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- PDB-5nkm: SMG8-SMG9 complex -

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基本情報

登録情報
データベース: PDB / ID: 5nkm
タイトルSMG8-SMG9 complex
要素
  • (Protein smg-8) x 2
  • (Protein smg-9) x 2
キーワードRNA BINDING PROTEIN / SMG8-SMG9 complex NMD effector proteins
機能・相同性
機能・相同性情報


Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / striated muscle dense body / molecular sequestering activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cytoplasm
類似検索 - 分子機能
Nonsense-mediated mRNA decay factor SMG8/SMG9 / Smg8_Smg9 / Nonsense-mediated mRNA decay factor SMG9 / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / Nonsense-mediated mRNA decay factor SMG8 / Nonsense-mediated mRNA decay factor SMG9
類似検索 - 構成要素
生物種Caenorhabditis elegans (センチュウ)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.493 Å
データ登録者Li, L. / Basquin, J. / Conti, E.
引用ジャーナル: RNA / 年: 2017
タイトル: Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins.
著者: Li, L. / Lingaraju, M. / Basquin, C. / Basquin, J. / Conti, E.
履歴
登録2017年3月31日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年4月19日Provider: repository / タイプ: Initial release
改定 1.12017年6月28日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
カテゴリ: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Protein smg-8
B: Protein smg-9
C: Protein smg-8
D: Protein smg-9
E: Protein smg-8
F: Protein smg-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)259,87621
ポリマ－258,7376
非ポリマー1,13915
水3,063170
1
A: Protein smg-8
B: Protein smg-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)87,7494
ポリマ－87,6252
非ポリマー1242
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-10 kcal/mol
Surface area26960 Å2
手法PISA
2
C: Protein smg-8
D: Protein smg-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)86,8219
ポリマ－86,2392
非ポリマー5837
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint6 kcal/mol
Surface area27210 Å2
手法PISA
3
E: Protein smg-8
F: Protein smg-9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)85,3058
ポリマ－84,8732
非ポリマー4326
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-6 kcal/mol
Surface area27140 Å2
手法PISA
単位格子
Length a, b, c (Å)111.085, 111.085, 374.474
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDモデル要素
11A-612-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain B and (resid 59 through 82 or (resid 83...
21(chain D and (resid 59 through 80 or (resid 81...
31(chain F and (resid 59 through 80 or (resid 81...
12(chain A and (resid 1 through 127 or (resid 128...
22(chain C and (resid 1 through 7 or (resid 8...
32(chain E and (resid 1 through 4 or (resid 5...

