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- PDB-8r61: Structure of IgE delta epsilon 3-4 in complex with a kappa bindin... -

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基本情報

登録情報
データベース: PDB / ID: 8r61
タイトルStructure of IgE delta epsilon 3-4 in complex with a kappa binding nanobody
要素
  • HMM5 IgE light chain
  • Immunoglobulin E VH-Ceps1-Ceps1
  • kappa binding nanobody
キーワードIMMUNE SYSTEM / adaptive immune system IgE allergy
生物種Homo sapiens (ヒト)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å
データ登録者Andersen, G.R. / Gandini, R.
資金援助 デンマーク, 1件
組織認可番号国
Danish Council for Independent Research0135-00061B デンマーク
引用
ジャーナル: Biorxiv / 年: 2023
タイトル: The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy
著者: Jensen, R.K. / Miehe, M. / Gandini, R. / Jorgensen, M.H. / Spillner, E. / Andersen, G.R.
#1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2023年11月20日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年11月29日Provider: repository / タイプ: Initial release
改定 1.12024年6月12日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
改定 1.22024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Immunoglobulin E VH-Ceps1-Ceps1
B: HMM5 IgE light chain
C: kappa binding nanobody
D: Immunoglobulin E VH-Ceps1-Ceps1
E: HMM5 IgE light chain
F: kappa binding nanobody
G: Immunoglobulin E VH-Ceps1-Ceps1
H: HMM5 IgE light chain
I: kappa binding nanobody
J: Immunoglobulin E VH-Ceps1-Ceps1
K: HMM5 IgE light chain
L: kappa binding nanobody
M: Immunoglobulin E VH-Ceps1-Ceps1
N: HMM5 IgE light chain
O: kappa binding nanobody
P: Immunoglobulin E VH-Ceps1-Ceps1
Q: HMM5 IgE light chain
R: kappa binding nanobody


分子量 (理論値)分子数
合計 (水以外)442,67218
ポリマ－442,67218
非ポリマー00
水00
1
A: Immunoglobulin E VH-Ceps1-Ceps1
B: HMM5 IgE light chain
C: kappa binding nanobody


分子量 (理論値)分子数
合計 (水以外)73,7793
ポリマ－73,7793
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Immunoglobulin E VH-Ceps1-Ceps1
E: HMM5 IgE light chain
F: kappa binding nanobody


分子量 (理論値)分子数
合計 (水以外)73,7793
ポリマ－73,7793
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: Immunoglobulin E VH-Ceps1-Ceps1
H: HMM5 IgE light chain
I: kappa binding nanobody


分子量 (理論値)分子数
合計 (水以外)73,7793
ポリマ－73,7793
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
J: Immunoglobulin E VH-Ceps1-Ceps1
K: HMM5 IgE light chain
L: kappa binding nanobody


分子量 (理論値)分子数
合計 (水以外)73,7793
ポリマ－73,7793
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
M: Immunoglobulin E VH-Ceps1-Ceps1
N: HMM5 IgE light chain
O: kappa binding nanobody


分子量 (理論値)分子数
合計 (水以外)73,7793
ポリマ－73,7793
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
P: Immunoglobulin E VH-Ceps1-Ceps1
Q: HMM5 IgE light chain
R: kappa binding nanobody


分子量 (理論値)分子数
合計 (水以外)73,7793
ポリマ－73,7793
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)154.100, 132.490, 154.530
Angle α, β, γ (deg.)90.000, 118.843, 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 "D"
d_3ens_1chain "G"
d_4ens_1chain "J"
d_5ens_1chain "M"
d_6ens_1chain "P"
d_1ens_2chain "B"
d_2ens_2chain "E"
d_3ens_2chain "H"
d_4ens_2chain "K"
d_5ens_2chain "N"
d_6ens_2chain "Q"
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"
d_4ens_3chain "L"
d_5ens_3chain "O"
d_6ens_3chain "R"

