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- PDB-8aht: Crystal structure of Plasmodium falciparum Ca2+/Calmodulin in com... -

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基本情報

登録情報
データベース: PDB / ID: 8aht
タイトルCrystal structure of Plasmodium falciparum Ca2+/Calmodulin in complex with melittin
要素
  • Calmodulin
  • Melittin
キーワードMETAL BINDING PROTEIN / hub protein / linear recognition motif
機能・相同性
機能・相同性情報


apical complex / calcium ion sensor activity / Neutrophil degranulation / other organism cell membrane / porin activity / molecular function inhibitor activity / protein kinase inhibitor activity / pore complex / localization / monoatomic ion transport ...apical complex / calcium ion sensor activity / Neutrophil degranulation / other organism cell membrane / porin activity / molecular function inhibitor activity / protein kinase inhibitor activity / pore complex / localization / monoatomic ion transport / enzyme regulator activity / enzyme activator activity / toxin activity / killing of cells of another organism / lipid binding / calcium ion binding / extracellular region / cytoplasm
類似検索 - 分子機能
Melittin/ Api allergen / Melittin / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
類似検索 - ドメイン・相同性
Melittin / Calmodulin
類似検索 - 構成要素
生物種Plasmodium falciparum (マラリア病原虫)
Apis mellifera (セイヨウミツバチ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者Durvanger, Z. / Harmat, V.
資金援助 ハンガリー, European Union, 3件
組織認可番号国
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 ハンガリー
European Regional Development FundVEKOP-2.3.2-16-2017-00014, VEKOP-2.3.3-15-2017-00018European Union
Hungarian National Research, Development and Innovation OfficeThematic Excellence Program Synth+ ハンガリー
引用ジャーナル: J.Biol.Chem. / 年: 2023
タイトル: Structures of calmodulin-melittin complexes show multiple binding modes lacking classical anchoring interactions.
著者: Durvanger, Z. / Juhasz, T. / Liliom, K. / Harmat, V.
履歴
登録2022年7月22日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年3月22日Provider: repository / タイプ: Initial release
改定 1.12023年4月26日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.22024年2月7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: _pdbx_initial_refinement_model.accession_code / _struct_ncs_dom_lim.beg_auth_asym_id ..._pdbx_initial_refinement_model.accession_code / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Calmodulin
B: Calmodulin
C: Calmodulin
D: Calmodulin
F: Melittin
G: Melittin
H: Melittin
I: Melittin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)79,83824
ポリマ－79,1978
非ポリマー64116
水3,333185
1
A: Calmodulin
B: Calmodulin
C: Calmodulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,32115
ポリマ－50,8403
非ポリマー48112
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Calmodulin
B: Calmodulin
C: Calmodulin
D: Calmodulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,42820
ポリマ－67,7874
非ポリマー64116
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
3
A: Calmodulin
B: Calmodulin
D: Calmodulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,32115
ポリマ－50,8403
非ポリマー48112
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
4
A: Calmodulin
B: Calmodulin
F: Melittin
G: Melittin
H: Melittin
I: Melittin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,62414
ポリマ－45,3036
非ポリマー3218
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)37.900, 60.680, 68.450
Angle α, β, γ (deg.)95.770, 89.990, 97.050
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 3 through 7 or resid 9...
d_2ens_1(chain "B" and (resid 3 through 5 or (resid 6...
d_1ens_2(chain "C" and (resid 2 through 12 or (resid 13...
d_2ens_2(chain "D" and ((resid 2 and (name N or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LYSLYSGLUGLUAA3 - 74 - 8
d_12ens_1ILEILEILEILEAA910
d_13ens_1GLUGLUMETMETAA11 - 3612 - 37
d_14ens_1SERSERLYSLYSAA38 - 7539 - 76
d_15ens_1LYSLYSTHRTHRAA77 - 11078 - 111
d_16ens_1LEULEUILEILEAA112 - 146113 - 147
d_17ens_1CACACACAAI201
d_18ens_1CACACACAAJ202
d_19ens_1CACACACAAK203
d_21ens_1LYSLYSGLUGLUBB3 - 74 - 8
d_22ens_1ILEILEILEILEBB910
d_23ens_1GLUGLUMETMETBB11 - 3612 - 37
d_24ens_1SERSERLYSLYSBB38 - 7539 - 76
d_25ens_1LYSLYSASPASPBB77 - 7878 - 79
d_26ens_1GLUGLUTHRTHRBB87 - 11088 - 111
d_27ens_1LEULEUILEILEBB112 - 146113 - 147
d_28ens_1CACACACABM201
d_29ens_1CACACACABN202
d_210ens_1CACACACAAL204
d_11ens_2ASPASPLYSLYSCC2 - 133 - 14
d_12ens_2ALAALAALAALACC15 - 7316 - 74
d_13ens_2ILEILEASNASNCC86 - 11187 - 112
d_14ens_2GLUGLUMETMETCC114 - 144115 - 145
d_15ens_2CACACACACQ201
d_16ens_2CACACACACR202
d_17ens_2CACACACACS203
d_21ens_2ASPASPLYSLYSDD2 - 133 - 14
d_22ens_2ALAALAASNASNDD15 - 11116 - 112
d_23ens_2GLUGLUMETMETDD114 - 144115 - 145
d_24ens_2CACACACADU201
d_25ens_2CACACACADV202
d_26ens_2CACACACADW203

