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- PDB-5jcz: Rab11 bound to MyoVa-GTD -

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基本情報

登録情報
データベース: PDB / ID: 5jcz
タイトルRab11 bound to MyoVa-GTD
要素
  • Ras-related protein Rab-11A
  • Unconventional myosin-Va
キーワードMOTOR PROTEIN / myosin / complex / Rab / motor cargo recognition
機能・相同性
機能・相同性情報


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / post-Golgi vesicle-mediated transport / regulation of cilium assembly / insulin-responsive compartment / exosomal secretion / melanosome transport / amyloid-beta clearance by transcytosis / astral microtubule organization / VxPx cargo-targeting to cilium / protein transmembrane transport / actin filament-based movement / neurotransmitter receptor transport, endosome to postsynaptic membrane / filopodium tip / vesicle transport along actin filament / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / multivesicular body assembly / dynein light intermediate chain binding / protein localization to cilium / Regulation of MITF-M-dependent genes involved in pigmentation / establishment of protein localization to membrane / protein localization to cell surface / myosin complex / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / microfilament motor activity / positive regulation of G2/M transition of mitotic cell cycle / Insulin processing / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / transport vesicle / vesicle-mediated transport / phagocytic vesicle / ruffle / Anchoring of the basal body to the plasma membrane / centriole / multivesicular body / small monomeric GTPase / G protein activity / regulation of cytokinesis / trans-Golgi network membrane / actin filament organization / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / trans-Golgi network / cytoplasmic vesicle membrane / cellular response to insulin stimulus / recycling endosome / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / actin filament binding / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / actin cytoskeleton / melanosome / protein transport / growth cone / cytoplasmic vesicle / microtubule binding / vesicle / calmodulin binding / neuron projection / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / Golgi apparatus / protein-containing complex / RNA binding / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
類似検索 - 分子機能
: / Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / small GTPase Rab1 family profile. / Myosin, N-terminal, SH3-like ...: / Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / small GTPase Rab1 family profile. / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif, EF-hand binding site / IQ motif profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Kinesin motor domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / 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
ACETATE ION / BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-11A / Unconventional myosin-Va
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.056 Å
データ登録者Pylypenko, O. / Attanda, W. / Gauquelin, C. / Malherbes, G. / Houdusse, A.
引用ジャーナル: Elife / 年: 2016
タイトル: Coordinated recruitment of Spir actin nucleators and myosin V motors to Rab11 vesicle membranes.
著者: Pylypenko, O. / Welz, T. / Tittel, J. / Kollmar, M. / Chardon, F. / Malherbe, G. / Weiss, S. / Michel, C.I. / Samol-Wolf, A. / Grasskamp, A.T. / Hume, A. / Goud, B. / Baron, B. / England, P. ...著者: Pylypenko, O. / Welz, T. / Tittel, J. / Kollmar, M. / Chardon, F. / Malherbe, G. / Weiss, S. / Michel, C.I. / Samol-Wolf, A. / Grasskamp, A.T. / Hume, A. / Goud, B. / Baron, B. / England, P. / Titus, M.A. / Schwille, P. / Weidemann, T. / Houdusse, A. / Kerkhoff, E.
履歴
登録2016年4月15日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年9月28日Provider: repository / タイプ: Initial release
改定 2.02018年10月24日Group: Atomic model / Data collection / Derived calculations
カテゴリ: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num
改定 2.12024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: Ras-related protein Rab-11A
B: Unconventional myosin-Va
C: Unconventional myosin-Va
D: Ras-related protein Rab-11A
E: Unconventional myosin-Va
I: Ras-related protein Rab-11A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)199,08833
ポリマ－196,3546
非ポリマー2,73427
水20,7891154
1
A: Ras-related protein Rab-11A
B: Unconventional myosin-Va
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,53813
ポリマ－65,4512
非ポリマー1,08711
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
C: Unconventional myosin-Va
D: Ras-related protein Rab-11A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,44013
ポリマ－65,4512
非ポリマー98911
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
E: Unconventional myosin-Va
I: Ras-related protein Rab-11A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,1097
ポリマ－65,4512
非ポリマー6585
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)215.790, 128.420, 89.020
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number5
Space group name H-MC121