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
111MSEMSESERSER(chain B and (resid 59 through 82 or (resid 83...BB59 - 821 - 24
121SERSERSERSER(chain B and (resid 59 through 82 or (resid 83...BB8325
131MSEMSEASPASP(chain B and (resid 59 through 82 or (resid 83...BB59 - 3641 - 306
141MSEMSEASPASP(chain B and (resid 59 through 82 or (resid 83...BB59 - 3641 - 306
151MSEMSEASPASP(chain B and (resid 59 through 82 or (resid 83...BB59 - 3641 - 306
161MSEMSEASPASP(chain B and (resid 59 through 82 or (resid 83...BB59 - 3641 - 306
211MSEMSELEULEU(chain D and (resid 59 through 80 or (resid 81...DD59 - 801 - 22
221THRTHRTHRTHR(chain D and (resid 59 through 80 or (resid 81...DD8123
231MSEMSETHRTHR(chain D and (resid 59 through 80 or (resid 81...DD59 - 3631 - 305
241MSEMSETHRTHR(chain D and (resid 59 through 80 or (resid 81...DD59 - 3631 - 305
251MSEMSETHRTHR(chain D and (resid 59 through 80 or (resid 81...DD59 - 3631 - 305
261MSEMSETHRTHR(chain D and (resid 59 through 80 or (resid 81...DD59 - 3631 - 305
311MSEMSELEULEU(chain F and (resid 59 through 80 or (resid 81...FF59 - 801 - 22
321THRTHRTHRTHR(chain F and (resid 59 through 80 or (resid 81...FF8123
331MSEMSETHRTHR(chain F and (resid 59 through 80 or (resid 81...FF59 - 3631 - 305
341MSEMSETHRTHR(chain F and (resid 59 through 80 or (resid 81...FF59 - 3631 - 305
351MSEMSETHRTHR(chain F and (resid 59 through 80 or (resid 81...FF59 - 3631 - 305
361MSEMSETHRTHR(chain F and (resid 59 through 80 or (resid 81...FF59 - 3631 - 305
112MSEMSEGLUGLU(chain A and (resid 1 through 127 or (resid 128...AA1 - 1271 - 127
122GLNGLNGLNGLN(chain A and (resid 1 through 127 or (resid 128...AA128128
132MSEMSESERSER(chain A and (resid 1 through 127 or (resid 128...AA1 - 4201 - 420
142MSEMSESERSER(chain A and (resid 1 through 127 or (resid 128...AA1 - 4201 - 420
152MSEMSESERSER(chain A and (resid 1 through 127 or (resid 128...AA1 - 4201 - 420
162MSEMSESERSER(chain A and (resid 1 through 127 or (resid 128...AA1 - 4201 - 420
212MSEMSEVALVAL(chain C and (resid 1 through 7 or (resid 8...CC1 - 71 - 7
222GLUGLUGLUGLU(chain C and (resid 1 through 7 or (resid 8...CC88
232MSEMSESERSER(chain C and (resid 1 through 7 or (resid 8...CC1 - 4201 - 420
242MSEMSESERSER(chain C and (resid 1 through 7 or (resid 8...CC1 - 4201 - 420
252MSEMSESERSER(chain C and (resid 1 through 7 or (resid 8...CC1 - 4201 - 420
262MSEMSESERSER(chain C and (resid 1 through 7 or (resid 8...CC1 - 4201 - 420
312MSEMSEALAALA(chain E and (resid 1 through 4 or (resid 5...EE1 - 41 - 4
322LYSLYSLYSLYS(chain E and (resid 1 through 4 or (resid 5...EE55
332MSEMSEGLNGLN(chain E and (resid 1 through 4 or (resid 5...EE1 - 4191 - 419
342MSEMSEGLNGLN(chain E and (resid 1 through 4 or (resid 5...EE1 - 4191 - 419
352MSEMSEGLNGLN(chain E and (resid 1 through 4 or (resid 5...EE1 - 4191 - 419
362MSEMSEGLNGLN(chain E and (resid 1 through 4 or (resid 5...EE1 - 4191 - 419

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 4種, 6分子 ACBDFE

#1: タンパク質 Protein smg-8 / Suppressor with morphogenetic effect on genitalia protein 8


分子量: 50393.395 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Caenorhabditis elegans (センチュウ)
遺伝子: smg-8, K04B12.3
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: O62301
#2: タンパク質 Protein smg-9 / Suppressor with morphogenetic effect on genitalia protein 9


分子量: 37231.883 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Caenorhabditis elegans (センチュウ)
遺伝子: smg-9, Y54E2A.2
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9XWJ1
#3: タンパク質 Protein smg-9 / Suppressor with morphogenetic effect on genitalia protein 9


分子量: 35845.445 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Caenorhabditis elegans (センチュウ)
遺伝子: smg-9, Y54E2A.2
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9XWJ1
#4: タンパク質 Protein smg-8 / Suppressor with morphogenetic effect on genitalia protein 8


分子量: 49027.074 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Caenorhabditis elegans (センチュウ)
遺伝子: smg-8, K04B12.3
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: O62301

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非ポリマー , 4種, 185分子

#5: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C2H6O2
#6: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#7: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H10O3
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 170 / 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: 3.07 Å3/Da / 溶媒含有率: 59.96 %
結晶化温度: 285 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5 / 詳細: 10% PEG3350, 0.1M Tris pH 8.5

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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: 0.979 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2015年5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: 0.979 Å / 相対比: 1
反射解像度: 2.493→52.36 Å / Num. obs: 188934 / % possible obs: 98 % / 冗長度: 39 % / Rmerge(I) obs: 0.1374 / Net I/σ(I): 27.25
反射 シェル解像度: 2.493→2.583 Å / Rmerge(I) obs: 2.587

