350.31830.795-0.04850.36460.5090.71240.1511.9236-0.27710.4119-3.3298-1.79530.01382.17240.53450.13851.5334-0.03441.7963-2.344443.642715.5418
354.2620.0268-2.12052.93931.35123.85670.3769-0.40850.0303-0.2249-0.43430.2256-0.4339-0.29780.21851.0259-0.1139-0.05460.9582-0.1310.7445-0.44217.76434.9484
360.7845-0.73920.21851.6944-0.52022.3344-0.02270.01140.43050.3814-0.2488-0.0819-0.6287-0.09490.22061.1404-0.0081-0.09140.75470.03670.83056.081321.801330.9745
371.0421-0.67620.12180.4865-0.39581.1037-0.26350.52990.5648-1.1845-0.0571-0.975-1.04870.99560.12751.5624-0.2245-0.40650.98470.13741.79613.54478.7993-5.2827
382.814-0.5541-1.42684.07741.61962.9112-0.07950.3578-0.3282-0.2508-0.07690.07660.2136-0.31220.18240.7415-0.03970.01170.94530.07041.148531.361-4.504910.9322
391.0782-0.8456-1.88272.8711.22453.84160.44430.37080.16490.2992-0.4765-0.50390.2282-0.9232-0.05780.8071-0.0204-0.02530.94080.01370.798823.70555.186113.5057
401.52480.67620.85992.71140.23091.54310.27710.1765-0.2035-0.0794-0.09810.1027-0.1745-0.3121-0.08250.7061-0.0307-0.08860.74210.13820.613222.29124.624114.0485
416.67690.21930.01486.10160.21645.39251.69551.04471.688-0.7248-1.751-0.6054-0.3379-0.18040.10011.22220.00490.12861.30690.19890.916717.157935.4725101.2024
422.4356-0.9075-2.07946.32594.23233.61811.20541.4479-0.9455-2.0593-1.55422.1443-1.1194-0.4938-0.61821.45820.70280.01881.56940.00811.2891-1.595535.61471.033
431.94320.3659-0.32773.45180.55616.7413-0.3887-1.03691.00650.43091.36720.0020.7933-1.0247-1.05921.51820.7707-0.33732.0052-0.20811.08082.694438.480657.4226
442.62430.82490.44542.21520.95561.7588-0.3443-0.42060.2222-0.4442-0.0870.4495-0.6691-0.67940.56871.34820.489-0.0371.3017-0.15140.902811.363832.929968.4207
452.84640.40360.83991.8488-0.06973.39360.1337-0.2893-0.4231-0.56710.13550.0432-0.4052-0.8793-0.34070.82960.22460.16581.5894-0.25331.05943.125617.497369.0003
462.2559-0.8926-0.22571.2981.1765.5522-0.22510.04540.2298-0.4586-0.33810.4814-0.0783-1.92160.45871.18840.3636-0.23861.4661-0.27980.898110.567325.963772.1467
471.4823-1.3398-0.35673.57170.22152.1766-0.11510.4117-0.1321-0.8781-0.28170.3602-0.5361-0.54710.25671.39980.2078-0.09121.2221-0.43680.881914.992144.137672.124
482.4404-1.00210.68390.3987-0.29960.2629-0.2303-0.5017-0.9013-0.8527-0.2216-1.1666-0.83780.28010.48132.9109-1.09990.3321.2229-0.12371.31746.22440.643777.0437
496.3801-0.2279-1.52594.36270.58845.0110.09810.40230.2246-0.2001-0.0968-0.2526-0.6805-0.06290.02780.99940.10470.03940.6083-0.01010.588941.604614.733657.8273
503.1603-0.0578-2.28922.0811-0.27652.48790.3440.14640.2424-0.1013-0.0244-0.2559-0.0735-0.4073-0.29851.39450.12730.0730.6845-0.04810.731327.91122.499353.8158
511.4141.06671.03211.18630.78331.9228-0.11130.15050.040.06280.2166-0.1207-0.0271-0.1806-0.13690.95980.03970.03310.6812-0.10880.647440.339316.998567.4936
524.83533.9060.40573.87042.0033.54331.51761.26690.05381.3779-1.7536-0.0420.1334-0.59740.13511.73820.2115-0.58440.99210.26172.5540.51797.163398.7649
532.16360.7594-1.69373.5319-0.69482.0118-0.5395-0.0234-0.53710.06280.17450.53010.5156-1.17870.35451.2036-0.26290.32481.5942-0.17731.033311.5707-4.487484.3861
540.61720.24740.03751.6490.82434.2150.0905-0.2486-0.04720.5376-0.04580.04550.5489-0.57120.11131.1225-0.12030.11611.2928-0.07420.740920.08082.78180.4349
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 50 )A30 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 65 )A51 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 106 )A66 - 106
