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- PDB-9gcn: Co-crystal VHH (TPL1158_01_C09) - alpha-cobratoxin (Naja kaouthia) -

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基本情報

登録情報
データベース: PDB / ID: 9gcn
タイトルCo-crystal VHH (TPL1158_01_C09) - alpha-cobratoxin (Naja kaouthia)
要素
  • Alpha-cobratoxin
  • Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)
キーワードTOXIN / nanobody / VHH / atibody / antitoxin / snake toxin / antivenom / neutralising / neutralizing
機能・相同性
機能・相同性情報


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
類似検索 - 分子機能
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
類似検索 - ドメイン・相同性
生物種Vicugna pacos (アルパカ)
Naja kaouthia (コブラ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å
データ登録者Rivera-de-Torre, E. / Burlet, N.J. / Laustsen, A.H. / Morth, J.P.
資金援助European Union, 英国, 2件
組織認可番号国
European Research Council (ERC)850974European Union
Wellcome Trust221702/Z/20/Z 英国
引用ジャーナル: Commun Chem / 年: 2025
タイトル: Structural mechanisms behind the neutralisation of long-chain alpha-neurotoxins by broadly neutralising V H Hs discovered using a consensus antigen.
著者: Damsbo, A. / Burlet, N.J. / Fernandez-Quintero, M.L. / Benard-Valle, M. / Overath, M.D. / Guadarrama-Martinez, A. / Vlamynck, A. / Bisbo, I. / Villalobos, C. / Tulika, T. / Alagon, A. / ...著者: Damsbo, A. / Burlet, N.J. / Fernandez-Quintero, M.L. / Benard-Valle, M. / Overath, M.D. / Guadarrama-Martinez, A. / Vlamynck, A. / Bisbo, I. / Villalobos, C. / Tulika, T. / Alagon, A. / Loeffler, J.R. / Ward, A.B. / Boddum, K. / Morth, J.P. / Rivera-de-Torre, E. / Laustsen, A.H.
履歴
登録2024年8月2日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年8月6日Provider: repository / タイプ: Initial release
改定 1.12025年8月13日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen

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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
D: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)
Y: Alpha-cobratoxin
V: Alpha-cobratoxin
X: Alpha-cobratoxin
Z: Alpha-cobratoxin
A: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)
B: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)
C: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)


分子量 (理論値)分子数
合計 (水以外)85,9178
ポリマ－85,9178
非ポリマー00
水181
1
D: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)
Z: Alpha-cobratoxin


分子量 (理論値)分子数
合計 (水以外)21,4792
ポリマ－21,4792
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
Y: Alpha-cobratoxin
B: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)


分子量 (理論値)分子数
合計 (水以外)21,4792
ポリマ－21,4792
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
V: Alpha-cobratoxin
C: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)


分子量 (理論値)分子数
合計 (水以外)21,4792
ポリマ－21,4792
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
X: Alpha-cobratoxin
A: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)


分子量 (理論値)分子数
合計 (水以外)21,4792
ポリマ－21,4792
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)65.370, 86.010, 75.920
Angle α, β, γ (deg.)90.000, 94.880, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_1ens_2chain "V"
d_2ens_2chain "X"
d_3ens_2chain "Y"
d_4ens_2chain "Z"

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLNGLNSERSERAF1 - 1121 - 122
d_2ens_1GLNGLNSERSERBG1 - 1121 - 122
d_3ens_1GLNGLNSERSERCH1 - 1121 - 122
d_4ens_1GLNGLNSERSERDA1 - 1121 - 122
d_1ens_2ILEILEPROPROVC1 - 661 - 66
d_2ens_2ILEILEPROPROXD1 - 661 - 66
d_3ens_2ILEILEPROPROYB1 - 661 - 66
d_4ens_2ILEILEPROPROZE1 - 661 - 66

