[日本語] English
万見
- PDB-6zhu: Yeast Uba1 in complex with Ubc3 and ATP -

+
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: 6zhu
タイトルYeast Uba1 in complex with Ubc3 and ATP
要素
  • Ubiquitin-activating enzyme E1 1
  • Ubiquitin-conjugating enzyme E2-34 kDa
キーワードLIGASE / Ubiquitin / E1 / Ubc3 / Cdc34
機能・相同性
機能・相同性情報


regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / E1 ubiquitin-activating enzyme / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin activating enzyme activity / positive regulation of D-glucose transmembrane transport / mitotic intra-S DNA damage checkpoint signaling / mitochondrial fusion / silent mating-type cassette heterochromatin formation ...regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / E1 ubiquitin-activating enzyme / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin activating enzyme activity / positive regulation of D-glucose transmembrane transport / mitotic intra-S DNA damage checkpoint signaling / mitochondrial fusion / silent mating-type cassette heterochromatin formation / regulation of metabolic process / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / protein autoubiquitination / regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / DNA replication / protein ubiquitination / cell division / DNA damage response / ATP binding / nucleus / cytoplasm
類似検索 - 分子機能
Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain ...Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Elongation Factor Tu (Ef-tu); domain 3 / Roll / Beta Barrel / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / Ubiquitin-conjugating enzyme E2-34 kDa / Ubiquitin-activating enzyme E1 1
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.18 Å
データ登録者Misra, M. / Schindelin, H.
資金援助 ドイツ, 1件
組織認可番号国
German Research Foundation (DFG)SCHI 425-6/1 ドイツ
引用ジャーナル: To Be Published
タイトル: ATP induced conformational changes facilitate E1-E2 disulfide bridging in the ubiquitin system
著者: Misra, M. / Schaefer, A. / Kuhn, M. / Pluska, L. / Tessmer, I. / Sommer, T. / Schindelin, H.
履歴
登録2020年6月23日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年1月12日Provider: repository / タイプ: Initial release
改定 1.12024年1月24日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
改定 1.22024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
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
B: Ubiquitin-conjugating enzyme E2-34 kDa
F: Ubiquitin-conjugating enzyme E2-34 kDa
D: Ubiquitin-conjugating enzyme E2-34 kDa
H: Ubiquitin-conjugating enzyme E2-34 kDa
A: Ubiquitin-activating enzyme E1 1
E: Ubiquitin-activating enzyme E1 1
C: Ubiquitin-activating enzyme E1 1
G: Ubiquitin-activating enzyme E1 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)596,09616
ポリマ－593,9708
非ポリマー2,1268
水1629
1
B: Ubiquitin-conjugating enzyme E2-34 kDa
A: Ubiquitin-activating enzyme E1 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,0244
ポリマ－148,4932
非ポリマー5312
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-24 kcal/mol
Surface area51010 Å2
手法PISA
2
F: Ubiquitin-conjugating enzyme E2-34 kDa
E: Ubiquitin-activating enzyme E1 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,0244
ポリマ－148,4932
非ポリマー5312
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-28 kcal/mol
Surface area51570 Å2
手法PISA
3
D: Ubiquitin-conjugating enzyme E2-34 kDa
C: Ubiquitin-activating enzyme E1 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,0244
ポリマ－148,4932
非ポリマー5312
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-23 kcal/mol
Surface area51110 Å2
手法PISA
4
H: Ubiquitin-conjugating enzyme E2-34 kDa
G: Ubiquitin-activating enzyme E1 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,0244
ポリマ－148,4932
非ポリマー5312
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-25 kcal/mol
Surface area52140 Å2
手法PISA
単位格子
Length a, b, c (Å)75.636, 152.408, 252.567
Angle α, β, γ (deg.)90.000, 90.448, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
12
22
32
42