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要素

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タンパク質 , 2種, 6分子 ADIBCE

#1: タンパク質 Ras-related protein Rab-11A / Rab-11 / YL8


分子量: 20100.598 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAB11A, RAB11 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P62491
#2: タンパク質 Unconventional myosin-Va / Dilute myosin heavy chain / non-muscle / Myosin heavy chain 12 / Myosin-12 / Myoxin


分子量: 45350.605 Da / 分子数: 3 / Fragment: UNP residues 1437-1828 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MYO5A, MYH12 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q9Y4I1

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非ポリマー , 7種, 1181分子

#3: 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
#4: 化合物 ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / コメント: GDP, エネルギー貯蔵分子*YM
#5: 化合物 ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


分子量: 66.007 Da / 分子数: 3 / 由来タイプ: 合成 / 式: BeF3
#6: 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: 13 / 由来タイプ: 合成 / 式: C2H6O2
#7: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H3O2
#8: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1154 / 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: 3.11 Å3/Da / 溶媒含有率: 60.43 %
結晶化温度: 290 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 7% (w/v) PEG-8000, 50 mM Bicine, 50 mM Tris, 30mM sodium fluoride, 20% (v/v) ethylene glycol

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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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.98011 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2012年6月6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: 0.98011 Å / 相対比: 1
反射解像度: 2.056→48.88 Å / Num. obs: 146774 / % possible obs: 98.6 % / 冗長度: 7.7 % / Net I/σ(I): 20.58
反射 シェル解像度: 2.056→2.18 Å / Rmerge(I) obs: 0.555

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
XDSデータ削減
XDSデータスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4LX1