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
XDSデータスケーリング
SHELXD位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.493→62.412 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 32.41
Rfactor反射数%反射
Rfree0.2602 8972 4.99 %
Rwork0.2247 --
obs0.2264 179816 99.76 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 264.81 Å2 / Biso mean: 96.4963 Å2 / Biso min: 49.12 Å2
精密化ステップサイクル: final / 解像度: 2.493→62.412 Å
タンパク質核酸リガンド溶媒全体
原子数14115 0 184 170 14469
Biso mean--115.86 75.87 -
残基数----1824
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00314373
X-RAY DIFFRACTIONf_angle_d0.56819433
X-RAY DIFFRACTIONf_chiral_restr0.042308
X-RAY DIFFRACTIONf_plane_restr0.0042500
X-RAY DIFFRACTIONf_dihedral_angle_d13.2558762
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11B4224X-RAY DIFFRACTION9.595TORSIONAL
12D4224X-RAY DIFFRACTION9.595TORSIONAL
13F4224X-RAY DIFFRACTION9.595TORSIONAL
21A5583X-RAY DIFFRACTION9.595TORSIONAL
22C5583X-RAY DIFFRACTION9.595TORSIONAL
23E5583X-RAY DIFFRACTION9.595TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4934-2.52180.4923170.43515383570094
2.5218-2.55140.3963060.386856335939100
2.5514-2.58260.33863160.360257816097100
2.5826-2.61530.41542720.356356355907100
2.6153-2.64970.34352620.342158066068100
2.6497-2.6860.35672940.334356215915100
2.686-2.72430.32133060.323957166022100
2.7243-2.7650.35143410.329456846025100
2.765-2.80820.33483320.312456375969100
2.8082-2.85420.32683140.306157626076100
2.8542-2.90350.37212340.291357916025100
2.9035-2.95630.33632570.295456695926100
2.9563-3.01310.31273020.278957846086100
3.0131-3.07460.2843040.271256685972100
3.0746-3.14150.30343000.270856945994100
3.1415-3.21450.26542980.262456695967100
3.2145-3.29490.2773040.251356976001100
3.2949-3.3840.28242960.254457816077100
3.384-3.48360.29032740.246557386012100
3.4836-3.5960.26123140.230456735987100
3.596-3.72450.25883000.217757126012100
3.7245-3.87360.2373180.198656445962100
3.8736-4.04990.23113520.195156315983100
4.0499-4.26340.21913300.187157386068100
4.2634-4.53040.22342680.166757095977100
4.5304-4.88010.20263340.168556866020100
4.8801-5.37090.21563060.189157106016100
5.3709-6.14750.25892510.218757646015100
6.1475-7.74290.25473010.216257066007100
7.7429-62.43190.23732690.191157225991100
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)
18.06460.8942-2.18043.33114.83738.56630.9057-1.68221.99470.79330.5667-2.5854-0.44961.8837-1.27380.7685-0.1358-0.20110.692-0.19921.6622100.6302196.5642421.3497
25.6357-3.0033-0.43725.8507-0.09391.9494-0.01780.0440.8172-0.0785-0.0346-1.251-0.44290.30640.01550.6707-0.08310.01540.62380.08620.94399.8085193.6927412.6272
33.1541-2.9468-4.0022.78983.61078.0077-0.3030.13910.72990.52250.1436-0.82560.27580.4560.31390.60150.0285-0.07760.70830.00410.8833102.4455171.6276420.7473
46.82860.63530.85628.3176-1.60222.397-0.02730.20680.7051-0.2234-0.1012-0.47380.25560.62270.09210.61320.07080.10740.63280.08990.6589.9864185.8831411.4945
51.8252-1.2901-0.2844.4640.26796.593-0.0903-0.1688-0.12590.47850.05810.9302-0.21320.05190.00050.5251-0.03320.09410.6330.01570.829981.811187.8307420.3169