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.99919530435, -0.0385547276427, -0.0110578813963), (-0.0384894476992, -0.999240650304, 0.00605683055291), (-0.0112830040498, -0.00562634490004, -0.999920515872)16.9386688186, -75.9748276977, -57.3354364551
2given(0.999777946058, -0.0209897077496, 0.00186835349719), (-0.0209781131038, -0.999761792977, -0.00602296227854), (0.00199432866028, 0.00598243032504, -0.999980116393)18.1607948641, -82.528462583, 11.884803575

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要素

#1: タンパク質
Calmodulin / CaM


分子量: 16946.721 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Plasmodium falciparum (マラリア病原虫)
株: isolate 3D7 / 遺伝子: PF14_0323 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62203
#2: タンパク質・ペプチド
Melittin / MEL / MLT / Allergen Api m 3 / Allergen Api m III


分子量: 2852.487 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Apis mellifera (セイヨウミツバチ) / 参照: UniProt: P01501
#3: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 16 / 由来タイプ: 合成 / 式: Ca
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 185 / 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N

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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: 1.96 Å3/Da / 溶媒含有率: 37.33 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6
詳細: 0.25M NaCl, 30w/v% PEG3350, 0.1M Bis-Tris buffer, pH 6.0

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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: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2015年2月22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: 1 Å / 相対比: 1
反射解像度: 2.2→47.43 Å / Num. obs: 28647 / % possible obs: 93.5 % / 冗長度: 1.796 % / Biso Wilson estimate: 28.52 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.09 / Net I/σ(I): 8.78
反射 シェル
解像度 (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.31.2532500.8321.0171
2.3-2.41.830890.7680.6241