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_1GLNGLNARGARGAA1 - 2231 - 223
d_2ens_1GLNGLNARGARGDD1 - 2231 - 223
d_3ens_1GLNGLNARGARGGG1 - 2231 - 223
d_4ens_1GLNGLNARGARGJJ1 - 2231 - 223
d_5ens_1GLNGLNARGARGMM1 - 2231 - 223
d_6ens_1GLNGLNARGARGPP1 - 2231 - 223
d_1ens_2GLUGLUCYSCYSBB1 - 2171 - 217
d_2ens_2GLUGLUCYSCYSEE1 - 2171 - 217
d_3ens_2GLUGLUCYSCYSHH1 - 2171 - 217
d_4ens_2GLUGLUCYSCYSKK1 - 2171 - 217
d_5ens_2GLUGLUCYSCYSNN1 - 2171 - 217
d_6ens_2GLUGLUCYSCYSQQ1 - 2171 - 217
d_1ens_3GLUGLUSERSERCC1 - 1201 - 120
d_2ens_3GLUGLUSERSERFF1 - 1201 - 120
d_3ens_3GLUGLUSERSERII1 - 1201 - 120
d_4ens_3GLUGLUSERSERLL1 - 1201 - 120
d_5ens_3GLUGLUSERSEROO1 - 1201 - 120
d_6ens_3GLUGLUSERSERRR1 - 1201 - 120

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.573140545431, -0.00810410713538, 0.819417011436), (0.00274797649503, 0.999964481817, 0.00796766781005), (-0.819452478066, -0.00231485478742, 0.573142458416)1.00052615455, -21.8358303932, 5.97794042702
2given(0.837148155857, -0.0118650638765, -0.546847497393), (-0.0229812122588, -0.999644857695, -0.0134915664908), (-0.546493210414, 0.0238616584181, -0.837123522683)-90.282703054, -14.5649488864, -132.669763882
3given(-0.0338096132503, -0.0193707770372, 0.999240553145), (-0.015401756689, -0.99968332818, -0.0199004836548), (0.999309609652, -0.0160628875292, 0.0335005627037)5.19338191464, 29.0549250789, -4.50414435948
4given(0.803123608821, -0.0160794795415, 0.595595432565), (0.00404966559378, -0.999465363327, -0.0324436082813), (0.59579868174, 0.0284681900971, -0.802629112972)-0.210537531383, 6.89311818382, -0.971108332241
5given(0.368849330378, 0.000636322247292, -0.929488981416), (-0.0138656733842, 0.999892260156, -0.00481779853503), (0.929385772745, 0.0146650323941, 0.368818413645)-159.563140025, 21.8473896949, -8.04008840688
6given(0.569488728381, -0.00448584931698, 0.821986900992), (-0.00300854199851, 0.999967036518, 0.00754152188715), (-0.821993635572, -0.00676779382343, 0.569456460184)1.04075903535, -21.8148889799, 5.8751250527
7given(0.844881482817, 0.00429732593577, -0.53493627002), (-0.00662113324257, -0.999807135531, -0.0184892492069), (-0.534912554151, 0.0191631086062, -0.84469008203)-89.6917447437, -14.8614227711, -132.949631513
8given(-0.0369992259897, -0.0221001089854, 0.999070889606), (-0.00767816550152, -0.999719630241, -0.0223988099309), (0.999285796482, -0.00849977026868, 0.0368191642312)4.99241066252, 28.8140933553, -4.35047794599
9given(0.795964497916, -0.00384984867712, 0.605331063734), (0.023793970013, -0.999008014104, -0.0376408653734), (0.604875495493, 0.0443640216865, -0.795083309177)0.290539316522, 6.8699725804, -0.612126481117
10given(0.380053936271, 0.000715404117859, -0.924964049962), (-0.035641664297, 0.999268355446, -0.0138717543839), (0.924277381142, 0.0382392730122, 0.379801370072)-159.145311895, 21.1030948918, -7.73044772248
11given(0.563782222074, -0.00449942381978, 0.825911230859), (-0.000378486415659, 0.999983648437, 0.00570610252474), (-0.825923400093, -0.0035295953422, 0.563771300382)1.22557005899, -21.8302442793, 5.39087436099
12given(0.85412963486, -0.0247481533674, -0.51947097682), (-0.0543632199931, -0.997643547147, -0.0418568172275), (-0.517210989022, 0.0639912630078, -0.853462307951)-88.2977713521, -17.5406368253, -132.971648844
13given(-0.0494225331466, -0.0560202651374, 0.997205667408), (-0.0381709972075, -0.997590429198, -0.0579336736695), (0.998048289508, -0.0409275636532, 0.0471650966696)4.47344851402, 25.8318739138, -3.68021121009
14given(0.784825447753, -0.031354005575, 0.618923212438), (0.00854591046561, -0.998076766664, -0.0613981698379), (0.619657957243, 0.0534761084928, -0.783048096765)0.741836262879, 5.12987077272, 0.630328378379
15given(0.415960872108, -0.0219915464653, -0.909116562801), (-0.0122960776328, 0.999480145585, -0.0298034403365), (0.909299378285, 0.0235756328676, 0.415474223249)-157.051615231, 20.6772187715, -6.00129581019