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.763924704021, 0.215361698483, 0.608307804827), (-0.216189385598, -0.97360400545, 0.0731941946244), (0.608014141399, -0.0755948371156, 0.790319064973)-32.1348046731, 44.3718867284, 2.43783918141
2given(0.763577991956, -0.250321167106, -0.59522093671), (-0.218401988882, -0.9675928681, 0.126746253809), (-0.607658803485, 0.0332167864299, -0.79350326001)20.8107515006, 45.250132584, -91.6708685191
3given(-0.999450104575, 0.0259415460643, 0.0206524733089), (0.0248539324004, 0.998374845155, -0.0512830440461), (-0.0219492712913, -0.0507415485593, -0.998470592827)-40.1735331962, -0.852257301122, -62.9517035236
4given(0.793419002581, -0.171964945841, -0.583878706364), (-0.188743454044, -0.981485515339, 0.0325897489154), (-0.578672787419, 0.084345957703, -0.811186516481)-62.3873049329, 52.9374872809, -65.302453492
5given(-0.997787674724, 0.0663736426485, 0.00378096950937), (0.066328745577, 0.997737539651, -0.0109681120261), (-0.00450040876392, -0.01069306003, -0.999932700129)-14.6772661312, -0.983535549184, -88.6939254655
6given(-0.792849858456, 0.136578878498, 0.593915239656), (-0.113355350984, -0.990606629692, 0.0764792103322), (0.598781818654, -0.00668693935905, 0.800884272846)24.2756744324, 54.84221017, -1.2709192761

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要素

#1: 抗体
Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)


分子量: 13637.082 Da / 分子数: 4 / 由来タイプ: 組換発現
詳細: Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)
由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌)
#2: タンパク質
Alpha-cobratoxin / Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long ...Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long neurotoxin 1 / Siamensis 3


分子量: 7842.094 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: Protein. Toxin alpha-cobratoxin from N. kaouthia. / 由来: (天然) Naja kaouthia (コブラ) / 参照: UniProt: P01391
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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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: 2.55 Å3/Da / 溶媒含有率: 51.8 % / 解説: The cristas were small, regular, spikes.
結晶化温度: 298.15 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 1.5 mM Tris and 6.5 mM NaCl, 17% (w/v) PEG1500. 20% (v/v) glycerol as cryopreservative.
PH範囲: 2-2.5