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1cdl

1cdl


解像度: 2.2→47.43 Å / SU ML: 0.4011 / 交差検証法: FREE R-VALUE / σ(F): 0.01 / 位相誤差: 34.1079
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2661 1194 4.77 %
Rwork0.2341 23814 -
obs0.2356 25008 81.72 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 52.4 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→47.43 Å
タンパク質核酸リガンド溶媒全体
原子数4794 0 16 185 4995
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00294894
X-RAY DIFFRACTIONf_angle_d0.54346621
X-RAY DIFFRACTIONf_chiral_restr0.0377775
X-RAY DIFFRACTIONf_plane_restr0.0036882
X-RAY DIFFRACTIONf_dihedral_angle_d12.1821769
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.729108885603
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.703473247819
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.5228720.46811663X-RAY DIFFRACTION50.42
2.29-2.390.40171050.31242489X-RAY DIFFRACTION76.45
2.39-2.520.30751490.28892557X-RAY DIFFRACTION79.22
2.52-2.680.29241420.27422560X-RAY DIFFRACTION80.34
2.68-2.880.29731460.27412782X-RAY DIFFRACTION85.69
2.88-3.170.29341450.2462914X-RAY DIFFRACTION90.26
3.17-3.630.2741250.21572993X-RAY DIFFRACTION92.41
3.63-4.570.2211550.18022880X-RAY DIFFRACTION88.74
4.58-47.430.21771550.20512976X-RAY DIFFRACTION92.5
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)
14.24547930848-3.49320543741.454578771192.352095927030.9511941083994.301517232640.3953129943880.181697444629-0.235486719739-0.286088610319-0.50142635811-0.004886522991060.3851243127460.09553564771920.07742402004210.322191174562-0.03514380170010.02973788033550.258921234909-0.04891752817040.282643683662-49.6853253673-49.6693955657-16.4710180838
22.444155289830.2635046113593.16077543541.797842758152.973882935188.33147505389-0.0775579985651-0.257140047003-0.0252499782724-0.963700006255-0.2574968997030.073345770333-0.714135177901-0.6686951768020.085089198720.596870894616-0.0705762915186-0.05887799692170.346143896830.05589896039120.257462683726-57.3244782616-38.6745660627-25.4477445503
34.240262864760.0976690815721.17950973863.086094158481.873046112818.36271241581-0.2519968865980.3988759859550.119539777982-0.759800986080.05008616820510.217114989593-0.919107392545-0.005138971722710.1233231920010.3781248220520.0314801535406-0.03457188552090.2855724585060.0167072143680.205127958395-59.897174865-36.0555842861-15.1536792308
44.006215782071.206404667080.8731846780954.15658552342-0.7227317212973.4432061830.1545874128450.5488965265220.1633358794050.183567758072-0.04190701909240.3779095192560.145853616894-1.00098618228-0.1079428067140.187731730104-0.0616636692877-0.06274713141430.4166121482830.07896854993130.320756704263-58.0825355843-46.6374598173-11.2640849541
54.64426315754.46047027181-1.098902869346.09704986152-2.726936374591.7696878779-0.6711872932420.701529707788-0.0792343792427-0.627036571403-0.1254902082732.242332278532.09852069331-0.2282528053710.6300876883250.751521769022-0.0769273174967-0.04112077021160.790474658746-0.5742870325930.760061095958-67.3259895727-52.8590368204-15.5966595553
62.941350813091.760949093460.313711656114.646219959330.9978709077953.48505351632-0.364451289840.03502148855370.323521900539-0.9287805060680.2449522159510.0590501826472-0.719655367836-0.4599373775010.108534584671.114083824160.126762106392-0.1672129723880.4245892941880.03326103082980.40157006989-64.1611565864-52.0259345571-36.8897174434
70.436138894453-0.395190392405-0.6056185572929.302752366934.710416383842.879587491190.3801277118750.7483644766341.08349300202-1.459453081490.480462140299-1.07331394681-0.3094964067860.0587735147032-0.7713489249380.679689961177-0.1452461105610.1293857343720.4922535781990.1598372579430.756090266247-50.9631469046-50.7400999032-33.8747957165
86.38209585981-0.7156553042943.030382927225.40289325934-0.5954589605786.362261536660.6040867812990.819576952006-0.0128574555934-0.776170387752-0.182382955845-0.3675233321230.1326821408610.988645639168-0.4250998997110.5912058209740.0248837871740.1003294785490.370525896801-0.04977155708310.312932955274-55.3426843568-63.2611831422-34.9530796232
97.800591685332.86875089288-4.189232732687.64916473463-1.980542993952.825447203760.852075203845-0.432969187673-0.6483306661030.0306297919213-0.9663766394220.21232395966-0.9752214321290.551671850235-0.0005740292749760.7221288542670.0953979127386-0.0008009001455790.4432137768820.05778373583090.317986096503-64.303661237-59.3323935109-28.2632398325