69.2445-0.52133.64497.9157-2.6512.19380.49080.31420.6032-1.2648-0.34750.50240.7366-1.31040.05871.0082-0.0516-0.00321.2461-0.1040.99883.3114183.3283393.4271
72.4884-0.93971.29811.89140.263.175-0.0460.11770.359-0.0067-0.04460.1324-0.37030.00860.13360.6102-0.00370.10660.62410.0580.803184.7553190.8435412.1427
84.5113-3.70293.31775.727-5.48855.2216-0.0294-0.9875-0.24440.63030.58621.15220.2779-0.045-0.4850.86530.06690.02240.84460.18830.599597.4957152.8172428.5623
98.79824.05672.7695.43370.57448.17281.2195-0.7468-0.89711.1584-0.3447-1.08930.99380.068-0.83690.90540.0521-0.15190.86150.18590.816105.5002149.9783427.204
100.73981.405-1.51794.3926-2.32733.2892-0.6426-0.40560.11890.87670.60850.0821-0.3613-0.4194-0.22051.91-0.5189-0.52132.13230.72630.8241103.6895142.8782440.6336
114.60395.3318-4.72876.1786-5.45194.8862-0.31971.0561-0.4676-1.0265-0.0021-0.50842.1714-0.8160.54660.8139-0.02670.06730.8548-0.15490.836293.7466147.5236390.1926
121.9880.3332-0.35862.4628-0.66681.27520.11720.49220.089-0.24460.1637-0.38160.53510.1069-0.14130.68060.03310.0060.697-0.25321.154793.9126140.8491396.7455
131.5649-2.2562.5434.8054-2.33837.211-0.18160.8418-0.0007-0.49030.008-0.7770.05160.48160.17120.5408-0.03280.17690.87320.05010.7232101.9956157.1964389.5318
149.3282-0.5308-0.41035.47040.87325.9867-0.14410.4048-0.5685-0.40730.12080.2235-0.18190.8053-0.0730.6257-0.07010.02140.8344-0.0370.813295.9897153.385393.2517
153.92013.4914-1.85358.4224-2.54364.03690.07840.1991-0.07450.0066-0.1292-0.27850.1651-0.04720.05010.39620.0469-0.01920.66990.00120.5001100.8534158.4546406.5789
168.695.0347-0.79125.8707-3.64938.5634-0.08560.6129-0.06080.24930.6892-0.6797-0.33750.3795-0.5590.62660.0468-0.00510.7720.08870.9488113.7033175.22402.2659
174.6958-0.73040.77543.2854-1.63516.71950.1770.1343-0.0526-0.1293-0.2462-1.1408-0.05781.00590.19160.53770.09240.09060.70730.05820.9667111.0812164.9524403.7883
183.5838-2.9966-3.99073.5164.13375.86070.38242.1298-0.1449-2.3376-1.0653-1.18330.02170.76570.22170.93680.19940.2141.4332-0.08790.8482112.501159.6323389.1354
193.3967-0.4618-1.25886.75021.3454.9867-0.02270.1671-0.7227-0.3843-0.0362-0.33790.4130.37090.03460.52380.0356-0.03790.5796-0.01390.9139100.731144.6257408.0397
206.8832-1.46874.65312.3273-1.76813.55150.6271-0.31672.0655-0.3815-0.1905-1.3661-0.9751-1.1223-0.30480.9723-0.00050.15311.16820.15121.900985.3529162.3669419.1383
218.43391.9131.16143.9010.49781.92960.20010.0157-1.2672-0.01730.0992-0.33290.25910.1539-0.36570.61670.1126-0.01070.4617-0.12390.792469.6149123.6651405.5877
224.1982-4.2437-1.48444.3372.01265.9316-0.4052-0.0884-2.75840.57720.13351.55860.8124-0.25120.10630.68660.0790.08930.64130.10331.162744.9713127.0148413.9481
238.4334-1.2738-2.36136.2024-1.9721.8306-0.2405-0.0975-0.13520.16920.24370.49590.2-0.48110.0390.56960.0853-0.05560.522-0.13960.461162.2922138.4461408.1219
243.51570.75820.50211.4576-0.60796.8238-0.0267-0.61930.14820.46130.1428-0.522-0.08710.2228-0.11620.67170.1337-0.07480.6563-0.14050.820275.6249141.0865416.2759
