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- PDB-5nkk: SMG8-SMG9 complex GDP bound -

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IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 5nkk
タイトルSMG8-SMG9 complex GDP bound
要素
  • Protein smg-8
  • Protein smg-9
キーワードTRANSCRIPTION / 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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / molecular sequestering activity / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / PYROPHOSPHATE 2- / 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 / 解像度: 2.64 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 1.22019年10月16日Group: Data collection / カテゴリ: reflns_shell
改定 1.32024年5月8日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)260,48610
ポリマ－259,7816
非ポリマー7064
水3,027168
1
A: Protein smg-8
B: Protein smg-9


分子量 (理論値)分子数
合計 (水以外)86,5942
ポリマ－86,5942
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-20 kcal/mol
Surface area26180 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)86,7703
ポリマ－86,5942
非ポリマー1761
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-21 kcal/mol
Surface area25640 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)87,1235
ポリマ－86,5942
非ポリマー5303
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-39 kcal/mol
Surface area27120 Å2
手法PISA
単位格子
Length a, b, c (Å)110.605, 110.605, 360.266
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-507-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 1 through 10 or (resid 11...
21(chain C and (resid 1 through 20 or (resid 21...
31(chain E and (resid 1 through 4 or (resid 5...
12(chain B and (resid 59 through 61 or (resid 62...
22(chain D and (resid 59 through 61 or (resid 62...
32(chain F and (resid 59 through 112 or (resid 113...

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
111METMETALAALA(chain A and (resid 1 through 10 or (resid 11...AA1 - 101 - 10
121ARGARGARGARG(chain A and (resid 1 through 10 or (resid 11...AA1111
131METMETGLNGLN(chain A and (resid 1 through 10 or (resid 11...AA1 - 4191 - 419
141METMETGLNGLN(chain A and (resid 1 through 10 or (resid 11...AA1 - 4191 - 419
151METMETGLNGLN(chain A and (resid 1 through 10 or (resid 11...AA1 - 4191 - 419
161METMETGLNGLN(chain A and (resid 1 through 10 or (resid 11...AA1 - 4191 - 419
211METMETTHRTHR(chain C and (resid 1 through 20 or (resid 21...CC1 - 201 - 20
221LYSLYSLYSLYS(chain C and (resid 1 through 20 or (resid 21...CC2121
231METMETMETMET(chain C and (resid 1 through 20 or (resid 21...CC1 - 4171 - 417
241METMETMETMET(chain C and (resid 1 through 20 or (resid 21...CC1 - 4171 - 417
251METMETMETMET(chain C and (resid 1 through 20 or (resid 21...CC1 - 4171 - 417
261METMETMETMET(chain C and (resid 1 through 20 or (resid 21...CC1 - 4171 - 417
311METMETALAALA(chain E and (resid 1 through 4 or (resid 5...EE1 - 41 - 4
321LYSLYSLYSLYS(chain E and (resid 1 through 4 or (resid 5...EE55
331METMETASPASP(chain E and (resid 1 through 4 or (resid 5...EE1 - 4211 - 421
341METMETASPASP(chain E and (resid 1 through 4 or (resid 5...EE1 - 4211 - 421