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データ収集

回折平均測定温度: 293 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: MAX IV / ビームライン: BioMAX / 波長: 0.976254 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年12月18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: 0.976254 Å / 相対比: 1
反射解像度: 3→37.82 Å / Num. obs: 16807 / % possible obs: 99.5 % / 冗長度: 3.6 % / Biso Wilson estimate: 63.23 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.28 / Rrim(I) all: 0.309 / Net I/σ(I): 6.49
反射 シェル解像度: 3→3.18 Å / Mean I/σ(I) obs: 2.11 / Num. unique obs: 2704 / CC1/2: 0.75 / Rrim(I) all: 0.83 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.2_5419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 / 解像度: 3→37.82 Å / SU ML: 0.4071 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 30.1039
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2918 1671 9.95 %
Rwork0.2382 15120 -
obs0.2435 16791 99.44 %
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: 57.7 Å2
精密化ステップサイクル: LAST / 解像度: 3→37.82 Å
タンパク質核酸リガンド溶媒全体
原子数5784 0 0 1 5785
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00285904
X-RAY DIFFRACTIONf_angle_d0.60858004
X-RAY DIFFRACTIONf_chiral_restr0.0441860
X-RAY DIFFRACTIONf_plane_restr0.00441048
X-RAY DIFFRACTIONf_dihedral_angle_d4.7146824
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2FAX-RAY DIFFRACTIONTorsion NCS0.214173791376
ens_1d_3FAX-RAY DIFFRACTIONTorsion NCS0.266914379916
ens_1d_4FAX-RAY DIFFRACTIONTorsion NCS0.169139184731
ens_2d_2CVX-RAY DIFFRACTIONTorsion NCS0.344167661176
ens_2d_3CVX-RAY DIFFRACTIONTorsion NCS0.356972511964
ens_2d_4CVX-RAY DIFFRACTIONTorsion NCS0.383256093082
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.090.33621340.29161267X-RAY DIFFRACTION99.86
3.09-3.190.35251400.29241260X-RAY DIFFRACTION99.93
3.19-3.30.34651410.28141254X-RAY DIFFRACTION99.93
3.3-3.440.33291300.27841252X-RAY DIFFRACTION99.86
3.44-3.590.3381470.27511239X-RAY DIFFRACTION99.07
3.59-3.780.32581400.23811251X-RAY DIFFRACTION99.5
3.78-4.020.30141350.23721274X-RAY DIFFRACTION99.58
4.02-4.330.26251380.21631246X-RAY DIFFRACTION99.21
4.33-4.760.25461470.19421262X-RAY DIFFRACTION99.16
4.76-5.450.25011420.20841257X-RAY DIFFRACTION99.29
5.45-6.860.28481430.24911264X-RAY DIFFRACTION99.58
6.86-37.820.25031340.21311294X-RAY DIFFRACTION98.41
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)
10.9745541930290.3671570361210.5732419870311.212828739270.09103505164362.209672771410.0500473116996-0.4018631701210.09041885289930.0185989334220.2562110173530.17446695046-0.3438597617550.191872502832-0.3814923033340.0382155005203-0.06295717337170.0954368554430.425946179275-0.1010830856060.34274474834-1.6151530003722.7445096568-27.6172216689
22.658068894050.288780001117-0.2456353859221.173786388910.5375319373621.29090264672-0.1268915857070.4569291462190.19388299258-0.25704622882-0.00307013772125-0.0378127969448-0.206197284171-0.1836222398960.07452670068170.119627209820.178741710520.08219635966620.363826241282-0.1223471906150.228814829248-2.7160502661514.298010644-31.8700852102
30.4306793163280.249483832338-0.7886330163360.305660119987-0.2769767825452.40331463878-0.04034561550410.0285664936399-0.1387611639090.11370312130.0006925950779740.04834950586440.366060313103-0.6679684668070.06912542572720.513315238633-0.02242408333120.5034411808370.5041342197610.2425915136330.585900913511-10.2745448157.99374410621-25.8223918808
41.442097621350.08502679113430.1132327350460.273033978298-0.1381360382780.6762709165540.0159810201050.02285986506610.1819010338570.01340221143850.09548102854310.0251968831056-0.01794003945-0.07741536543030.03245837004240.05620202678910.02760499714870.03421805380860.578249852285-0.06097006134340.563133119795-12.488768518616.1322182561-28.6743149132
53.04991834877-0.186920093136-2.849053807914.38951413868-2.707649773724.89284169209-0.4347772947690.363425212578-0.177388035138-0.7492432284730.6656171309040.09150342719750.5816636382-0.520681602623-0.09681357575430.428824917625-0.2462274200860.1773484518170.45658267588-0.09772244409020.401124280673-11.358591586520.2567035567-32.4390456483