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要素

#1: タンパク質
Immunoglobulin E VH-Ceps1-Ceps1


分子量: 37231.449 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト)
#2: 抗体
HMM5 IgE light chain


分子量: 23384.795 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト)
#3: 抗体
kappa binding nanobody


分子量: 13162.396 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli (大腸菌)
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: 3.12 Å3/Da / 溶媒含有率: 60.6 %
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.2 / 詳細: 0.2 M Ammonium nitrate, 20% PEG 3350, pH 6.2

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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: PETRA III, EMBL c/o DESY / ビームライン: P13 (MX1) / 波長: 0.97626 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2023年10月12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: 0.97626 Å / 相対比: 1
反射解像度: 3.1→32.46 Å / Num. obs: 98556 / % possible obs: 99.68 % / 冗長度: 6.8 % / Biso Wilson estimate: 73.74 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.3116 / Net I/σ(I): 5.65
反射 シェル解像度: 3.1→3.211 Å / 冗長度: 6 % / Rmerge(I) obs: 1.598 / Num. unique obs: 9783 / CC1/2: 0.336 / % possible all: 99.33

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21rc1_4903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: 3.1→32.46 Å / SU ML: 0.474 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 29.5979
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2752 2327 2.36 %
Rwork0.2324 96207 -
obs0.2334 98534 99.78 %
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: 74.95 Å2
精密化ステップサイクル: LAST / 解像度: 3.1→32.46 Å
タンパク質核酸リガンド溶媒全体
原子数25344 0 0 0 25344
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006125914
X-RAY DIFFRACTIONf_angle_d0.887135280
X-RAY DIFFRACTIONf_chiral_restr0.05554002
X-RAY DIFFRACTIONf_plane_restr0.00924506
X-RAY DIFFRACTIONf_dihedral_angle_d5.12693618
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.896912523708
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.926574781435
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.893814194155
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.545162233671
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.616628855694
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.490137344717
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.434013243639
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.476830398488
ens_2d_5BBX-RAY DIFFRACTIONTorsion NCS0.487333331519
ens_2d_6BBX-RAY DIFFRACTIONTorsion NCS0.452942921897
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.591059458035
ens_3d_3CCX-RAY DIFFRACTIONTorsion NCS0.695805013296
ens_3d_4CCX-RAY DIFFRACTIONTorsion NCS0.593482175597
ens_3d_5CCX-RAY DIFFRACTIONTorsion NCS0.474839786281
ens_3d_6CCX-RAY DIFFRACTIONTorsion NCS0.61276706674
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.160.3761390.33695613X-RAY DIFFRACTION99.09
3.16-3.230.36381300.30955625X-RAY DIFFRACTION99.64
3.23-3.310.35541380.30345600X-RAY DIFFRACTION99.79
3.31-3.390.31761150.28985657X-RAY DIFFRACTION99.91
3.39-3.480.29741370.26615642X-RAY DIFFRACTION99.83
3.48-3.580.34031380.26035672X-RAY DIFFRACTION99.97
3.58-3.70.2891270.25865650X-RAY DIFFRACTION99.93
3.7-3.830.28331550.24795610X-RAY DIFFRACTION99.93
3.83-3.980.25861190.22495686X-RAY DIFFRACTION99.86
3.98-4.170.25411660.21575613X-RAY DIFFRACTION99.95
4.17-4.380.24591320.20085649X-RAY DIFFRACTION99.88
4.38-4.660.25631320.19095666X-RAY DIFFRACTION99.6
4.66-5.020.2361610.19015666X-RAY DIFFRACTION99.91
5.02-5.520.2487980.20085719X-RAY DIFFRACTION99.95
5.52-6.310.24311750.21725644X-RAY DIFFRACTION99.83
6.31-7.930.3009930.23785753X-RAY DIFFRACTION99.85
7.94-32.460.27171720.23735742X-RAY DIFFRACTION99.29
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)
11.066369263410.5035115708510.03934069645943.73802146488-0.4387606720333.487905659010.306166364411-0.0155282077498-0.1849707846120.0997905307506-0.207059711641-0.4407032729260.1096229929790.5848962917-0.05200071897130.4149250871130.000963843096392-0.09088158637160.602412089869-0.04283265220390.6575431750989.0090424902324.4476886518-61.2042195087