351METMETASPASP(chain E and (resid 1 through 4 or (resid 5...EE1 - 4211 - 421
361METMETASPASP(chain E and (resid 1 through 4 or (resid 5...EE1 - 4211 - 421
112METMETGLUGLU(chain B and (resid 59 through 61 or (resid 62...BB59 - 611 - 3
122SERSERSERSER(chain B and (resid 59 through 61 or (resid 62...BB624
132METMETTHRTHR(chain B and (resid 59 through 61 or (resid 62...BB59 - 3631 - 305
142METMETTHRTHR(chain B and (resid 59 through 61 or (resid 62...BB59 - 3631 - 305
152METMETTHRTHR(chain B and (resid 59 through 61 or (resid 62...BB59 - 3631 - 305
162METMETTHRTHR(chain B and (resid 59 through 61 or (resid 62...BB59 - 3631 - 305
212METMETGLUGLU(chain D and (resid 59 through 61 or (resid 62...DD59 - 611 - 3
222SERSERSERSER(chain D and (resid 59 through 61 or (resid 62...DD624
232METMETASPASP(chain D and (resid 59 through 61 or (resid 62...DD59 - 3641 - 306
242METMETASPASP(chain D and (resid 59 through 61 or (resid 62...DD59 - 3641 - 306
252METMETASPASP(chain D and (resid 59 through 61 or (resid 62...DD59 - 3641 - 306
262METMETASPASP(chain D and (resid 59 through 61 or (resid 62...DD59 - 3641 - 306
312METMETARGARG(chain F and (resid 59 through 112 or (resid 113...FF59 - 1121 - 54
322GLNGLNTYRTYR(chain F and (resid 59 through 112 or (resid 113...FF113 - 11855 - 60
332METMETASPASP(chain F and (resid 59 through 112 or (resid 113...FF59 - 3641 - 306
342METMETASPASP(chain F and (resid 59 through 112 or (resid 113...FF59 - 3641 - 306
352METMETASPASP(chain F and (resid 59 through 112 or (resid 113...FF59 - 3641 - 306
362METMETASPASP(chain F and (resid 59 through 112 or (resid 113...FF59 - 3641 - 306

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 , 2種, 6分子 ACEBDF

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


分子量: 49783.762 Da / 分子数: 3 / 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 / プラスミド: multibac pFL
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: 36809.828 Da / 分子数: 3 / 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 / プラスミド: multibac pFL
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9XWJ1

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非ポリマー , 5種, 172分子

#3: 化合物 ChemComp-POP / PYROPHOSPHATE 2-


分子量: 175.959 Da / 分子数: 1 / 由来タイプ: 合成 / 式: H2O7P2
#4: 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: 1 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物 ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / コメント: GDP, エネルギー貯蔵分子*YM
#6: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 168 / 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: 3.01 Å3/Da / 溶媒含有率: 59.13 %
結晶化温度: 285 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 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: 0.9785 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2015年6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: 0.9785 Å / 相対比: 1
反射解像度: 2.6→47.893 Å / Num. obs: 152344 / % possible obs: 99 % / 冗長度: 10 % / Net I/σ(I): 12.39

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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