103.68999278670.05231404578870.06541098069935.674223988550.9241435447225.68131560442-0.1614082068690.04864680998280.3526333974550.2404524357080.167014359441-0.0648750406999-0.3409204565280.2855482513510.04557849471220.271040403772-0.04286036416-0.03286526539120.302735539551-0.03287041817680.235569850806-30.5056633636-24.4381544441-40.1265866938
112.14021005193-4.55875164146-5.773715481862.426154904640.5221188161815.88265953554-1.40343548828-0.236195270253-0.07787375422520.4588204461130.875648762007-0.001129248230081.06214936339-0.3191372408220.584611302360.638112572104-0.01916339554130.03272447672920.392326170926-0.01910291679070.246756817303-38.5994195653-34.7163178965-31.4873888623
122.823662372670.681232869959-0.8769766032822.57842846564-0.1810289177763.93423360796-0.026986518038-0.769521870712-0.2588514105451.14221125576-0.2893593271220.4900351918061.41093111326-2.080159789370.3107440008220.872957381711-0.3495949200560.07647750901590.7162957285180.00586635142440.357426526392-44.2848716741-38.3362669586-38.3578050788
133.86819552110.7304333758351.274678458253.417361220520.7965789409822.484374954470.1471623319140.0880613709135-0.06437008208830.0549071183633-0.02103266800020.1398154678840.486550021945-0.269608993152-0.09520344889350.335330160783-0.0558690541082-0.01230415017720.3530738184120.01205698946050.193212176589-37.2898452497-31.4617335309-46.2977885598
142.356757742940.460662458645-0.440339591122.56825895610.6224551878088.69880449760.288150078874-0.000409892218594-0.303400746850.495358967604-0.3848281140130.559247722126-1.19213799971-0.621708806708-0.01232414219780.452208337023-0.08919240620990.144053452720.525181119171-0.06523652854270.469624167108-45.2310807634-21.1177146523-22.9001985068
153.907537174850.533264101682.951148339643.814173007260.9407135857722.263181039060.7335578635120.366449981547-0.366504037790.721028322779-0.351240758398-0.5152526641090.447979874466-0.0573054958802-0.3627127106530.418699202258-0.0293392539445-0.127480947460.250412136050.03358258678740.432464243962-32.0737127985-23.6320451083-22.4714158632
162.08537998748-4.1349024178-1.585990200152.13602682987-0.4811359060927.22310958514-0.447885537206-0.06499176775590.5078886729432.000405865790.345163788426-0.519076624919-0.5210368575750.4211498402840.03177432942060.692772720965-0.0762750624996-0.006288236936650.3758132557580.0006981045217360.429137102602-30.9188037086-12.3031148169-22.2305309351
175.588177487010.492789719694-0.4164926575197.052288374280.1882538223693.867961152390.3414761840080.7728750745711.26455722649-0.1062174472771.02731702829-0.186430650226-1.03374673581-0.224764938225-0.9510805101320.5038884435390.08939594518490.1314362429140.468817003710.05534254091890.639518925373-43.402753639-11.735858241-23.0962746551
189.61882299727-1.87898063111-5.405353051832.569172051561.404913983965.849198062560.220801074360.789544964412-0.141297357206-0.243028363755-0.2565057604460.303629258132-0.420145131934-0.54812884178-0.03683640775620.292349093255-0.10080028989-0.07232898403180.3583880069450.06146354963050.278205648685-73.1234485359-30.380978686913.5860323812
193.004985339321.96560362624-1.956275184023.74162895765-1.925188595591.436578136120.156530497329-0.750811605042-0.217386163007-0.731324656585-0.0315023692150.08296605680541.682396898570.201691462076-0.2321619526990.3735696258490.0345826688871-0.06951330745210.3887060129880.03214124557480.25455834911-61.017083842-39.59948513711.864845876
201.379208506831.773052658940.2686505110135.12419551699-5.080218963342.07027218226-0.360858088755-0.8457130635820.09782989997390.2674529321340.0746571907008-0.311981254214-0.186793821810.4819454587180.2564783330130.1506897555920.0821284849631-0.007930561529950.409243505193-0.007640330535770.227505755868-54.265475467-35.46782576084.752962204
212.67859427922.37351163989-1.154154760532.319981508170.7846971210932.11326696703-0.1984426128810.2985651795620.110842320099-0.1543149369180.0251678864706-0.0181204887244-0.00280179849289-0.2715835037190.1629850668560.2677328753040.0669416764043-0.01062807218160.43490037449-0.04427724313470.350642621309-48.585161141-31.564173254410.5805742915
222.027755434991.521773698510.1273104685082.776403610584.82041633112.039651637490.0951028157118-0.584123533902-0.1783773986830.6054532052060.360387006054-0.1284837576141.588332700991.84157459409-0.3275676724510.4026173524060.071538573979-0.04806331547650.5212382830940.03573782357930.299020463099-56.0328510018-34.872420988321.5633860823