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
111ALAALAPROPRO(chain 'A' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))AE10 - 77210 - 772
121GLUGLULEULEU(chain 'A' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))AE797 - 1024797 - 1024
131ATPATPATPATP(chain 'A' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))AI1101
241ALAALAPROPRO(chain 'C' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))CG10 - 77210 - 772
251GLUGLULEULEU(chain 'C' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))CG797 - 1024797 - 1024
261ATPATPATPATP(chain 'C' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))CM1101
371ALAALAPROPRO(chain 'E' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))EF10 - 77210 - 772
381GLUGLULEULEU(chain 'E' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))EF797 - 1024797 - 1024
391ATPATPATPATP(chain 'E' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))EK1101
4101ALAALAPROPRO(chain 'G' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))GH10 - 77210 - 772
4111GLUGLULEULEU(chain 'G' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))GH797 - 1024797 - 1024
4121ATPATPATPATP(chain 'G' and (resid 10 through 772 or resid 797 through 1024 or resid 1101 through 1102))GO1101
1132SERSERPROPRO(chain 'B' and resid 6 through 178)BA6 - 1786 - 178
2142SERSERPROPROchain 'D'DC6 - 1786 - 178
3152SERSERPROPRO(chain 'F' and resid 6 through 178)FB6 - 1786 - 178
4162SERSERPROPRO(chain 'H' and resid 6 through 178)HD6 - 1786 - 178

NCSアンサンブル:
ID
1
2

-
要素

#1: タンパク質
Ubiquitin-conjugating enzyme E2-34 kDa / Cell division control protein 34 / E2 ubiquitin-conjugating enzyme 3 / E3 ubiquitin ligase complex ...Cell division control protein 34 / E2 ubiquitin-conjugating enzyme 3 / E3 ubiquitin ligase complex SCF subunit CDC34 / Ubiquitin carrier protein / Ubiquitin-protein ligase


分子量: 34098.750 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: CDC34, DNA6, UBC3, YDR054C, D4211, YD9609.08C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P14682, E2 ubiquitin-conjugating enzyme
#2: タンパク質
Ubiquitin-activating enzyme E1 1


分子量: 114393.844 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: UBA1, YKL210W / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P22515, E1 ubiquitin-activating enzyme
#3: 化合物
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: ATP, エネルギー貯蔵分子*YM
#4: 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: 4 / 由来タイプ: 合成 / 式: Mg
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 9 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationY

-
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: 2.45 Å3/Da / 溶媒含有率: 49.81 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: ammonium chloride, PEG 3350

-
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: ESRF / ビームライン: ID23-2 / 波長: 0.873 Å
検出器タイプ: DECTRIS PILATUS3 X 2M / 検出器: PIXEL / 日付: 2017年11月3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: 0.873 Å / 相対比: 1
反射解像度: 3.18→49.81 Å / Num. obs: 96004 / % possible obs: 99.66 % / 冗長度: 3.8 % / Biso Wilson estimate: 87.41 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.1
反射 シェル解像度: 3.18→3.294 Å / Num. unique obs: 9585 / CC1/2: 0.33

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
Aimlessデータスケーリング
PDB_EXTRACT3.25データ抽出
XDSデータ削減
PHASER位相決定
PARROTモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 3CMM