精密化解像度: 2.64→47.893 Å / SU ML: 0.41 / 交差検証法: FREE R-VALUE / σ(F): 1.14 / 位相誤差: 30.8
Rfactor反射数%反射
Rfree0.2741 7231 5 %
Rwork0.232 --
obs0.2341 144590 99.83 %
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: 191.86 Å2 / Biso mean: 81.4195 Å2 / Biso min: 30 Å2
精密化ステップサイクル: final / 解像度: 2.64→47.893 Å
タンパク質核酸リガンド溶媒全体
原子数13529 0 42 168 13739
Biso mean--124.72 64.93 -
残基数----1784
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00313755
X-RAY DIFFRACTIONf_angle_d0.70718662
X-RAY DIFFRACTIONf_chiral_restr0.0462259
X-RAY DIFFRACTIONf_plane_restr0.0042393
X-RAY DIFFRACTIONf_dihedral_angle_d5.0478348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4343X-RAY DIFFRACTION12.662TORSIONAL
12C4343X-RAY DIFFRACTION12.662TORSIONAL
13E4343X-RAY DIFFRACTION12.662TORSIONAL
21B3168X-RAY DIFFRACTION12.662TORSIONAL
22D3168X-RAY DIFFRACTION12.662TORSIONAL
23F3168X-RAY DIFFRACTION12.662TORSIONAL
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 (%)
2.6398-2.66980.37252320.36814348458096
2.6698-2.70120.3982470.353246474894100
2.7012-2.73420.39152350.347445354770100
2.7342-2.76880.34492470.324146574904100
2.7688-2.80520.32742400.309344614701100
2.8052-2.84360.34582460.302946544900100
2.8436-2.88420.35692410.298445204761100
2.8842-2.92730.342430.302646264869100
2.9273-2.9730.34542450.305546244869100
2.973-3.02180.3422360.289745424778100
3.0218-3.07390.34882460.28946544900100
3.0739-3.12970.33192330.293845154748100
3.1297-3.18990.34132400.29546354875100
3.1899-3.2550.32432370.282146334870100
3.255-3.32580.34542390.272445254764100
3.3258-3.40310.29682390.255146004839100
3.4031-3.48820.27372430.252846084851100
3.4882-3.58250.26352400.236245764816100
3.5825-3.68790.26292420.224146084850100
3.6879-3.80690.26572430.222845764819100
3.8069-3.94290.26632340.212245564790100
3.9429-4.10070.28012450.204246234868100
4.1007-4.28720.2452370.201545714808100
4.2872-4.5130.24652420.196245444786100
4.513-4.79550.20732460.192446354881100
4.7955-5.16540.25452480.204945414789100
5.1654-5.68450.24862460.218645704816100
5.6845-6.50530.29332410.235746244865100
6.5053-8.18930.2652400.216145624802100
8.1893-47.90120.2172380.184745894827100
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)
14.7949-1.83850.10835.811.79152.33610.02550.25930.6513-0.3767-0.0181-0.9247-0.48380.4389-0.05830.5218-0.17290.11360.54060.02690.6728155.6445288.9502396.7562
22.78710.5196-2.43182.88913.73737.3022-0.11680.1733-0.18190.2780.3204-0.39680.43590.724-0.07440.4687-0.0208-0.08330.5903-0.14080.5334159.2792266.8311404.3371
33.87730.50120.76564.2946-3.83767.0126-0.23750.38450.0477-0.17410.1962-0.04310.4330.29310.03730.4542-0.07690.01540.3904-0.02870.5386145.9149280.6835394.9567
41.9556-1.8482-0.57266.05524.78617.0886-0.17550.0581-0.28080.418-0.22450.82130.2566-0.24250.50550.3423-0.07330.07320.376-0.02540.4563140.4676278.3226406.676
57.26395.268-1.08877.9047-4.04247.2630.2234-0.25840.69310.22840.43041.6795-0.7165-0.8605-0.56560.43570.10140.00090.6464-0.11610.9494132.2435289.5046405.4008