62.236893681980.2750053930080.5858368142571.6592452481.231228491182.81773406611-0.282561493564-0.535266337099-0.304311999204-0.08651272668970.2480726930440.328767349521-0.0143213855201-0.0934653413080.0337665385310.1943542545120.0928531801324-0.02038479305030.2596472348160.08355843331490.295921816033-2.8440477942713.2884130919-29.6210365789
70.6791986837490.0748725265443-0.3894304145851.223388320471.124103693173.44738291851-0.1329003963820.098047734218-0.133205426652-0.2484970538050.101923278605-0.05657123854960.0996806205876-0.3073154300920.2882478000130.20748055481-0.1081653351010.435935898570.191926458563-0.1433568643670.25447019026-0.51662707146311.8765929649-36.5454714653
81.87730307723-1.53881252031-0.8216372406811.39327507731.229256214352.62416951178-0.17958586686-0.398774207595-0.2664792701620.547544929195-0.04466190034380.5071448161420.132130913727-1.436700104270.1342164456090.509137564640.06966243545810.07402811651991.010359798740.05325191700960.179976937663-19.459549689539.5767435904-14.4439848283
91.20479924253-0.855501627005-1.183808004471.630146771221.368640815714.388624097530.132884507521-0.399233775882-0.297250593568-0.125602489494-0.5527474596720.366919319493-0.509785253913-0.5845777418420.1492782034320.2990277238-0.02797787881280.0457339565910.7381436815590.08052007964090.316800780139-9.6767167507740.3211563551-17.1187289028
101.76321696650.655387403834-1.442814797520.969175052061-1.498742740213.04565028480.08149188860510.0384563076073-0.0508783914547-0.2926713632060.143942209102-0.258492353951-0.1721076137290.470820929315-0.08007006393670.58737951260.2314541816740.1389335640561.04529730365-0.1176922092570.23429364940910.661538869942.1131917038-73.5080052028
114.1135272562-3.86440545685-1.888875205219.662914935290.467144422711.150931880650.154321988154-0.218132168290.4474586298920.3695850844890.223014392054-0.469329988874-0.2069217546950.238468357912-0.3270817559510.8222878641040.1751902190920.1983181752581.94329773973-0.4659198132420.96575417130711.132349166932.1636608404-80.6635307622
124.36384890259-0.383385724816-3.207076553481.575750736741.501893316945.37188376425-0.05980316444830.747143737438-0.1492904645940.225328109286-0.111233633218-0.5306827070020.608894416784-0.4700008068270.0500364976820.2506506517140.124409310086-0.0439369242720.2403215713140.04124369421190.213840544367-3.4840378146141.6370446992-67.4366903498
131.13655379639-1.49865208871-1.122070085972.060884929581.358263831241.26665439253-0.01432405747920.368996064084-0.294033449961-0.03839994312410.1061881700760.1532710855920.1886272308950.09887117917910.07055481348251.1643337705-0.286821270818-0.01641686051960.631390898717-0.3178343035580.82194120394-5.5512967136832.5410815704-74.9387427365
142.383501381112.444074949390.5640111526592.78157382852-0.1497032928972.07484749795-0.2590088770680.113877433904-0.07460540996860.06670808390370.308396356375-0.180585824275-0.1011549410040.393210113624-0.1139718063690.775588185736-0.163053872450.1675576465460.847607774895-0.06809654785140.3282235237941.6295791389943.291406374-78.778182659
151.03898834338-1.632334883520.6906029831952.5649487301-1.087527972440.460537703286-0.4372019579190.4809280524270.02388735459030.3135915043320.00792792570326-0.5533530600180.0191716143825-0.05164026778290.3370100068290.9866519766860.05486815423950.06848562449931.28197471480.2048839205220.522201853086-18.20095475137.18084977901-8.25679940988
163.50733463119-1.39994105113-1.34065899352.245493673851.391627399969.99166611719-0.0630591422070.648670822117-0.148858360579-0.645439855386-0.124956992748-0.286714514242-0.01878458020490.1327193739940.1756688871661.73626981869-0.3161085988920.4738656791941.724569092130.06604039675411.19404106624-12.123395648216.6791063843-3.52643883378
173.83638486377-1.821560528971.108502011281.27766725071-0.8311503816621.49345823477-0.205221587349-0.2088786265470.09441042561430.0330767487725-0.1843917836360.0612247404530.1147856812410.3155293811690.3174197840570.6208774197030.006675933607950.1228189390850.82480332728-0.1588979350710.358492997003-27.199877051412.6396825433-2.03651562147