253.1429-0.8553-0.17190.7861-1.92327.0810.32551.4356-0.16490.00580.1735-1.2346-0.9718-0.7957-0.70650.7557-0.02630.01760.8590.10850.780365.3475145.3505389.6864
264.7384-0.53460.55164.0845-0.86633.0672-0.1460.02170.11720.03230.216-0.4308-0.090.0056-0.09970.58160.0297-0.010.5403-0.15590.59172.4221138.3324406.1325
271.20630.5677-0.91183.69572.30342.86080.0474-1.50180.34011.01540.9075-0.2554-0.7702-0.3647-0.22971.11850.44640.69081.33130.35120.626933.2019143.2907424.5675
283.31112.97681.72983.01192.56483.899-0.0739-0.60770.31540.7094-0.82311.2135-0.1567-2.37070.35631.11770.44911.08361.71820.48981.887117.2145140.6057424.2406
297.2713-3.4192.56883.66572.60947.9630.1628-2.1984-0.98551.83781.09862.53360.4362-1.1335-0.96020.98760.01380.37651.05970.36711.404329.2768137.1656419.2416
304.73942.99835.00354.59426.51939.4495-0.9106-1.7792-1.35910.896-1.636-0.71412.1809-0.90952.02151.84450.40860.51051.65210.50571.138823.5429138.0675433.6554
318.00170.5179-0.23257.09863.07888.530.16410.538-0.4488-1.3097-0.44541.1246-0.2331-0.51480.19990.71760.1347-0.19140.723-0.00610.891628.3029156.4268392.195
323.7457-1.5375-4.93595.42430.12559.0226-0.33881.5985-0.392-1.2224-00.84860.4947-0.69590.30950.75250.0066-0.16950.7882-0.21670.794932.5914141.915388.7292
332.00226.83792.42996.37584.30694.59820.0412.8525-1.0223-3.76992.40890.89571.98960.5066-2.08082.41720.3859-0.60941.3569-0.24051.284237.9219145.0691374.5828
342.93030.21640.34742.89531.07313.42880.07920.5072-0.1451-1.3384-0.21860.5849-0.2074-0.2530.00880.87310.0628-0.13510.6321-0.08230.760334.4209149.8621390.6865
356.15330.05020.67374.3642-4.33674.701-0.87590.0767-0.5171-0.5471-0.4512-0.506-2.82640.86161.40891.30970.0523-0.23940.94410.06790.88550.0481151.1718404.2112
362.9448-2.17841.549.0799-0.5474.72880.0784-0.141-0.60870.1346-0.06080.42840.06810.07950.04660.4798-0.06340.00820.4792-0.00350.578938.2286141.2741403.3231
374.6143-2.6424-1.82065.68551.98154.59410.07710.2515-1.437-0.3298-0.12391.45490.0334-0.13120.16650.5794-0.0704-0.13460.5925-0.10431.139935.919130.4872398.7074
385.18662.86012.0053.1358-0.65552.93751.34990.6479-1.2263-1.1931-0.91210.52451.4552-1.1359-0.10491.45820.1491-0.40081.1385-0.16191.197331.4028131.4157382.6019
394.70572.2484-1.00196.88044.66784.5427-0.06540.4813-1.3358-0.0142-0.55171.95790.1579-0.89920.54990.62520.042-0.07450.792-0.02531.494821.3381145.762402.352
403.72851.91793.79439.33133.88744.31350.33650.0565-0.90490.21180.9283-2.30960.23590.1854-1.2770.81820.1467-0.08320.8343-0.02741.044541.7328149.9251414.3332
416.35230.79510.86028.88330.14041.7932-0.00190.03990.48420.2283-0.07760.9097-0.1042-0.45460.06210.43560.12450.00220.610.04460.676220.8155183.5236407.9236
428.49767.88652.76419.69783.94893.4930.01470.05850.18360.20.21940.3691-0.1927-0.2905-0.19490.59490.08890.0470.66170.12310.748527.2514189.8737410.4214
435.30224.53062.49754.23562.96422.8524-0.0183-0.33480.3362-0.028-0.24070.4826-0.2982-0.17830.29930.56340.111-0.02320.5870.03460.558335.5375187.9881414.7307
442.69270.6568-1.17774.2674-0.51772.87180.0205-0.3229-0.42170.3125-0-0.38730.0601-0.0535-0.00950.56780.0326-0.08940.64470.10310.700936.8557173.0657414.6664