3cmm


解像度: 3.18→49.81 Å / SU ML: 0.4866 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.7927
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2627 4764 4.96 %
Rwork0.217 91208 -
obs0.2192 95972 99.7 %
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 mean: 92.43 Å2
精密化ステップサイクル: LAST / 解像度: 3.18→49.81 Å
タンパク質核酸リガンド溶媒全体
原子数37086 0 128 9 37223
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.016438026
X-RAY DIFFRACTIONf_angle_d1.450551519
X-RAY DIFFRACTIONf_chiral_restr0.06635699
X-RAY DIFFRACTIONf_plane_restr0.00966742
X-RAY DIFFRACTIONf_dihedral_angle_d20.002114219
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.220.36021480.3543046X-RAY DIFFRACTION99.94
3.22-3.250.34831690.33433038X-RAY DIFFRACTION99.97
3.25-3.290.32311540.323028X-RAY DIFFRACTION99.97
3.29-3.340.33661880.31353020X-RAY DIFFRACTION99.91
3.34-3.380.36051670.30522979X-RAY DIFFRACTION99.94
3.38-3.430.35321470.29843080X-RAY DIFFRACTION99.91
3.43-3.470.31831640.28353029X-RAY DIFFRACTION99.75
3.47-3.530.34321670.27562973X-RAY DIFFRACTION99.87
3.53-3.580.31171640.26323047X-RAY DIFFRACTION99.94
3.58-3.640.32981680.26713044X-RAY DIFFRACTION99.97
3.64-3.70.30451730.25013022X-RAY DIFFRACTION99.81
3.7-3.770.30861560.25743089X-RAY DIFFRACTION99.85
3.77-3.840.29651670.24292966X-RAY DIFFRACTION99.87
3.84-3.920.28911440.23233039X-RAY DIFFRACTION99.59
3.92-4.010.29091550.22053071X-RAY DIFFRACTION99.72
4.01-4.10.25871750.21022954X-RAY DIFFRACTION99.87
4.1-4.20.24791460.20443124X-RAY DIFFRACTION99.79
4.2-4.320.23391420.20383001X-RAY DIFFRACTION99.87
4.32-4.440.24171440.193088X-RAY DIFFRACTION99.78
4.44-4.590.21491550.17933014X-RAY DIFFRACTION99.56
4.59-4.750.20381730.17053063X-RAY DIFFRACTION99.57
4.75-4.940.21631570.17762981X-RAY DIFFRACTION99.34
4.94-5.160.25021820.18513054X-RAY DIFFRACTION99.54
5.16-5.440.25481530.19813055X-RAY DIFFRACTION99.63
5.44-5.780.24571430.19933052X-RAY DIFFRACTION99.81
5.78-6.220.26431520.19383056X-RAY DIFFRACTION99.78
6.22-6.850.26291550.1923075X-RAY DIFFRACTION99.51
6.85-7.830.25071310.20433039X-RAY DIFFRACTION99
7.83-9.860.20681650.18493070X-RAY DIFFRACTION99.17
9.86-49.810.24311600.20843111X-RAY DIFFRACTION98.76
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)
10.01347367028520.065192677038-0.066235261660.966385030799-0.7917436750090.660488768270.613502463402-0.0852280589331-0.138803772443-0.190648131694-0.02211873811870.4741689542460.369739046154-0.952085251979-0.5106533885870.910959643645-0.111319967972-0.2099093784841.68706347932-0.04739722572611.03754844147-29.846623031551.2886035168-50.9163247649
20.500831038157-0.253402394363-1.676208548033.774720817381.589943581115.728456874370.839906661563-0.9054699739920.4950046478661.03327028975-0.19912593247-0.2333866151850.452584608602-0.0637686729871-0.7754692978320.998671911061-0.105250675376-0.1671393106341.2358741001-0.3246929683230.864849218787-26.144973272344.1244068814-41.3918055297
33.624330803781.63241829455-2.185094366562.68192354561-0.3626485928361.641399624660.6928827924570.1640533096110.0494131190871-0.08591858011510.1199720245360.0318073577881-0.09195604538260.372871358698-0.717090926471.646316358840.056457377924-0.1572742352851.37386749523-0.09499125342910.84597298035-31.911595104335.8365213701-43.7164692923
40.160499739479-1.143308713540.9930694200459.00348845551-7.788267521116.741381586180.118523441441-0.5947258751240.0689553869060.963516328549-0.0255846286356-0.2939050448760.7593102841130.668510957013-0.2807197416661.33354103974-0.386784093959-0.01290625024611.40963405116-0.2463814260440.690401588243-27.419864870228.1312371775-43.9007321849
53.593797151730.509666717204-4.496786360631.44788712538-0.6409262685186.515525811780.985736168072-0.0963169879364-0.6823329377380.04596447212410.8488875756680.3729472578281.14932577845-0.0797618572211-1.506694171311.47166307156-0.0338840379274-0.1619759839051.429848365310.2441564066710.732463796854-30.31801637323.3462524279-47.1946836333