24.005689556921.735238812791.136831614916.38020609348-0.3537594670982.168804034570.189010998383-0.354262449381-0.80057132816-0.147781095368-0.273138573792-0.9029007893380.366034068803-0.07362183514810.1992270385370.5892537134940.0162457044549-0.04826137632530.6339907005910.02381340648780.897620818143-3.57641662617-2.51376068292-44.565259685
34.59075373561-0.1580703811450.1744796199340.5890216528890.9224991456783.400845300050.1393832173440.282431104888-0.227580748019-0.121590476318-0.205379241528-0.24704160958-0.044005715787-0.0444182159033-0.00236425150710.518075383153-0.06017264220520.04685398923290.441860825587-0.05151432192210.477047460537-5.0754052345417.4332607688-76.3790950163
41.665638378660.7148588570470.9214049866030.7183828543881.110128990717.12726886322-0.079438206978-0.297523331544-0.1387364402820.220394351907-0.0542948249164-0.2308619045240.3859776243770.4092188332780.05578747190650.4968394830570.0355099871913-0.01695841193460.4148155128260.08372918753950.649411870966-19.22757763980.545162664235-46.3035135127
54.226250678912.022805211240.405477407796.446554411972.048538945225.308335499940.06475811011730.05758931907720.0968307822023-0.1799073632430.1711365264930.011727817185-0.1029513543890.110213855413-0.1989410280850.419002192237-0.03446944385940.05644430166120.3837671626790.009582104431120.45244757782-36.5812143056-2.65186224449-69.2097897389
64.46415356742-0.9065247417511.430878123082.35047803602-1.779888382891.39632537409-0.06806630903770.284491570848-0.0957398113361-0.3478386930430.0909079910562-0.231670114915-0.261567714745-0.01983948780310.01399598161030.668938186884-0.08161187036710.1022976044220.465239472608-0.03136278886540.539833066763-44.2192441792.1543371689-36.5508432247
72.99561046599-0.672548986489-0.8545781535473.639612238621.277504572823.72277462175-0.288131492210.0132237826474-0.729873706369-0.2604781501620.0790738757573-0.2217927542760.7539949698610.1283311829420.1138881477550.7001997972650.03531720017010.08286131563210.7058279599590.01100061041310.783297253228-37.5209431754-24.7217006962-16.6088684884
83.41465566377-0.539593846369-0.5462706926174.03143579152-2.983100373071.810448490610.04455579734240.0195098955170.0146784438423-0.227300836953-0.004721011825360.1656487210030.0366045044846-0.0505179095180.002938415894520.582976860471-0.0257196875197-0.00803424394830.464011612703-0.1000556707210.376517341581-64.7421282269-4.93686977351-33.5915739622
94.99039503210.5995691318351.154604565732.90542240686-0.7266787482423.928369043270.001841203816480.06421502432720.0141253078088-0.201266567126-0.167386839644-0.5053747315430.5079056981920.7813224664720.2152864880730.5201579054770.05755406755910.1097173390560.4640207618770.02565893835840.508464074957-47.9423338179-21.571881786-4.66134377981
104.090291217461.93011365860.8927758227517.796393700190.3598711402433.16098811129-0.116151546863-0.173120915958-0.09115977622230.2209041986190.2401620031540.03433771430440.0778912307112-0.0820470092752-0.1167593508520.483712036655-0.01625701477520.01360159990550.4653316809330.01807872673730.464477824555-76.5465205087-24.8645777308-3.40535604547
112.71552483524-1.79451147619-0.3501124195755.286051736961.146307565924.283224158510.03294769585890.146341337644-0.302982760431-0.2978320755360.164708895344-0.4665324852130.1973627837160.315516820094-0.1950333456140.444238265372-0.063133117236-0.0005817066263980.328729504953-0.03999558726610.437857729071-49.6804393151-38.2366572444-85.8083421412
125.20133855117-1.31484287991-1.014033884954.399476139210.09906856966913.02876304192-0.0531576081530.269798059841.04354748622-0.1573926408310.220784088091-0.727876703182-0.4168383769310.0542490649239-0.1810284366790.640668294591-0.121427195722-0.03355664985590.5781000766660.00275630180020.669456363468-68.7469652894-11.5346208256-93.4207183119
132.8833398941-1.192093487080.3618253530032.302786310990.4173173441561.39193340359-0.0363288529668-0.248380363420.31088122228-0.0239528730397-0.0267545722866-0.214676684244-0.100019155103-0.1087546082940.04377600008460.452341051971-0.05015584266540.006759042004440.402201397086-0.05224176961320.453618858263-53.1380796137-30.7910436334-65.4245488901