455.70360.58321.9925.3466-0.35042.8226-0.64562.21661.6101-0.98161.09810.01010.06720.0267-0.40161.7542-0.0108-0.12471.10040.09871.1238.0014185.4276384.6868
466.82770.53843.24125.64770.07766.0341-0.02070.7122-0.0409-0.81450.0733-0.5255-0.08180.38280.00420.56440.06490.12910.54960.01230.552239.0152174.9828397.751
477.47033.96093.50174.4884.02088.96630.1019-0.4575-0.03930.59410.04761.10950.3229-0.3742-0.12890.59090.0675-0.01260.66170.14910.659225.124174.0292419.2546
487.2764.17683.3712.98942.59142.2660.4414-0.4878-0.2580.9292-0.30560.55430.0444-0.2919-0.37991.08990.032-0.17630.81190.03850.656855.5511202.4723432.5111
497.3374-1.3468-0.19016.4089-2.92356.06340.6535-1.59680.42531.5173-0.135-0.4802-1.2466-0.2583-0.57991.3553-0.0923-0.0491.0909-0.16170.667254.8325211.5207432.138
509.36853.2741.24414.9102-3.06953.42230.09711.3427-2.139-3.2542-1.5622-0.06434.4532.10991.22182.02480.4969-0.19171.4816-0.43271.076957.4833212.1849446.3383
517.7405-2.27582.87554.3594-5.53016.9127-0.44650.84430.4987-0.1643-0.0946-0.4539-0.48740.43160.80660.69810.04710.07770.77540.19870.914769.9606204.0047399.7936
522.7623-2.3692-1.10783.07593.53646.9768-0.37010.90411.60180.1143-0.3472-0.2932-1.20860.81060.57340.802-0.1748-0.0820.71160.28861.555372.505214.7492402.4142
535.6861.68691.20761.71362.81837.9853-0.25020.79110.4524-0.404-0.11850.0227-0.81170.1540.54340.66740.0258-0.11470.68610.22250.783959.1452208.3655395.1402
541.56970.0395-0.33315.6475-4.9117.68830.45120.1959-2.93430.7913-0.8103-0.12232.0193-0.16070.45741.41530.1662-0.21530.8671-0.13171.280855.7492193.3775404.9792
554.58761.86431.77993.22860.70515.1336-0.31890.01520.460.10670.0448-0.0528-0.39630.04410.41040.66220.0747-0.07760.48150.02060.722950.1127206.1778408.8433
562.70133.084-0.07496.47473.24023.9375-0.2406-0.0131.73020.1390.02060.4571-0.4596-0.43560.32650.74180.0897-0.11170.5681-0.0691.047941.5545211.6088411.7377
578.50663.7525-1.89457.01-3.01731.3291-0.75151.42011.0559-0.83810.79790.57030.3016-0.039-0.051.0732-0.0918-0.15380.85160.34540.870246.2809215.083394.208
588.8089-2.8421-2.48477.10441.61443.3471-0.3947-0.41662.12370.04720.5999-0.4279-1.13750.1483-0.19631.03710.0269-0.11090.73510.06531.515263.782220.8802410.9632
599.7709-0.4854-0.81197.7037-5.2433.80920.24670.1861-0.19270.6418-0.2729-0.34620.35151.8280.23750.90430.1189-0.1920.7553-0.11061.180167.4776206.4809416.5038
603.3314.8351-3.82547.2513-5.83494.72871.41890.3242-1.167-1.6833-0.76293.611.50470.8697-0.83060.91940.1363-0.32680.7895-0.07761.506856.4472192.0732420.1106
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:6)A1 - 6
2X-RAY DIFFRACTION2(chain A and resid 7:92)A7 - 92
3X-RAY DIFFRACTION3(chain A and resid 93:109)A93 - 109
4X-RAY DIFFRACTION4(chain A and resid 110:133)A110 - 133
5X-RAY DIFFRACTION5(chain A and resid 134:191)A134 - 191
6X-RAY DIFFRACTION6(chain A and resid 192:221)A192 - 221
7X-RAY DIFFRACTION7(chain A and resid 222:329)A222 - 329
8X-RAY DIFFRACTION8(chain A and resid 330:388)A330 - 388
9X-RAY DIFFRACTION9(chain A and resid 389:413)A389 - 413