239.135802487342.423193403111.974631818772.046416557632.915253957157.23338884052-0.899325812380.1466149764570.42933576549-0.3875878655441.29627625429-0.190542214943-0.5381647112290.0299693342949-0.3498492268440.235218824302-0.00951759438372-0.08293256182030.282460934323-0.006099693369790.44320913421-63.3843032356-28.219762797117.5883804939
241.302567056570.900907664203-2.407187253850.684234584807-0.7465058442535.62005069299-0.261675184292-0.9518934641920.3953540572040.650800409864-0.1417663114550.377725136511-0.7612359363790.2519422123080.4360295559740.645265361268-0.0341688968929-0.1435237120060.478012167953-0.01288416695280.526126542998-55.7746720781-20.03449327341.82346573645
258.139296610844.126518056530.3325450567819.75399583889-2.244868941417.68716491844-0.6748542398560.007803929283150.357525351009-1.25025978630.180475032165-0.674050426268-0.4669773502111.117411184640.4148044213830.45626475961-0.07106745441740.01219505618960.4199171478640.03539529666680.328579545379-57.356268683-20.2511244609-10.1323849931
266.192194564293.06891661737-3.116994098984.32135126102-2.75600951683.932804015460.518134452283-0.557832627184-0.01941587253480.1610882888-0.2402496368080.4364524596190.02877853928730.383517023518-0.2377303019080.261667049933-0.0283902300387-0.04277539459460.2269102219-0.01644251034940.249973044171-65.4295435823-29.6906067667-5.49483125489
278.64036458601-0.286635223914-1.811274466282.158437549625.835863099662.10360176581-0.1122033696680.05018654800520.903237591247-1.302105461690.2769586611450.393352622805-1.60522370567-0.593859913219-0.2548842489640.510940108912-0.0200705809355-0.05326954892370.3944939698020.08804219761570.413735035495-73.7672580578-22.1216010192-7.53920463179
285.47719294975-0.07549659843754.157533843423.687756873341.43481282987.02420364840.764601813111.110799580960.6612457909260.754233808581-0.0646444293940.592654490863-1.075474108380.608913289861-0.7429571561710.8491690228850.00635771394993-0.03625887571810.4500022544720.1652827368540.532627841696-65.8773719728-12.5591284482-8.62881856122
295.60093205867-2.786590774140.9519323875951.37968077438-0.4411317005930.1530575384-1.31354247379-0.6542319846510.05739658357480.7132005448360.567281775138-0.0050003667022-0.711624424919-0.5943770026670.7439234964451.288251032680.165047014403-0.04161612675660.656609930768-0.2279548113370.653525117181-61.7347231761-13.67786818820.450173302776
306.701655828291.95657480061.970680671732.07835911738-0.679905900694.81143704438-0.214086389035-0.07963973098280.135707190334-0.1351783175180.1458676128120.324889711317-0.222103548288-0.5403772538410.09722624733640.2503871711470.0808896437948-0.001844461866750.2997998294630.03575546247020.31669845517-50.0530696445-47.9119970712-1.52366035228
313.10078496195-2.36602390649-1.733717583282.770258537122.198240445916.522642128310.0219006285591-0.1036813870470.1345654626430.0397997878250.344510378385-0.28646911713-0.1050119208471.03831229614-0.3539477360520.161968731477-0.05522234933680.02364572833380.398090701989-0.01358041834670.358304489758-35.2956976258-48.6637189439-1.17543228433
32-0.102657617095-0.1248437223230.5371800139831.11888768236-0.909026549940.63725335828-0.102108010887-1.163369504240.4870265816361.21959621995-1.30085885492-1.455925327681.829791087071.128441564850.5490721562711.62998053067-0.184217418446-0.5445866971680.3558613986020.08069923137791.68252751735-37.9517426219-60.133701548717.1036081154
336.544687407680.786914834136-2.905124018272.3773353541-0.1234088685092.45976221860.2055166290041.26745804774-0.9801417836230.9459580088680.1144271504771.212493792131.08780986322-1.3464770209-0.3049428827591.04201035798-0.4755110931990.1658036247660.8394268256870.05284388485370.687637451039-49.7459563121-54.257372452417.776924948
345.36526031290.0271516593263-1.357325508882.34704375692-2.666372788766.18406238563-0.321384288104-0.641354274384-2.14020431428-1.009957413690.1005243514740.06758231438562.87860502218-0.4937374401550.03606194632751.13398731737-0.162602215996-0.1124482227060.4728125121360.06809184884071.16485380237-45.4361277588-67.155914033716.3678334775