63.7251-0.5651-1.5195.6228-1.32294.14660.12920.6313-0.1283-0.65030.02590.5738-0.0509-0.4543-0.11720.4496-0.0565-0.08650.4622-0.04840.5775136.6861279.7798388.1581
76.57962.30542.89685.3558-4.30077.7994-0.6448-0.02590.632-1.1289-0.0010.57540.14380.00910.17840.9222-0.09330.11870.60540.18730.7673146.2576289.9654379.9368
82.27381.6870.34566.8706-0.28625.4067-0.11950.01430.61190.5823-0.0576-0.2499-0.87960.36530.17850.3213-0.01850.13460.4443-0.06150.5488144.2389290.7599404.6914
97.1281-2.47520.29117.6918-1.78413.58470.151-1.0461-0.89590.92070.0939-0.69980.240.2726-0.23830.58990.01-0.11790.66650.07950.6223155.7415247.7454410.2136
102.23571.9043-3.07637.096-0.28225.22111.0388-1.46860.12141.2286-0.745-0.1398-0.25931.5422-0.44571.2204-0.0408-0.24381.14110.13460.8107160.5332241.974421.2407
116.8394-2.1289-5.6936.24694.5526.8725-0.04750.3187-0.7849-0.43470.1936-0.284-1.0870.1659-0.08710.5969-0.00770.11520.8348-0.25370.8626146.3224240.2998378.4062
123.68430.281.16966.28481.64284.0929-0.4280.7484-0.6471-0.5210.42870.04920.30850.7387-0.00440.4415-0.04550.15990.6168-0.09290.5858158.1702246.421377.3171
139.1772.508-3.26965.3821-3.5582.9871-0.0840.3937-0.2173-1.39710.05690.23840.20380.7403-0.26380.8235-0.15680.03680.7102-0.22970.7879150.4881250.7915370.6781
147.85353.63050.40516.0111-2.78762.8438-0.13660.2269-0.4364-0.85640.3975-0.3536-0.47111.3609-0.41670.6327-0.11280.09450.747-0.14480.5307153.1727248.2442379.3579
153.01891.3936-1.07766.5616-0.85853.1306-0.05460.2448-0.5778-0.0165-0.0966-0.50790.24550.06110.20150.3020.02510.02810.5555-0.14170.6567157.4046253.3526389.8911
164.95615.1166-5.16725.6397-5.41465.29470.10370.0683-0.32080.1767-0.3096-0.3708-0.09060.7340.16340.4629-0.04050.14470.736-0.04390.9631168.7131269.2289387.0079
174.11473.0317-1.24145.2165-2.75513.0737-0.5130.3625-0.1883-0.184-0.0271-1.23220.1515-0.04240.62630.43050.04720.02970.8057-0.11041.2714168.1967257.4428392.7604
186.7366-2.2907-4.77753.45794.42257.09570.01880.6241-1.3964-1.25310.4521-1.4268-0.531.2328-0.30290.6582-0.13640.18781.0701-0.28761.0404167.4064257.0203375.0154
192.5941-2.94360.79663.6820.65236.3348-0.26860.24830.19470.28-0.0103-1.09370.65630.96450.21330.67280.18110.00250.6396-0.10691.3866163.0733237.0069387.3568
201.82430.819-2.38537.41652.39975.19680.2156-0.04540.1272-0.1465-0.39871.00470.3994-0.32010.30140.4457-0.0211-0.0490.5594-0.10461.1651146.2364245.8184398.6456
211.35772.8778-0.37077.80551.10972.30560.5632-1.0439-2.73991.1793-0.5778-0.60230.0984-0.3448-0.36470.72550.2514-0.05010.6850.1181.1386128.0753215.0126398.793
228.25211.1659-0.80751.1139-0.18442.32520.27890.3696-1.5945-0.06140.0649-0.29790.42850.0425-0.41040.58530.1173-0.05390.3978-0.19190.9848126.6586218.4685387.2363
234.8038-1.58392.74074.7721-0.60543.18880.11840.4865-0.7950.19060.2031-0.32880.27570.3284-0.2470.54940.0802-0.00690.4025-0.17220.9521123.8374220.2307390.1257
245.0458-3.34291.56222.55630.39687.35930.1368-0.898-2.64320.38390.12321.94040.8267-0.5249-0.23490.61310.04270.05960.5710.13541.181101.3454221.7169397.645
254.0174-0.3685-0.78731.843-1.63992.4048-0.074-0.3406-0.05510.24920.1622-0.12110.16090.1312-0.07540.54730.07090.00630.3834-0.17020.5923124.9896234.5712396.0658