60.260123725663-0.165907798890.4596910253770.7446637421070.1718871304221.437849385710.225951295011-0.3313814286-0.1048742583230.0259161584781-0.0972103244070.4686152129340.47157011297-0.161976824746-0.07518020125121.55211910887-0.801062566201-0.023187895981.01084292034-0.3385402080391.84922722635-37.433134500532.7098419775-57.8599538211
72.05288715684-0.7496840482331.859516603921.04192424943-0.06900575718562.14542091452-0.4407267974790.8830437966130.869954642286-0.05217060975830.2110575137310.9507253760810.255826044272-0.3266257517060.1267748286571.26792418966-0.3263625518420.4361075019471.15541195340.09748132880041.83940832394-40.645607875238.2154758274-52.4148753215
82.904303639-1.87821483339-1.775382473342.806067640050.5831166270573.369503624510.1629762981040.4621044031630.517977831676-0.3720433957590.6203310791220.7081015344390.0361680657016-0.663311192051-0.6659996040541.72380945414-0.749772370810.414893285231.201094483020.2719161796610.950065712874-40.137278528721.4128233078-47.5622067563
92.198181131570.645865557061-0.5232083966656.713807180630.682977304891.555551823140.201902146544-0.571625594132-0.6264336845841.993988686090.142176273460.6342062323520.320050124262-0.856088972324-0.3271184123511.77971160107-0.06451390687370.009199895853221.93443909273-0.001662066198711.27406395741-40.055534266913.7790230597-39.7613587172
103.95725697622-0.781755154634-0.6399933059881.35786914577-0.3902228675754.75040332790.125261342371-0.2066835787590.631430808852-0.2609321847740.624771111518-0.1352675362530.9601561215660.395313584292-0.5803646489261.49195041559-0.0817089398860.08679685082741.634876406720.2028055012540.858429864274-28.971414295627.4793526902-30.3157836154
115.019061202691.10292126127-0.8854224539186.182309760741.272515838633.24483188827-0.1487130872190.152341126257-0.470002330322-0.717534170155-0.2023558390260.224697831415-0.589146796132-1.064945915960.2874000886250.656918647420.139174720243-0.006333376306231.18846003112-0.137744898830.643254235038-65.241829237566.305291008-77.0473599509
120.01033496271060.0008412331610780.0124828134967-0.000944985332315.18372777581E-50.00794658417482-0.3013559999280.251290500917-0.332690864346-0.9883321413110.4307456179180.7138971922350.288457971280.444973338763-0.1061073404271.320248906120.293558072688-0.2829618495671.38864478371-0.4295702612711.31152224995-74.249916046878.5974908294-93.8648295192
132.319912935730.3616908079450.4572912215037.36260055459-2.138107820883.649289063440.2107002018230.389616050450.33332345306-0.508613147112-0.309833003499-0.303403666708-1.84687942453-1.107575513170.1024268259521.374348312830.621863509164-0.1719563989951.3822026989-0.2760103751630.652236517463-65.311346198481.7452494198-77.1085424777
142.94591232686-0.356345803036-1.77311929830.365212819241-0.3157258803881.933797885690.543273603422-0.9235394262830.8423796986760.8400189310210.530560227880.400699598805-1.1758129751-1.0797621415-1.036296438291.552641349950.4941049514430.1704495038691.88213433234-0.09666146056731.85346301082-78.947031593777.9112237047-67.8840318106
154.114489733161.42518077898-2.694794840463.50792987086-0.04778761919612.44476571735-0.4158897924760.246929307383-0.569796237994-0.0398804835230.1200126726740.691682604810.465237935304-0.2552920255620.2620843990580.830260177210.3903897348210.2631667512711.58327127143-0.2088954057420.769659926889-75.021434012977.034509664-81.5046278476
166.285322314972.007687624786.070672816410.7458727609342.296754535017.088799093590.3068418983531.296871094540.129893494031-0.559287968213-0.410915503127-0.3381422368830.245380220880.5205184251590.08437485527841.51051458610.818653477573-0.1533049279251.581775254120.2947986750710.665488448316-76.834870476792.0944231099-80.7019777489