4lx1


解像度: 2.056→48.879 Å / SU ML: 0.2 / 交差検証法: FREE R-VALUE / σ(F): 2 / 位相誤差: 21.55
Rfactor反射数%反射
Rfree0.2083 7338 5 %
Rwork0.1797 --
obs0.1811 146754 98.57 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.056→48.879 Å
タンパク質核酸リガンド溶媒全体
原子数12385 0 172 1154 13711
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00212915
X-RAY DIFFRACTIONf_angle_d0.59317456
X-RAY DIFFRACTIONf_dihedral_angle_d12.5434791
X-RAY DIFFRACTIONf_chiral_restr0.0222027
X-RAY DIFFRACTIONf_plane_restr0.0032212
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0558-2.07920.27762300.23844371X-RAY DIFFRACTION93
2.0792-2.10360.2452410.23314579X-RAY DIFFRACTION98
2.1036-2.12930.2752450.22014656X-RAY DIFFRACTION98
2.1293-2.15620.25212400.21084559X-RAY DIFFRACTION98
2.1562-2.18460.25252410.20684581X-RAY DIFFRACTION98
2.1846-2.21450.24592450.1964656X-RAY DIFFRACTION98
2.2145-2.24620.22252420.19314587X-RAY DIFFRACTION98
2.2462-2.27970.21642440.19154647X-RAY DIFFRACTION98
2.2797-2.31530.23942390.19014545X-RAY DIFFRACTION98
2.3153-2.35330.21692470.1894684X-RAY DIFFRACTION98
2.3533-2.39390.24982410.1864577X-RAY DIFFRACTION98
2.3939-2.43740.2192450.18074660X-RAY DIFFRACTION99
2.4374-2.48430.23382450.18164649X-RAY DIFFRACTION98
2.4843-2.5350.232440.18664633X-RAY DIFFRACTION99
2.535-2.59010.22992440.19044643X-RAY DIFFRACTION99
2.5901-2.65030.23752440.18424629X-RAY DIFFRACTION99
2.6503-2.71660.22652460.18944674X-RAY DIFFRACTION99
2.7166-2.79010.25932460.1984681X-RAY DIFFRACTION99
2.7901-2.87220.24412440.20224641X-RAY DIFFRACTION99
2.8722-2.96480.23632460.19624661X-RAY DIFFRACTION99
2.9648-3.07080.23732460.19184681X-RAY DIFFRACTION99
3.0708-3.19370.21622460.19244683X-RAY DIFFRACTION99
3.1937-3.3390.22012460.18874660X-RAY DIFFRACTION99
3.339-3.5150.20042460.18624680X-RAY DIFFRACTION99
3.515-3.73520.21452470.1724703X-RAY DIFFRACTION99
3.7352-4.02350.1692490.16044727X-RAY DIFFRACTION99
4.0235-4.42810.17732470.14984696X-RAY DIFFRACTION100
4.4281-5.06830.18242490.14674720X-RAY DIFFRACTION100
5.0683-6.38330.21862500.18954754X-RAY DIFFRACTION100
6.3833-48.89320.1882530.18714799X-RAY DIFFRACTION99
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)
11.21870.37490.32530.894-0.83560.8531-0.0510.241-0.2691-0.29350.05510.0631-0.0346-0.1675-0.00010.43580.0109-0.00840.30190.01910.453139.24776.087423.6072
2-0.01990.0407-0.01880.1836-0.12080.0521-0.09970.10550.2324-0.20980.31450.7030.0056-0.8396-0.00050.49890.0291-0.05140.39710.11950.613428.244314.554124.2261
30.3892-0.110.61730.5344-0.23670.83360.10780.483-0.2797-0.3122-0.09080.2013-0.2483-0.0109-0.00010.5104-0.0538-0.02590.39310.02470.507541.55261.664920.3488
40.42840.14450.30540.4364-0.14670.23290.1421-0.9909-0.30040.51140.09140.0053-0.1969-0.02080.00010.53390.0061-0.01920.46050.13840.535335.34450.163737.7625
50.53390.3186-0.10630.33510.17380.6576-0.0543-0.4331-0.0730.26820.0363-0.2245-0.01850.0455-0.00010.51480.0586-0.04940.36730.11660.402741.961213.147439.0585
61.27210.84710.21150.47190.13790.3017-0.03740.0081-0.0193-0.23450.0464-0.2067-0.00180.0784-0.00010.48320.0077-0.03780.29680.0410.415844.563617.250331.2864
70.117-0.06680.03140.0052-0.03280.0279-0.17790.1550.53240.1613-0.2457-1.6075-0.41311.05980.00050.5469-0.0007-0.07470.42330.04910.597953.167719.55636.362
80.1817-0.2455-0.27920.26840.27760.29020.23310.3507-0.0572-0.3513-0.14-0.15390.21680.3866-0.00020.4831-0.0106-0.04610.30130.06280.419545.832217.703926.3875
90.21620.24210.27140.26990.30820.25390.32780.6341-0.2423-0.5628-0.4848-0.58780.17550.49490.00020.51650.00440.00810.38720.01560.584751.3775.096222.5457
101.1832-0.2594-0.48461.03060.350.93770.07011.0308-0.6022-0.167-0.01880.15310.7083-0.3772-0.00010.789-0.32520.03771.1519-0.27530.713714.5318-9.1887-22.5256
111.24950.5261-0.6630.4406-0.35673.1154-0.19530.5059-0.3041-0.06590.1715-0.08260.43-0.5596-0.00040.5088-0.15150.01680.6503-0.11060.649317.396-5.2054-1.212
123.5014-0.50930.28161.63551.1892.0159-0.0826-0.4609-0.28840.21070.03950.16770.0492-0.20720.00010.4037-0.01350.00470.42670.09730.557218.9522-1.568329.7316