356.404358982280.642861090135-2.459395918898.418111729883.474502593977.28356029524-0.2662302611510.3834880169690.341131375285-0.8874541180310.9842069569150.565617516068-0.0433931989921-0.328827321797-0.6877220500640.531901995306-0.1328041756930.01020125581940.5376522494360.120171539660.276471659922-61.6715398629-49.1066559696-21.4478672651
362.060729666734.293691121372.392937761691.585216015790.1613934652944.704757087311.64803018994-1.08823712342-1.45741308620.429437535003-0.852847560373-1.01356099860.386170627117-0.361724853519-0.7111501435090.707946472027-0.0390385410513-0.07507515708250.3819486301010.01723321416840.634697604741-47.1087640381-59.7784397876-24.3996484891
377.79442199685-1.686197154135.420464122796.411078243634.999450892889.98777696856-0.7938092449681.313226896090.194879190759-0.306994370033-0.171142578030.590618408463-0.637936807065-0.3808817309970.8121392878960.326672545172-0.05699388271160.04532069069350.563027470778-0.02612061792210.273957427302-42.6509520355-24.3609157193-35.0334464763
389.636327054150.200745371114-0.759644331177.982532280290.3901514900998.60393632620.3972275456280.760011733980.123862232974-0.75557718699-0.2057191194970.0177737186392-0.786160308483-0.67207434125-0.1887052928460.3260454361930.05836246331810.01330962167890.370898610168-0.0261267828610.300808340066-28.7079355225-14.5144539719-31.6747844152
392.138905884561.394556423453.368791511263.51252821197-0.1052462063643.921109481370.106998894007-0.35403767302-0.46951518726-0.006471234515340.0923021913528-0.2543914816680.202277444370.197719901398-0.33138690390.2683020496570.0774078457825-0.04279613180230.357870966421-0.03852626058750.365834290071-68.950110798-24.93704656894.74705535747
402.06780671861-1.62181175971-3.32427595851.785817348640.3761257585721.60306847784-0.3392213649151.29124153019-0.6239451456250.0287734050185-0.06872924781670.1630505619360.510530350944-0.7217991687910.2345438851240.716123355642-0.1374057907330.08771778717290.7208092946960.003644260202190.610844072001-49.9864657537-56.07550257126.61252100947
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 28 )AA3 - 281 - 26
22chain 'A' and (resid 29 through 39 )AA29 - 3927 - 37
33chain 'A' and (resid 40 through 64 )AA40 - 6438 - 62
44chain 'A' and (resid 65 through 75 )AA65 - 7563 - 73
55chain 'A' and (resid 76 through 78 )AA76 - 7874 - 76
66chain 'A' and (resid 84 through 101 )AA84 - 10177 - 94
77chain 'A' and (resid 102 through 117 )AA102 - 11795 - 110
88chain 'A' and (resid 118 through 137 )AA118 - 137111 - 130
99chain 'A' and (resid 138 through 147 )AA138 - 147131 - 140
1010chain 'B' and (resid 3 through 28 )BF3 - 281 - 26
1111chain 'B' and (resid 29 through 39 )BF29 - 3927 - 37
1212chain 'B' and (resid 40 through 55 )BF40 - 5538 - 53
1313chain 'B' and (resid 56 through 75 )BF56 - 7554 - 73
1414chain 'B' and (resid 76 through 101 )BF76 - 10174 - 95
1515chain 'B' and (resid 102 through 117 )BF102 - 11796 - 111
1616chain 'B' and (resid 118 through 128 )BF118 - 128112 - 122
1717chain 'B' and (resid 129 through 146 )BF129 - 146123 - 140
1818chain 'C' and (resid 2 through 18 )CK2 - 181 - 17
1919chain 'C' and (resid 19 through 28 )CK19 - 2818 - 27
2020chain 'C' and (resid 29 through 39 )CK29 - 3928 - 38
2121chain 'C' and (resid 40 through 55 )CK40 - 5539 - 54
2222chain 'C' and (resid 56 through 64 )CK56 - 6455 - 63
2323chain 'C' and (resid 65 through 73 )CK65 - 7364 - 72
2424chain 'C' and (resid 74 through 92 )CK74 - 9273 - 83
2525chain 'C' and (resid 93 through 101 )CK93 - 10184 - 92
2626chain 'C' and (resid 102 through 117 )CK102 - 11793 - 108
2727chain 'C' and (resid 118 through 127 )CK118 - 127109 - 118
2828chain 'C' and (resid 128 through 137 )CK128 - 137119 - 128
2929chain 'C' and (resid 138 through 145 )CK138 - 145129 - 136
3030chain 'D' and (resid 2 through 28 )DP2 - 281 - 27
3131chain 'D' and (resid 29 through 72 )DP29 - 7228 - 71
3232chain 'D' and (resid 73 through 101 )DP73 - 10172 - 88
3333chain 'D' and (resid 102 through 127 )DP102 - 12789 - 114
3434chain 'D' and (resid 128 through 144 )DP - T128 - 144115
3535chain 'F' and (resid 1 through 11 )FU1 - 111 - 11
3636chain 'F' and (resid 12 through 25 )FU12 - 2512 - 25
3737chain 'G' and (resid 1 through 11 )GV1 - 111 - 11
3838chain 'G' and (resid 12 through 24 )GV12 - 2412 - 24
3939chain 'H' and (resid 3 through 26 )HW3 - 261 - 24
4040chain 'I' and (resid 3 through 26 )IX3 - 261 - 24

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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