170.8382066129380.2695420778530.6904205248410.104393598540.3996759353812.241462333960.422420045328-0.0346934416826-0.380013125964-0.1067105863740.1209473757860.03724066770630.170413687555-0.2205768194280.07301087205261.847990856460.725546709904-0.1290133293261.963746293560.4172388137040.195974705029-68.771970329187.5467566366-93.9179422504
182.448581629952.993004780550.4521091951353.97833036457-0.8083921077135.9112050686-0.420863657642-0.1608586867730.4825919448340.459648868923-0.4241189154380.769027280953-0.252673024335-0.2187763803210.8241522918951.49405873291-0.1664802179790.1080872361170.552649054706-0.133817710730.655062621112-89.47518996940.542487452139-124.791480263
194.486305580011.975562356711.879140535374.75904447385-2.099509406814.18274698638-0.2452329865570.541961234421-0.0910209568191-1.050901331240.251482185760.3473252902630.569884929065-0.09515979383550.06833104861410.84704511732-0.155989000191-0.2031485492630.357397774573-0.415763568161.01734680836-83.15250330064.72467480548-132.840614206
20-0.00168294328026-0.003606036807610.00117466538140.00939333372163-0.01414383250430.0111159953847-0.392224421039-0.334985759341.322523937130.202129106633-0.552653723094-0.150225092909-0.263229049114-0.1865481726870.8932584447161.034365223890.220885265807-0.3263313038461.38130841837-0.3399274960212.35497498001-95.37137801622.2692191546-129.517798904
213.86444654012-0.4086638223271.913939031981.27459107921-0.6841239080393.60133215013-0.230161105876-0.241999861480.2096282660230.0431551178407-0.175620424854-0.2523246691240.152640850633-0.07780721149610.3708131523550.832581023054-0.0624426186746-0.1088318146860.599919339162-0.1698010203930.986397253401-77.397116491415.1958507337-125.125567313
220.2184996217310.4534600850160.2023250971570.9322329743150.4173976301430.1952126639390.3216529654-1.316908546070.5834947628790.8747427797810.474091773472-0.281471979018-1.83184731031-0.34521640558-0.6849812517541.759719761560.1987914374210.126126975921.15988005579-0.07790564270481.00607370211-80.693307526510.6952361981-108.999079006
231.934269105891.648617697651.346633838512.528092469641.46888856632.26892373326-0.430600781555-0.1101475370760.537054473424-0.619734808304-0.6284798084231.83785481841-0.290812215299-0.1006344030531.103359516170.5541119758080.132265357421-0.05330925609820.808899534066-0.09688477699021.61264507284-85.605865500627.6387148678-128.432995573
240.929049450105-0.22342911642-0.4580966289414.11638012987-1.044627751370.553591366631-0.216753793070.202500162407-0.07055809295010.754813969886-0.8131653905641.882614090690.262646584521-0.8930143207950.9472187881811.56372179062-0.3591350839840.3498362351972.29434056079-0.8005550112641.17217460025-97.079171646112.030458788-140.767546357
254.33305460970.7438410301240.2332647820883.610547274371.271306869585.31621259804-0.8120302018280.1030495704460.676029233096-0.483348574898-0.229807055247-0.4761955967360.2377093398511.179717407771.003010476481.49835995106-0.105105082963-0.2052090929611.252946627880.5823668481081.20060505108-30.741593093650.71653376255.863848786
260.227143988097-0.236426120779-0.2410601986860.2425890549750.2520757873920.252972304097-0.193445309395-0.665134322496-0.09533702938370.24954020899-0.01433496615211.18331715457-0.4818709776190.1933615233650.1777327932251.5069756999-0.01883411068140.5105971981791.26960078693-0.03171241541641.81626664569-19.721023401631.0304397166-0.172942600198
273.6992029572-1.81822183639-0.7193358770112.902518536472.225581500081.90754747675-0.524184111516-0.344200523956-0.0661704348880.267219636337-0.2489396627670.2798126185920.3551217882940.3444462726990.5747065564621.51976824171-0.05073170194450.1312696252081.352499732590.362031628640.997324510138-37.902617740.94725215713.03054003157
281.73977082718-0.4410798157090.8188846910571.581794851720.5496687613482.306979698230.244805393098-0.2721929389580.512810284430.988517361007-0.447845356364-0.132969091411-0.6321958888130.9771799031250.1033438277381.23738059228-0.1990620889860.09047098018631.152272659370.5233763629591.27559670457-35.868876049833.426236183811.0200131734