130.51260.28580.86391.0927-1.42211.7301-0.28510.7483-0.0843-0.22220.3078-0.07170.3421-1.344100.5227-0.1804-0.00830.9478-0.06130.628215.0548-2.6198-5.1943
140.4603-0.21510.12370.42190.30880.4263-0.1166-0.22990.16390.39480.0631-0.26350.06440.413700.60930.0264-0.07610.41740.02050.489247.406445.694748.878
151.3226-0.49170.70212.79771.31282.3234-0.00060.0214-0.00660.22880.0479-0.08630.02110.106700.38280.0007-0.03850.2240.07540.353440.410844.208238.5684
160.42610.69950.0081.0581-0.30340.54390.22360.37010.2088-0.0781-0.0817-0.042-0.8018-0.23010.00020.4802-0.0043-0.020.39350.12770.462642.499149.674819.3188
170.9511-0.04660.81351.53540.00910.635-0.08720.17640.0681-0.01430.1623-0.30690.3630.73890.00010.4089-0.00390.01650.61040.03630.489450.978437.35159.5939
180.6399-0.3403-0.2041.40710.70771.46120.03840.140.0075-0.06460.0131-0.12380.09420.1588-00.3569-0.01450.02410.43210.08550.33541.218338.31681.4743
190.1982-0.2694-0.1310.29060.27430.45110.09780.2657-0.1752-0.3923-0.18910.14050.0276-0.4553-0.00010.59130.00710.00630.62960.0940.408131.669942.3268-14.553
200.58680.5380.64710.85150.1731.23040.84620.4862-0.1761-1.1368-0.56020.0915-0.3384-0.11010.00220.81230.1314-0.02330.78890.05280.441835.121345.0548-21.0402
210.3060.1872-0.45310.11560.81911.3051-0.0280.1575-0.07010.12560.0926-0.0801-0.0227-0.0005-0.00010.42290.0162-0.01020.35170.07130.440938.828542.554626.0177
221.01-0.1945-0.8621.5838-0.14490.5552-0.0558-0.0856-0.06050.18510.0376-0.2318-0.10210.093300.4413-0.01850.0220.54420.02580.461544.842819.3352-3.9304
230.45380.7232-0.35441.59960.60691.08370.03360.0878-0.05870.27750.03710.2021-0.1749-0.2149-00.45860.00940.05720.51570.07110.476438.454721.734-2.6255
241.19970.5685-0.44741.99831.14511.0738-0.04460.502-0.1049-0.53410.0743-0.4284-0.23560.097500.5121-0.01370.11370.59470.06620.49347.899423.5674-12.0212
250.0040.0449-0.00190.10680.02940.047-0.27790.09310.1331-0.11390.24150.18960.1856-0.1909-0.00020.4691-0.01470.05660.682-0.09870.502336.950710.9939-13.5378
260.1009-0.09260.06520.1358-0.06190.4108-0.11270.7575-0.1814-1.22450.1768-0.11330.1408-0.07520.00350.7093-0.01950.18720.8676-0.05990.49541.226514.0679-22.2978
270.8284-0.44830.83871.49210.28531.2150.12130.1269-0.4394-0.0317-0.0806-0.19270.39090.107900.4608-0.02170.06860.611-0.1020.52939.38625.8923-11.9081
280.0650.0684-0.00140.121-0.11590.10890.0736-0.0345-0.874-0.2635-0.347-0.64070.29690.22570.00020.46560.02030.07210.60970.04240.794352.777410.4962-3.8701
291.25760.1990.60021.1699-0.71990.96190.24620.67410.424-0.7134-0.0242-0.3852-1.0166-0.59460.04770.76920.22570.08050.84310.22650.541122.836172.7868-2.2549
301.8169-1.2898-1.82551.99560.20723.52430.14970.52970.0655-0.3245-0.1245-0.0883-0.2691-0.72760.00460.38760.0643-0.00290.65480.11980.371921.990965.19744.7729
310.1349-0.0160.0543-0.0927-0.1750.77230.04090.26960.08710.21150.3023-0.29960.30730.33530.00010.38850.0514-0.0150.47270.04490.529129.518869.017921.9787
320.956-0.60270.06120.6438-0.0724.9821-0.0856-0.10180.15540.09450.05030.1264-0.3006-0.9677-0.00010.38910.09950.00470.47650.02550.465721.511173.207641.8932
330.8818-0.1354-0.02170.51190.12112.50610.06310.05970.08910.07860.04890.172-0.2023-0.57470.00130.48850.07540.02580.4660.05710.472623.582666.848933.6849
340.4090.598-0.2910.943-0.27190.2337-0.09720.36310.2171-0.29030.22660.64750.0618-0.39890.01230.07690.12650.16580.29080.06360.48962.722980.920550.2931
350.46530.64870.79595.57211.89311.5541-0.27130.1836-0.3338-1.3963-0.2291.055-0.1216-0.2326-0.3469-0.5610.00540.4990.45470.13290.01042.904171.333549.1233
360.9370.45640.62170.20830.28250.40340.2283-0.5995-0.35420.3392-0.04450.1804-0.1243-0.5970.08240.28630.09960.12260.2762-0.01420.41579.982582.806247.9739
370.06270.01190.00790.5386-0.69440.93380.1501-0.16470.14050.15120.66720.16680.0067-0.3340.07840.3448-0.02480.05120.4008-0.25130.526812.988984.467359.1054
380.143-0.13560.00620.1135-0.05690.0137-0.4622-0.31180.3033-0.31090.57950.2546-0.1309-0.22910.0060.3361-0.03420.04310.4491-0.09970.3721-0.199383.346863.3598