180.414762901183-0.2523301330660.03362103891460.66653468844-0.1535804701280.03678140710920.199828015926-0.7125687129220.2284129353260.446159035681-0.040208553118-0.10920976799-0.192979294440.218411207544-0.09176484666190.5144656740340.03210363238620.1714471382740.712965265771-0.005042101195440.291583757648-35.68312586419.50535559126-6.56912663101
192.354107852650.2303711005641.083643903780.604130404818-0.4234517466510.980086536439-0.2083369965740.1130888614380.04600860702110.159096424424-0.438250414892-0.661073162533-0.132024928692-0.09534140737580.5707079107771.13375967222-0.308247270946-0.4398384516870.779163588619-0.1544307425621.29641022795-28.604328896519.69413282981.5869896701
207.61980493104-3.032490845541.655307912197.85834144005-0.4491179501545.48210381435-0.04215459770460.1866735501510.0369012694418-0.1442880987390.05849677589620.428366248369-0.319183837124-0.319656489836-0.06410883346660.7910212015740.0774646069554-0.3895997420341.098945761750.07165128721320.485917392716-26.53032530711.86944748523.57710366669
210.6189824790660.0389300096118-0.1026041437270.06207992480820.007638672622210.0200825274744-0.08562696828880.01035570901130.1009955591310.2350692827680.0637977413366-0.337002425103-0.2820634438530.516096692823-0.0008513954963950.4949921123850.143862950655-0.3953128955810.845612614712-0.286280096460.43408214065-20.39742150394.97405073006-0.202480769224
220.701671363517-0.227700378420.5295065329491.9745765072-0.26574724190.40313187142-0.035252414727-0.3215681004060.1910348398870.2187638503930.4084770590050.6090542028640.0476792701039-0.0561207942382-0.3062269846110.7275036481810.08915268007910.4982755710731.420144728930.1419226340311.09911138224-22.0221902676.22875867083-54.0691290752
230.704238931876-0.277868927976-0.03862930553660.6765506399660.04832283136880.552170312801-0.000501028386358-0.2878566957330.0511337408109-0.200395970379-0.1531816838780.213672746116-0.31099551674-0.892314627438-0.1121810161220.6160613663420.271489432126-0.001814490447641.081756198220.03516823003840.22028083838-18.474080597712.6160107136-60.3379339586
241.188843412930.7025527351410.5974044487492.24504007886-1.314874263412.43314283433-0.269742952744-0.2092574487880.169197679486-0.726761437286-0.2946526911670.221267736056-0.201669082835-0.4316433055870.3276152936910.353987472060.0565355409297-0.01699555877090.328143573115-0.08170877089650.329189823137-4.623273288137.83531938964-56.083789625
251.45568099441-0.694111296750.1428985331011.49792177588-0.8676454900992.27124735914-0.0769440259720.024853187451-0.4054205177240.356105930987-0.446233681591-0.1091161680270.274456154235-0.1241338198810.376515987381.077435470190.0046330262577-0.237952265350.3035827994850.006681671415310.886122546179-11.494421084817.5282208147-64.9579148473
262.759256579170.1264979122394.260965529248.409791114490.9795439602877.08285661126-0.02217398321220.548727985447-0.942173554468-0.08052290024180.3918834422280.5293929317930.426809136745-0.434955539579-0.3300027785810.671008273507-0.146399932542-0.100889682410.7553520225170.0471802646470.651847746139-13.9237727979.74799116324-66.4382639573
273.260128733520.7586393526622.82138655822.67146869389-0.7830037641885.148076727480.1536756871640.566180104588-0.0991151875889-0.2482306727240.4128763906320.4469939056310.134152247203-0.399599270843-0.419024441960.713838794218-0.423101860554-0.3591775667081.33528386580.3284289571830.906885452228-20.13482208623.47475412772-61.8822486169
281.14258188609-0.6288314371441.191770574781.694735861070.06738495994463.52076771509-0.277101675818-0.148987120438-0.3223263521830.2283199552330.4407151731550.161242091038-0.661730358454-0.0083607327841-0.1185840896050.3776501288290.03598530073580.1649914393720.4474806076950.06866498567940.312689260227-38.097894191517.3876782295-32.6586716275