291.03743464758-0.533303526261.023058087280.266880740862-0.5267834880380.9931693408080.3141790201160.4928663772840.100880376601-0.1286168335630.00902748317888-0.569595801482-0.3989500898230.364544872938-0.3451640164741.703269196050.1072909074870.6543459056150.9448903883460.02403996358291.22134233915-25.690105419726.7054333288-6.2046690219
301.42739316936-0.4106165398440.5628783158432.650003723380.1129512308482.1331895907-0.07514214875610.0806452057256-0.184401384917-0.3014259742330.264298962694-0.4806141305010.1455496810040.331780173156-0.1828373068920.3519702875670.0008023098614980.05746506856510.458613842645-0.06205684077520.540049804499-26.681981571337.0917805012-105.521688052
313.24825008771.24167743288-1.87675313813.94191796856-2.648682257473.422818601630.205457377419-0.4353548656280.04762351638961.330101276050.0508172173693-0.191794334514-0.692417896734-0.342671142385-0.2393496170770.99211326462-0.0567376555713-0.04496177093810.833584626584-0.05887708542880.532110061717-52.805438219623.6440070756-76.9518277824
321.10353217665-0.1755636160660.5578886565220.9128608178220.3228193996971.116219336090.0144525173837-0.3902011763390.09135297884530.1186499145820.105873133002-0.1821359521180.08947966217840.206054172537-0.09138567626640.381787740221-0.008988896985460.01306843937510.713242376101-0.1006731458250.623480279818-23.689583609144.715778748-84.4404526005
330.9501476733040.2967992698030.2976169885981.226199344440.146396395761.195693669080.167910075467-0.553296287241-0.04706147550640.45355689846-0.061668619598-0.1258133639220.2378518385290.0122520639342-0.1224080686290.577351826693-0.0117971918321-0.01349295288640.967351816085-0.04451492919830.704076799972-22.246891151634.7337235106-62.7302070814
341.58694999639-0.942568787223-0.4798417037992.482691966341.101571259791.756035194250.0005329972695930.0795602198316-0.08282548860120.364104868535-0.1056179290890.130756433314-0.0745591547037-0.2070409638010.04562138374170.543774946031-0.0111199118729-0.05376586476080.637017470361-0.08210136391950.523932958047-67.734638544878.5336111252-29.4597435632
351.089604974940.154153588862-0.7657763806551.641664699440.5560581359331.3147089440.4195819410590.6058207156390.213861846502-1.04853713175-0.185019798911-0.431848880997-0.924691542483-0.0384553157919-0.2691857973851.292206905850.2433286408730.1929232989681.291913746020.04695429711060.680638146051-56.820081121986.6243073345-63.5893280954
360.757763267719-0.796130075836-0.7147348299011.302082638241.050075448982.035409521940.291086789640.5987047988980.0676602707809-0.459534160692-0.198199468943-0.161929192625-0.758580761068-0.366896553686-0.07029952009140.6964786984070.1449817480460.02321718153891.003448328550.03135384731630.736820582358-59.182662864980.7144316897-62.6673579718
371.167451478880.3243149905120.395747422751.743831471060.6664421560141.579464013370.14205098669-0.134945818574-0.3380367408830.457241642109-0.0690163222501-0.2861806745090.5470211116180.10721249152-0.05468764383090.7917587282220.00355657700843-0.03206085031970.5450377672080.04303100397490.742722719317-45.8502082404-4.80555670407-97.8793235801
38-0.0386334002174-0.00567089618333-0.03447031286410.698123815151-0.10476742836-0.02951820509950.0332529271098-0.0104391440964-0.0797944761131-0.109306363041-0.1075454390380.263225483110.2463597281320.06467266129730.04575462722050.77231853888-0.0109796702071-0.006575184742240.545931660692-0.07564322942880.808005691841-63.37003708382.64752249557-116.414292119
392.188309254760.6816129921510.05836456394651.91640806422-0.3653270933812.63918694333-0.1428106265820.4121254350580.0211247124531-0.5919821553570.1789762350370.0392909222693-0.0203415359855-0.203628706767-0.0302568228530.624462092322-0.0414238463352-0.0069619399210.47072775296-0.08124986429510.491469777819-55.880595567526.6033238353-131.402121236