10X-RAY DIFFRACTION10(chain A and resid 414:420)A414 - 420
11X-RAY DIFFRACTION11(chain B and resid 59:66)B59 - 66
12X-RAY DIFFRACTION12(chain B and resid 67:84)B67 - 84
13X-RAY DIFFRACTION13(chain B and resid 85:117)B85 - 117
14X-RAY DIFFRACTION14(chain B and resid 118:155)B118 - 155
15X-RAY DIFFRACTION15(chain B and resid 172:247)B172 - 247
16X-RAY DIFFRACTION16(chain B and resid 248:257)B248 - 257
17X-RAY DIFFRACTION17(chain B and resid 258:307)B258 - 307
18X-RAY DIFFRACTION18(chain B and resid 308:320)B308 - 320
19X-RAY DIFFRACTION19(chain B and resid 321:358)B321 - 358
20X-RAY DIFFRACTION20(chain B and resid 359:364)B359 - 364
21X-RAY DIFFRACTION21(chain C and resid 1:86)C1 - 86
22X-RAY DIFFRACTION22(chain C and resid 87:105)C87 - 105
23X-RAY DIFFRACTION23(chain C and resid 106:148)C106 - 148
24X-RAY DIFFRACTION24(chain C and resid 149:191)C149 - 191
25X-RAY DIFFRACTION25(chain C and resid 192:222)C192 - 222
26X-RAY DIFFRACTION26(chain C and resid 223:329)C223 - 329
27X-RAY DIFFRACTION27(chain C and resid 330:384)C330 - 384
28X-RAY DIFFRACTION28(chain C and resid 385:393)C385 - 393
29X-RAY DIFFRACTION29(chain C and resid 394:406)C394 - 406
30X-RAY DIFFRACTION30(chain C and resid 407:420)C407 - 420
31X-RAY DIFFRACTION31(chain D and resid 59:81)D59 - 81
32X-RAY DIFFRACTION32(chain D and resid 82:109)D82 - 109
33X-RAY DIFFRACTION33(chain D and resid 110:118)D110 - 118
34X-RAY DIFFRACTION34(chain D and resid 119:154)D119 - 154
35X-RAY DIFFRACTION35(chain D and resid 155:174)D155 - 174
36X-RAY DIFFRACTION36(chain D and resid 175:219)D175 - 219
37X-RAY DIFFRACTION37(chain D and resid 220:284)D220 - 284
38X-RAY DIFFRACTION38(chain D and resid 305:320)D305 - 320
39X-RAY DIFFRACTION39(chain D and resid 321:351)D321 - 351
40X-RAY DIFFRACTION40(chain D and resid 352:363)D352 - 363
41X-RAY DIFFRACTION41(chain E and resid 1:67)E1 - 67
42X-RAY DIFFRACTION42(chain E and resid 68:92)E68 - 92
43X-RAY DIFFRACTION43(chain E and resid 93:129)E93 - 129
44X-RAY DIFFRACTION44(chain E and resid 130:191)E130 - 191
45X-RAY DIFFRACTION45(chain E and resid 192:207)E192 - 207
46X-RAY DIFFRACTION46(chain E and resid 208:302)E208 - 302
47X-RAY DIFFRACTION47(chain E and resid 303:328)E303 - 328
48X-RAY DIFFRACTION48(chain E and resid 329:386)E329 - 386
49X-RAY DIFFRACTION49(chain E and resid 387:413)E387 - 413
50X-RAY DIFFRACTION50(chain E and resid 414:419)E414 - 419
51X-RAY DIFFRACTION51(chain F and resid 59:71)F59 - 71
52X-RAY DIFFRACTION52(chain F and resid 72:84)F72 - 84
53X-RAY DIFFRACTION53(chain F and resid 85:151)F85 - 151
54X-RAY DIFFRACTION54(chain F and resid 152:173)F152 - 173
55X-RAY DIFFRACTION55(chain F and resid 174:256)F174 - 256
56X-RAY DIFFRACTION56(chain F and resid 257:277)F257 - 277
57X-RAY DIFFRACTION57(chain F and resid 278:322)F278 - 322
58X-RAY DIFFRACTION58(chain F and resid 323:339)F323 - 339
59X-RAY DIFFRACTION59(chain F and resid 340:353)F340 - 353
60X-RAY DIFFRACTION60(chain F and resid 354:363)F354 - 363

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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