263.9345-4.0242-0.09116.8294-4.30717.3302-0.87422.0335-0.18210.3410.03390.8249-1.0329-1.19590.63410.79440.0814-0.0061.18040.15740.6831120.1325237.6933374.5467
273.9224-0.33341.02631.5860.16971.8324-0.06130.17310.044-0.04930.3093-0.4748-0.13570.3445-0.29680.545-0.0340.01910.4194-0.11910.6647129.7713235.1798384.7935
282.814-1.95362.9522.8457-0.29065.0811-0.1366-1.61150.00820.96580.4193-0.89080.2511-0.0131-0.14450.77150.1171-0.07640.7269-0.00130.7442123.3013226.3874406.4174
298.5451-2.7331-6.10131.40752.04848.5128-0.3868-1.13460.12610.60680.620.3308-0.5819-0.4571-0.12890.82350.14580.23290.78490.18930.704189.6009237.7655406.5462
306.5196-4.6884-5.76884.17094.44035.3261-0.1502-1.4511-1.18770.86471.24250.34162.1287-0.8482-0.45130.8273-0.04360.31311.16760.55261.154384.1661231.3511408.4033
314.57390.53270.49394.717-1.50534.33060.32060.52540.0665-0.6156-0.53781.4076-0.0301-0.66750.42970.51450.0997-0.14260.6045-0.07571.050982.169248.0585376.3698
328.2332-1.67438.28866.74480.34299.499-0.7751.61821.4714-1.3041-0.1065-1.90350.08410.83620.70780.54970.14210.14060.69870.03711.198196.5335237.1663375.3094
334.2874-3.82385.50469.7134-4.70797.04090.30450.91071.1477-2.4471-0.2650.55261.1418-0.6087-0.25610.9438-0.1005-0.11660.9539-0.03860.918491.0941236.6178362.9336
349.49384.08793.89622.76643.64987.56320.31980.62441.05430.0524-0.29590.4676-0.93980.5149-0.13380.95180.1189-0.13150.6552-0.00571.023294.6843247.7607371.4209
358.54110.02392.79763.28441.74253.5365-0.0649-0.4872-0.8489-0.4070.2757-0.8833-0.83540.3619-0.19320.6805-0.0961-0.10040.6838-0.10230.962790.8569242.7465377.0821
362.66212.7732-1.2263.0998-1.8692.1765-0.2686-0.32931.68030.7509-0.2031-1.1401-1.67481.33720.66650.5594-0.07440.06040.5472-0.04020.638198.362244.6183388.6395
373.2479-0.88791.10454.98880.15542.4934-0.19720.1815-1.24450.13470.00291.08510.2743-0.27090.20220.43-0.04820.06690.4583-0.01350.902392.2042229.0293385.4011
383.5458-3.53513.2178.14210.59766.25160.12561.4137-1.5626-1.1244-0.79082.0082-0.0842-1.15860.41950.7714-0.0005-0.34630.99-0.32561.257392.1573223.5993369.4083
398.1364-1.20474.87452.39081.18614.92720.765-0.3013-1.6714-0.7534-0.17432.3829-0.0303-0.4573-0.85770.8586-0.09430.23090.7037-0.01161.751177.8433229.7022382.778
400.23320.4007-0.25313.42711.09983.3328-0.10750.0235-1.02270.6330.36361.0072-0.5209-0.4749-0.32590.61940.05670.15820.50840.01130.945185.1105244.3578391.1288
417.55130.6918-0.91196.96090.90922.7390.07880.13750.75720.0625-0.00191.2373-0.1904-0.559-0.13890.38880.1163-0.06460.4789-0.02070.714376.9179276.105391.2911
424.81463.1472.53722.46130.93573.6516-0.4171-0.25240.7758-0.15880.05530.5297-0.5555-0.69380.36040.47560.0727-0.03990.623-0.05540.935979.5983281.7607391.8947
434.1778-1.37465.05215.8338-3.38747.41080.0367-0.72040.90560.8675-0.50181.2428-0.4691-1.17290.40960.5030.1206-0.03390.6524-0.13440.897492.2923296.2088403.9141
443.26740.7371.80886.57924.09648.70090.03480.0865-0.1655-0.677-0.3182-0.1245-0.6196-0.15890.22780.33170.06180.01380.38390.04580.574491.3849277.2899393.28