290.675887125255-0.0477042172546-0.3572543654320.0479264289819-0.03095774228660.777657594770.08766744995110.02661796453240.0341132681056-0.007140962880030.0641285108767-0.04719300116210.04341961709920.4720157554330.2165413422170.4858906371440.0277005161020.6272082886370.722357422182-0.02842686283550.403603860706-30.52449151917.76834032993-36.9314855322
303.595850828543.476012493450.75412191225.527565585130.3153562405567.25383822295-0.176873633781-1.366931732150.5370388206930.342842229426-0.6800130930940.112374260517-0.1279656956291.253596937350.8030429318330.425916874728-0.2535141707980.1418178786670.833227713708-0.04157616457720.499142978535-28.022737467415.9099959126-34.4744205865
317.641098085412.55143624712-4.724734831987.09140052873-3.334449492773.41671926571-0.171326870873-0.3678102509320.05223809704641.14034499857-0.500526591791-0.4343570955440.2469571230951.635976410650.6740685365140.389374160618-0.02263079365810.01276622912360.484138175143-0.03933050195250.274949211495-28.978081615320.2589832729-30.9394768496
320.489207064912-0.08387416467440.3861133180811.7882538754-2.462999567243.80712733520.139781817258-0.07665986683190.1646224194840.2136980214970.1958498678270.0281536415647-0.3375925067240.200791424799-0.2697039807540.4041781300060.03777835109080.1515583962490.558718794779-0.07275629518410.396891992684-37.645779487113.4143722731-33.236897277
331.16559708397-0.6522180882930.6654862862412.89243927927-3.258544454454.79068791701-0.121267228371-0.5753085241540.38232376497-0.1167996154730.054702407729-0.2929090131070.156270427083-0.1940596881120.01175269532630.0399360179250.1391268820280.1165236481630.617155210332-0.0020858210060.410619231908-39.842559531912.3478115025-26.1979998755
340.408192986663-0.07943776664010.1003385826121.987683672291.047023268882.13982092380.005677653048250.228883594151-0.551090953383-0.05042842298930.2038054051180.00523021147230.47270686429-0.0778014753556-0.2025388632510.568975853451-0.08450269539170.1429206108550.149529590559-0.07098341272710.331669299627-19.389681239527.9435374722-51.0206529473
351.02873934190.438846149831-0.2949407257071.09455450569-0.7573757965041.98349962823-0.0142451758758-0.2569550481480.1023338211020.0609168961073-0.139118132329-0.185195970806-0.04267636220190.09016818792810.01523996631560.164143551068-0.2134281519090.008301626254520.639085378347-0.1888658269620.35822563555-19.048434462136.1190640603-46.1375831143
364.374839730880.08728802272020.1972046554543.74982391716-1.665819306417.03744380981-0.296171915802-0.05711841723670.6017668460330.3519363854230.6416343440260.923082505442-0.568546552102-1.03589238695-0.3085253486860.2444332240050.05234987344980.02816482158650.3974842075740.1156148534960.515646452043-29.643974747540.7483572666-45.8940812255
374.813977610352.72885685174-1.113372955621.741977782720.07347519164472.7861941180.134562071594-0.451511254868-0.3467433978970.064569278116-0.206705016781-0.355773276370.2371019651010.08663323805680.240773508630.457425120758-0.1246004663980.1577703312960.2991685672430.2194273632720.806844642874-28.313756467532.4029454658-43.0996285278
387.031491029072.065822921294.084423140673.41309563525-0.4467439700766.902030818440.30026486933-1.06280150634-0.2860256278470.1149624548590.02598733967430.03471562473430.411014880717-0.913127050065-0.3781432445450.177186336212-0.1183914762270.200259925650.304980135027-0.07614512090690.593411441578-24.382112427628.6623676411-41.145109883
392.699766131461.342869744922.897205917571.323239563021.605523052935.25195354669-0.0742227290993-0.211819509802-0.0160101919873-0.3521033755920.0472071885401-0.1234302490870.323462945384-0.6650988423770.1530435747980.325206464923-0.1553226784380.05539231510690.2218175761050.2078405528490.400687148465-20.715590715337.033282755-47.7157329827
401.42561905971.239111638242.564584804873.164317250574.448720885219.15853708430.169393521758-0.0167618222281-0.05690477929020.05590190869190.144079233136-0.5132727895010.185189357818-0.199928627281-0.2621662721170.2189495761520.09386314036640.05483179875890.179309466808-0.09681085103470.447816683649-14.918132836139.0101483955-43.4710133331