391.1864-0.23411.04691.2916-0.04962.32270.0919-0.0576-0.28560.25770.30920.05530.4401-0.31760.46130.06820.1530.18560.1201-0.1260.5379-0.146689.8456.6149
400.3738-0.78470.86411.6761-1.84072.0080.14090.081-0.1469-0.5137-0.1722-0.01350.6216-0.07850.0043-0.2103-0.15780.1680.59090.04780.3107-14.30677.406556.8092
410.0672-0.04880.1580.1968-0.24560.45150.0715-0.2060.1320.09320.29510.1664-0.3332-0.20160.0498-0.1730.20070.31540.4322-0.28170.5355-10.517690.811462.4617
420.39130.488-0.3560.5887-0.41590.3076-0.05990.79030.0425-0.5877-0.0590.19430.318-0.5772-0.00970.25380.0748-0.02540.46850.04660.4809-7.748485.080452.0764
430.57310.4853-0.9940.7819-1.15781.9161-0.38670.4388-0.8286-0.26540.25540.10580.7943-0.2844-0.037-0.56710.32070.31740.1302-0.09660.3687-0.995692.977546.4259
440.0464-0.0141-0.04580.1515-0.01520.08180.0167-0.0919-0.22190.16450.1830.4497-0.1323-0.28730.00110.48750.0259-0.06320.31180.0770.499932.256217.045328.4256
450.08890.03170.03020.1212-0.03390.0573-0.2629-0.1347-0.24670.31560.3269-0.01690.04640.20740.00060.4587-0.03760.03060.6190.00850.449931.321517.8517-8.6289
460.05180.01030.00140.006-0.00420.00890.1121-0.0319-0.0172-0.11180.338-0.21290.2144-0.14440.00040.2794-0.10220.06910.231-0.05180.5416-0.691173.327553.505
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 67 )
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 112 )
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 135 )
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 145 )
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 160 )
9X-RAY DIFFRACTION9chain 'A' and (resid 161 through 177 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1471 through 1544 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1545 through 1702 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1703 through 1807 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1808 through 1853 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1469 through 1489 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1490 through 1593 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1594 through 1627 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1628 through 1679 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1680 through 1753 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1754 through 1783 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1784 through 1808 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1809 through 1853 )
22X-RAY DIFFRACTION22chain 'D' and (resid 5 through 33 )
23X-RAY DIFFRACTION23chain 'D' and (resid 34 through 55 )
24X-RAY DIFFRACTION24chain 'D' and (resid 56 through 85 )
25X-RAY DIFFRACTION25chain 'D' and (resid 86 through 95 )
26X-RAY DIFFRACTION26chain 'D' and (resid 96 through 112 )
27X-RAY DIFFRACTION27chain 'D' and (resid 113 through 160 )
28X-RAY DIFFRACTION28chain 'D' and (resid 161 through 177 )
29X-RAY DIFFRACTION29chain 'E' and (resid 1471 through 1523 )
30X-RAY DIFFRACTION30chain 'E' and (resid 1524 through 1593 )
31X-RAY DIFFRACTION31chain 'E' and (resid 1594 through 1627 )
32X-RAY DIFFRACTION32chain 'E' and (resid 1628 through 1783 )
33X-RAY DIFFRACTION33chain 'E' and (resid 1784 through 1853 )
34X-RAY DIFFRACTION34chain 'I' and (resid 11 through 33 )
35X-RAY DIFFRACTION35chain 'I' and (resid 34 through 45 )
36X-RAY DIFFRACTION36chain 'I' and (resid 46 through 67 )
37X-RAY DIFFRACTION37chain 'I' and (resid 68 through 86 )
38X-RAY DIFFRACTION38chain 'I' and (resid 87 through 112 )
39X-RAY DIFFRACTION39chain 'I' and (resid 113 through 124 )
40X-RAY DIFFRACTION40chain 'I' and (resid 125 through 135 )
41X-RAY DIFFRACTION41chain 'I' and (resid 136 through 145 )
42X-RAY DIFFRACTION42chain 'I' and (resid 146 through 160 )
43X-RAY DIFFRACTION43chain 'I' and (resid 161 through 174 )
44X-RAY DIFFRACTION44chain 'F'
45X-RAY DIFFRACTION45chain 'G'
46X-RAY DIFFRACTION46chain 'H'

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万見について

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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://pdbjlvh1.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