452.7770.5434-0.21472.75880.42373.9250.1574-0.4776-0.45090.4824-0.3003-0.73090.3979-0.01660.17020.4835-0.0206-0.08430.50570.1080.812992.1797266.5163399.9968
464.27794.88311.91855.9743.68546.9575-0.38260.3956-0.2901-1.58210.35380.2095-1.3589-0.0981-0.13211.15130.0278-0.03310.53480.12980.785696.7449275.4886371.957
475.49181.4782.3235.51350.71267.63480.48440.5281-0.1786-0.7237-0.095-1.05580.36120.4277-0.40010.57550.12080.12160.42520.0140.847496.1303269.924383.1823
484.49342.87531.96495.59712.19986.48110.554-0.72070.05460.6816-0.54150.23490.4448-0.4762-0.00910.4032-0.0305-0.00290.51320.10480.71282.1096268.3256400.2864
495.52034.54521.48816.31334.57525.65080.385-0.93590.33490.5653-0.30950.0623-0.41590.0567-0.00380.78960.0219-0.08860.7707-0.05240.8677111.2863301.1137416.2032
501.96030.06263.18071.291-2.00313.99531.0877-3.66190.6572-1.8737-2.7816-0.3879-0.15160.87361.28232.17390.1912-0.36651.2397-0.12751.0827113.6791306.0087432.0326
515.37150.77951.33013.0988-3.62094.7985-0.15670.17940.2896-0.27580.0913-0.3464-0.35570.30050.07430.68530.03170.11520.65150.18941.1767128.0703303.2116385.3418
528.57797.8935-1.2778.3107-1.59985.5418-0.47040.99230.8231-0.24960.4821-0.9753-0.88180.347-0.25260.78670.0388-0.03110.53460.11951.0797113.0339304.7364384.4257
537.3463.3-2.93153.3731-4.24645.5996-0.45090.93070.3248-1.2997-0.1097-0.4022-0.2365-0.25780.64091.0446-0.07130.03570.69170.12771.1339113.7633303.3678371.9696
548.54373.019-0.42247.6325-2.63088.28830.03090.43340.1457-0.46030.2190.1319-0.17520.4147-0.18470.6930.1620.02020.5450.05341.172118.3388301.1751384.9868
552.6053-0.4761-3.5271.41842.32067.0226-1.7980.1496-3.05720.72451.6919-1.94382.39171.81380.44040.772-0.0834-0.01140.48280.26631.1276114.275291.5733394.6588
565.00731.73710.96554.71411.11612.0412-0.0461-0.15931.2720.1596-0.27110.3317-0.32150.15640.34250.53340.0449-0.05850.3977-0.01940.9431110.467301.9022396.4603
573.49320.77812.42380.08320.23874.0195-0.46870.02730.9528-0.1325-0.00070.3508-0.8074-0.17020.53420.75520.1145-0.09280.44390.03281.036297.9414304.5967389.0645
586.8517-2.0292-5.19543.8917-3.05872.0209-1.1342-0.99620.07660.43941.1919-0.5954-0.65971.40970.61931.1462-0.2014-0.26950.40291.13891.8393104.5702312.4587375.8067
591.04890.90370.44352.54951.11945.957-0.5025-0.01281.2437-0.40220.0849-0.0496-1.0889-0.16780.34280.8929-0.0754-0.09860.50130.06661.484119.2013312.6529395.0525
604.2615.14250.92627.71-1.10395.01550.1462-0.2612-1.58980.04760.3515-1.07310.258-0.3274-0.42650.67860.1233-0.1310.54660.00761.3684116.5203290.6932404.8335
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:90)A1 - 90
2X-RAY DIFFRACTION2(chain A and resid 91:109)A91 - 109
3X-RAY DIFFRACTION3(chain A and resid 110:133)A110 - 133
4X-RAY DIFFRACTION4(chain A and resid 134:163)A134 - 163
5X-RAY DIFFRACTION5(chain A and resid 164:181)A164 - 181
6X-RAY DIFFRACTION6(chain A and resid 182:250)A182 - 250
7X-RAY DIFFRACTION7(chain A and resid 251:296)A251 - 296
8X-RAY DIFFRACTION8(chain A and resid 297:329)A297 - 329
9X-RAY DIFFRACTION9(chain A and resid 330:407)A330 - 407