411.654266107050.0712458804618-0.08816190821840.199276441594-0.09206961581262.432240893330.07248508465650.756410369188-0.0969792705222-0.219115444091-0.2504947500930.1745781312960.206391018395-0.4048760840360.09184153177140.4699705042010.1092547943450.2238127407130.401348641355-0.1160360854360.4082588803126.8080011101132.5980839553-42.0604999043
425.41202846922-0.3607582770980.6939202217823.125374817980.8045459571626.42126658191-0.6424004087480.9238386227650.2274894703710.06438971904520.242026975602-0.43345588199-0.7079948374990.3301015501330.3142587969560.328080878708-0.03158281953790.05669999247410.2493214144950.0876533461370.34793582577817.608401873939.737156501-43.5721328925
437.96811357954-1.02104713184-1.718740379742.091449620150.2505758982912.841536713910.02889917593631.0333600866-0.378832450157-0.243144002998-0.1226590753630.235120142660.104793545898-0.3033576232970.323371168030.1666094667310.1529457043740.04599284945970.705843109929-0.1643933103570.46522239278115.990885045431.599343294-46.735064617
441.34386187566-1.332381801291.491006590241.78296818971-0.8670368945012.582651697890.1043241813870.372256159515-0.0657476725528-0.211768100881-0.2951521963070.07901445567840.0909677803370.3506874910550.1250849143180.348975175102-0.04830808132790.2230842699230.4615061259460.05606310487640.3128966403947.1295114327235.4195071692-44.998880943
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 'D' and (resid 1 through 17 )DA1 - 171 - 17
22chain 'D' and (resid 18 through 45 )DA18 - 4518 - 45
33chain 'D' and (resid 46 through 66 )DA46 - 6646 - 66
44chain 'D' and (resid 67 through 72 )DA67 - 7267 - 72
55chain 'D' and (resid 73 through 82 )DA73 - 8273 - 82
66chain 'D' and (resid 82A through 100 )DA82 - 10083 - 103
77chain 'D' and (resid 100A through 112 )DA100 - 112104 - 122
88chain 'Y' and (resid 1 through 25 )YB1 - 251 - 25
99chain 'Y' and (resid 26 through 66 )YB26 - 6626 - 66
1010chain 'V' and (resid 1 through 13 )VD1 - 131 - 13
1111chain 'V' and (resid 14 through 18 )VD14 - 1814 - 18
1212chain 'V' and (resid 19 through 42 )VD19 - 4219 - 42
1313chain 'V' and (resid 43 through 52 )VD43 - 5243 - 52
1414chain 'V' and (resid 53 through 66 )VD53 - 6653 - 66
1515chain 'X' and (resid 1 through 13 )XE1 - 131 - 13
1616chain 'X' and (resid 14 through 18 )XE14 - 1814 - 18
1717chain 'X' and (resid 19 through 25 )XE19 - 2519 - 25
1818chain 'X' and (resid 26 through 42 )XE26 - 4226 - 42
1919chain 'X' and (resid 43 through 52 )XE43 - 5243 - 52
2020chain 'X' and (resid 53 through 57 )XE53 - 5753 - 57
2121chain 'X' and (resid 58 through 66 )XE58 - 6658 - 66
2222chain 'Z' and (resid 1 through 13 )ZF1 - 131 - 13
2323chain 'Z' and (resid 14 through 25 )ZF14 - 2514 - 25
2424chain 'Z' and (resid 26 through 42 )ZF26 - 4226 - 42
2525chain 'Z' and (resid 43 through 52 )ZF43 - 5243 - 52
2626chain 'Z' and (resid 53 through 57 )ZF53 - 5753 - 57
2727chain 'Z' and (resid 58 through 66 )ZF58 - 6658 - 66
2828chain 'A' and (resid 1 through 45 )AG1 - 451 - 45
2929chain 'A' and (resid 46 through 66 )AG46 - 6646 - 66
3030chain 'A' and (resid 67 through 72 )AG67 - 7267 - 72
3131chain 'A' and (resid 73 through 82 )AG73 - 8273 - 82
3232chain 'A' and (resid 82A through 100 )AG82 - 10083 - 103
3333chain 'A' and (resid 100A through 112 )AG100 - 112104 - 122
3434chain 'B' and (resid 1 through 17 )BH1 - 171 - 17
3535chain 'B' and (resid 18 through 45 )BH18 - 4518 - 45
3636chain 'B' and (resid 46 through 66 )BH46 - 6646 - 66
3737chain 'B' and (resid 67 through 72 )BH67 - 7267 - 72
3838chain 'B' and (resid 73 through 82 )BH73 - 8273 - 82
3939chain 'B' and (resid 82A through 100 )BH82 - 10083 - 103
4040chain 'B' and (resid 100A through 112 )BH100 - 112104 - 122
4141chain 'C' and (resid 1 through 45 )CI1 - 451 - 45
4242chain 'C' and (resid 46 through 66 )CI46 - 6646 - 66
4343chain 'C' and (resid 67 through 72 )CI67 - 7267 - 72
4444chain 'C' and (resid 73 through 112 )CI73 - 11273 - 122

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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://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