401.734378683411.218673487441.322686953172.010275719150.3392037775492.109750701530.231058130405-0.156541616988-0.2185043802240.0622426355581-0.1454960406340.4207809732320.526151141916-0.5403310912-0.09144198009110.620907184716-0.0284247418350.09693861219140.546761768171-0.1884782098050.820204229336-75.6650500616-14.919119437-120.419670801
411.369809032690.344326488253-0.2308059689531.80471795234-0.4891655855741.214716552620.219355225021-0.3680547237380.222562584190.740853674415-0.3285470377970.218818017359-0.7315213254680.1486132930890.128682131031.46601978596-0.2875680538450.03920091246110.833926111928-0.1158813227670.745917214077-70.888997678550.275473064734.8058066828
420.7383840314610.3742483050040.0768711338362.083199723450.3836552256610.9761489318680.02013380889840.0784820573649-0.101025065156-0.323199234443-0.321513002859-0.472104526637-0.04819725762840.3505030676420.3133655327841.309958035210.0169438862110.1699669150630.8617274434280.2496492428610.826973743732-56.642783106931.39527799781.94674584973
431.435105944670.66940503502-0.7069432187512.04042795442-0.3297358925581.057735585820.1482359745-0.04720528227960.2972240938680.142145786117-0.464527011677-0.469482490631-0.2901892916290.4560513655170.3281053201621.06218756971-0.147403639664-0.2213534153230.981071742220.3805672832490.874670600839-47.730007319755.400233290510.4529848803
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 20 )
2X-RAY DIFFRACTION2chain 'B' and (resid 21 through 46 )
3X-RAY DIFFRACTION3chain 'B' and (resid 47 through 75 )
4X-RAY DIFFRACTION4chain 'B' and (resid 76 through 84 )
5X-RAY DIFFRACTION5chain 'B' and (resid 85 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 104 )
7X-RAY DIFFRACTION7chain 'B' and (resid 105 through 133 )
8X-RAY DIFFRACTION8chain 'B' and (resid 134 through 143 )
9X-RAY DIFFRACTION9chain 'B' and (resid 144 through 154 )
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 178 )
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 46 )
12X-RAY DIFFRACTION12chain 'F' and (resid 47 through 59 )
13X-RAY DIFFRACTION13chain 'F' and (resid 60 through 94 )
14X-RAY DIFFRACTION14chain 'F' and (resid 95 through 120 )
15X-RAY DIFFRACTION15chain 'F' and (resid 121 through 133 )
16X-RAY DIFFRACTION16chain 'F' and (resid 134 through 143 )
17X-RAY DIFFRACTION17chain 'F' and (resid 144 through 178 )
18X-RAY DIFFRACTION18chain 'D' and (resid 6 through 28 )
19X-RAY DIFFRACTION19chain 'D' and (resid 29 through 46 )
20X-RAY DIFFRACTION20chain 'D' and (resid 47 through 59 )
21X-RAY DIFFRACTION21chain 'D' and (resid 60 through 104 )
22X-RAY DIFFRACTION22chain 'D' and (resid 105 through 120 )
23X-RAY DIFFRACTION23chain 'D' and (resid 121 through 170 )
24X-RAY DIFFRACTION24chain 'D' and (resid 171 through 178 )
25X-RAY DIFFRACTION25chain 'H' and (resid 1 through 46 )
26X-RAY DIFFRACTION26chain 'H' and (resid 47 through 59 )
27X-RAY DIFFRACTION27chain 'H' and (resid 60 through 84 )
28X-RAY DIFFRACTION28chain 'H' and (resid 85 through 143 )
29X-RAY DIFFRACTION29chain 'H' and (resid 144 through 178 )
30X-RAY DIFFRACTION30chain 'A' and (resid 10 through 166 )
31X-RAY DIFFRACTION31chain 'A' and (resid 167 through 264 )
32X-RAY DIFFRACTION32chain 'A' and (resid 265 through 684 )
33X-RAY DIFFRACTION33chain 'A' and (resid 685 through 1024 )
34X-RAY DIFFRACTION34chain 'E' and (resid 10 through 545 )
35X-RAY DIFFRACTION35chain 'E' and (resid 546 through 684 )
36X-RAY DIFFRACTION36chain 'E' and (resid 685 through 1024 )
37X-RAY DIFFRACTION37chain 'C' and (resid 10 through 545 )
38X-RAY DIFFRACTION38chain 'C' and (resid 546 through 624 )
39X-RAY DIFFRACTION39chain 'C' and (resid 625 through 866 )
40X-RAY DIFFRACTION40chain 'C' and (resid 867 through 1024 )
41X-RAY DIFFRACTION41chain 'G' and (resid 10 through 545 )
42X-RAY DIFFRACTION42chain 'G' and (resid 546 through 797 )
43X-RAY DIFFRACTION43chain 'G' and (resid 798 through 1024 )

+
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