10X-RAY DIFFRACTION10(chain A and resid 408:419)A408 - 419
11X-RAY DIFFRACTION11(chain B and resid 59:76)B59 - 76
12X-RAY DIFFRACTION12(chain B and resid 77:107)B77 - 107
13X-RAY DIFFRACTION13(chain B and resid 108:138)B108 - 138
14X-RAY DIFFRACTION14(chain B and resid 139:174)B139 - 174
15X-RAY DIFFRACTION15(chain B and resid 175:247)B175 - 247
16X-RAY DIFFRACTION16(chain B and resid 248:259)B248 - 259
17X-RAY DIFFRACTION17(chain B and resid 260:277)B260 - 277
18X-RAY DIFFRACTION18(chain B and resid 278:320)B278 - 320
19X-RAY DIFFRACTION19(chain B and resid 321:342)B321 - 342
20X-RAY DIFFRACTION20(chain B and resid 343:363)B343 - 363
21X-RAY DIFFRACTION21(chain C and resid 1:9)C1 - 9
22X-RAY DIFFRACTION22(chain C and resid 10:58)C10 - 58
23X-RAY DIFFRACTION23(chain C and resid 59:85)C59 - 85
24X-RAY DIFFRACTION24(chain C and resid 86:105)C86 - 105
25X-RAY DIFFRACTION25(chain C and resid 106:190)C106 - 190
26X-RAY DIFFRACTION26(chain C and resid 191:221)C191 - 221
27X-RAY DIFFRACTION27(chain C and resid 222:312)C222 - 312
28X-RAY DIFFRACTION28(chain C and resid 313:330)C313 - 330
29X-RAY DIFFRACTION29(chain C and resid 331:394)C331 - 394
30X-RAY DIFFRACTION30(chain C and resid 395:417)C395 - 417
31X-RAY DIFFRACTION31(chain D and resid 59:88)D59 - 88
32X-RAY DIFFRACTION32(chain D and resid 89:100)D89 - 100
33X-RAY DIFFRACTION33(chain D and resid 101:117)D101 - 117
34X-RAY DIFFRACTION34(chain D and resid 118:135)D118 - 135
35X-RAY DIFFRACTION35(chain D and resid 136:174)D136 - 174
36X-RAY DIFFRACTION36(chain D and resid 175:183)D175 - 183
37X-RAY DIFFRACTION37(chain D and resid 184:274)D184 - 274
38X-RAY DIFFRACTION38(chain D and resid 275:319)D275 - 319
39X-RAY DIFFRACTION39(chain D and resid 320:328)D320 - 328
40X-RAY DIFFRACTION40(chain D and resid 329:364)D329 - 364
41X-RAY DIFFRACTION41(chain E and resid 1:46)E1 - 46
42X-RAY DIFFRACTION42(chain E and resid 47:85)E47 - 85
43X-RAY DIFFRACTION43(chain E and resid 86:105)E86 - 105
44X-RAY DIFFRACTION44(chain E and resid 106:133)E106 - 133
45X-RAY DIFFRACTION45(chain E and resid 134:189)E134 - 189
46X-RAY DIFFRACTION46(chain E and resid 190:215)E190 - 215
47X-RAY DIFFRACTION47(chain E and resid 216:297)E216 - 297
48X-RAY DIFFRACTION48(chain E and resid 298:329)E298 - 329
49X-RAY DIFFRACTION49(chain E and resid 330:413)E330 - 413
50X-RAY DIFFRACTION50(chain E and resid 414:421)E414 - 421
51X-RAY DIFFRACTION51(chain F and resid 59:82)F59 - 82
52X-RAY DIFFRACTION52(chain F and resid 83:101)F83 - 101
53X-RAY DIFFRACTION53(chain F and resid 102:124)F102 - 124
54X-RAY DIFFRACTION54(chain F and resid 135:175)F135 - 175
55X-RAY DIFFRACTION55(chain F and resid 176:184)F176 - 184
56X-RAY DIFFRACTION56(chain F and resid 185:227)F185 - 227
57X-RAY DIFFRACTION57(chain F and resid 228:309)F228 - 309
58X-RAY DIFFRACTION58(chain F and resid 310:317)F310 - 317
59X-RAY DIFFRACTION59(chain F and resid 318:346)F318 - 346
60X-RAY DIFFRACTION60(chain F and resid 347:364)F347 - 364

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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