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 118 )A107 - 118
6X-RAY DIFFRACTION6chain 'A' and (resid 119 through 144 )A119 - 144
7X-RAY DIFFRACTION7chain 'A' and (resid 145 through 192 )A145 - 192
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 217 )A193 - 217
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 27 )C2 - 27
10X-RAY DIFFRACTION10chain 'C' and (resid 28 through 118 )C28 - 118
11X-RAY DIFFRACTION11chain 'C' and (resid 119 through 156 )C119 - 156
12X-RAY DIFFRACTION12chain 'C' and (resid 157 through 217 )C157 - 217
13X-RAY DIFFRACTION13chain 'E' and (resid 3 through 27 )E3 - 27
14X-RAY DIFFRACTION14chain 'E' and (resid 28 through 85 )E28 - 85
15X-RAY DIFFRACTION15chain 'E' and (resid 86 through 217 )E86 - 217
16X-RAY DIFFRACTION16chain 'B' and (resid 3 through 29 )B3 - 29
17X-RAY DIFFRACTION17chain 'B' and (resid 30 through 50 )B30 - 50
18X-RAY DIFFRACTION18chain 'B' and (resid 51 through 65 )B51 - 65
19X-RAY DIFFRACTION19chain 'B' and (resid 66 through 106 )B66 - 106
20X-RAY DIFFRACTION20chain 'B' and (resid 107 through 144 )B107 - 144
21X-RAY DIFFRACTION21chain 'B' and (resid 145 through 173 )B145 - 173
22X-RAY DIFFRACTION22chain 'B' and (resid 174 through 217 )B174 - 217
23X-RAY DIFFRACTION23chain 'D' and (resid 2 through 27 )D2 - 27
24X-RAY DIFFRACTION24chain 'D' and (resid 28 through 118 )D28 - 118
25X-RAY DIFFRACTION25chain 'D' and (resid 119 through 156 )D119 - 156
26X-RAY DIFFRACTION26chain 'D' and (resid 157 through 217 )D157 - 217
27X-RAY DIFFRACTION27chain 'F' and (resid 3 through 27 )F3 - 27
28X-RAY DIFFRACTION28chain 'F' and (resid 28 through 106 )F28 - 106
29X-RAY DIFFRACTION29chain 'F' and (resid 107 through 173 )F107 - 173
30X-RAY DIFFRACTION30chain 'F' and (resid 174 through 217 )F174 - 217
31X-RAY DIFFRACTION31chain 'G' and (resid 3 through 35 )G3 - 35
32X-RAY DIFFRACTION32chain 'G' and (resid 36 through 95 )G36 - 95
33X-RAY DIFFRACTION33chain 'G' and (resid 96 through 217 )G96 - 217
34X-RAY DIFFRACTION34chain 'H' and (resid 3 through 27 )H3 - 27
35X-RAY DIFFRACTION35chain 'H' and (resid 28 through 118 )H28 - 118
36X-RAY DIFFRACTION36chain 'H' and (resid 119 through 217 )H119 - 217
37X-RAY DIFFRACTION37chain 'I' and (resid 3 through 29 )I3 - 29
38X-RAY DIFFRACTION38chain 'I' and (resid 30 through 85 )I30 - 85
39X-RAY DIFFRACTION39chain 'I' and (resid 86 through 118 )I86 - 118
40X-RAY DIFFRACTION40chain 'I' and (resid 119 through 217 )I119 - 217
41X-RAY DIFFRACTION41chain 'J' and (resid 5 through 18 )J5 - 18
42X-RAY DIFFRACTION42chain 'J' and (resid 19 through 50 )J19 - 50
43X-RAY DIFFRACTION43chain 'J' and (resid 51 through 65 )J51 - 65
44X-RAY DIFFRACTION44chain 'J' and (resid 66 through 118 )J66 - 118
45X-RAY DIFFRACTION45chain 'J' and (resid 119 through 144 )J119 - 144
46X-RAY DIFFRACTION46chain 'J' and (resid 145 through 192 )J145 - 192
47X-RAY DIFFRACTION47chain 'J' and (resid 193 through 217 )J193 - 217
48X-RAY DIFFRACTION48chain 'K' and (resid 2 through 27 )K2 - 27
49X-RAY DIFFRACTION49chain 'K' and (resid 28 through 118 )K28 - 118
50X-RAY DIFFRACTION50chain 'K' and (resid 119 through 156 )K119 - 156
51X-RAY DIFFRACTION51chain 'K' and (resid 157 through 217 )K157 - 217
52X-RAY DIFFRACTION52chain 'L' and (resid 3 through 27 )L3 - 27
53X-RAY DIFFRACTION53chain 'L' and (resid 28 through 95 )L28 - 95
54X-RAY DIFFRACTION54chain 'L' and (resid 96 through 217 )L96 - 217

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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