144.47272917321-0.9310122080271.866324863891.63900122347-1.441345785224.04753982349-0.02273405586010.545751089630.162589329716-0.4967682118270.1197752378860.102377179874-0.192759356066-0.253851966576-0.1818088238090.6316138997830.0056378215972-0.0255771655960.5144444731930.03616697870380.612803552671-81.07683603-14.4760715973-83.5001072374
153.039050076430.145059553560.3194657303516.261493461381.056993738712.21400299279-0.0883030171856-0.325207943719-0.0272392157109-0.0590774840043-0.2074133052510.512276761772-0.467231939851-0.5725364887260.2824209947410.7395031339150.110529871195-0.01087160696410.682199736141-0.038141512620.646032519903-83.526664367-10.0081947022-55.1549971973
163.2588252183-0.2135373124320.5614541693353.22460881732-2.037117773232.24871833442-0.248452080109-0.309143304140.02691687983220.0913905121810.1534713698420.121513007761-0.0711059927465-0.07230717420230.1381827126960.6013722196110.0827672708456-0.02232632060950.4309331028790.009289269473810.540907657371-56.68023555995.774086099021.98563477703
173.96610378924-0.886116030672-0.08212562745996.05944562391-1.704027013072.5043511409-0.09129011258040.09452878744660.5172973823180.710848291172-0.101482844625-0.402420292746-0.567244216825-0.1444162485920.08598590233380.730301616997-0.0137466140753-0.06350036119840.645297775877-0.009699939130680.690187091597-39.243307518932.4204066907-9.46191738939
184.509148629060.209441263825-0.3792012424445.32854741349-2.571669017832.666829509990.1357136690640.4165998262840.1665128290840.0192344614643-0.09111950431140.244969094051-0.157238319314-0.0152697139562-0.1433969577440.5457054376950.0553879128782-0.001802615979420.40389440793-0.03202095486920.404300687828-71.475061468713.2020908287-12.4419065745
196.77171444088-0.0516864582861-0.2335614522310.107750995184-0.3202987021121.56997258930.237962922496-0.2375423802420.2004478085250.168812768854-0.105361172196-0.0672796278952-0.04786410730630.289836984959-0.1902126286160.664837054860.01649425837580.002950913544470.456821754381-0.01585911605470.604007066219-40.603970273829.3862204319-25.2162710486
205.68494485684-2.49276042134-0.203398106913.903462702410.6428404723222.39405524144-0.05849349498810.2957314423630.269812846223-0.2468141237140.162622602617-0.02413676237620.102423425179-0.206030422553-0.06850540597820.523856622604-0.07794770918410.06653559987770.5042210261710.06003119237640.479352982251-62.585025719633.8849823153-43.3438149525
213.11555484698-0.779378556144-0.7824509407572.2290168965-1.32344039951.261444557840.137836738425-0.4575568462620.08265996724680.0481231889058-0.366045802863-0.114065523873-0.3144964420180.4601872859520.2714589428470.600514299391-0.0153665271638-0.1722884797050.729632777907-0.024463175790.622853472234-29.8134319879-15.394320428254.1177789442
224.441840245790.8872824237031.306492554865.291243922270.2712462186983.82999449328-0.2574853352970.1566140824240.7856450189470.452449949877-0.03164252231330.0418032410711-0.69095303496-0.03053787429560.3792277633570.5492170454780.0282959059404-0.1047196618450.6507489076150.04622444236110.683799368708-29.595702920710.696668690632.7075959663
232.4907253876-0.676862998340.3009548177164.46939845861-1.481396915961.877625076480.0276244689948-0.4601863919280.03456716830960.489857968466-0.02165547101930.247311049035-0.3762660880840.0779678960976-0.01924189970760.814808435566-0.00569342466242-0.04035457534360.887433667804-0.01857208353120.499559128857-50.0407421119-7.7394895364357.7133369764
243.55958686476-0.436300213503-1.795275090060.45670541495-0.1296433700514.195175059660.0113347433824-0.2240701412010.06700985895560.107145358518-0.160984194052-0.248601082205-0.4391045500420.6586907174180.1573282063090.640856912931-0.00351502510756-0.1059478154220.5418427188790.008445997316430.619139052674-43.0577005257.5603979180124.6988209922
255.75279063792-0.6397139383420.7173671411594.10164934887-2.516364245853.626197288360.0667669857428-0.08461756317970.225321647240.7864552335690.2395704872280.5274447192-0.903866440365-0.464744481539-0.2990163932730.7879755950230.1846541760450.1466463222980.6010160912970.03790196478730.490042631733-70.718118693411.714616762832.0157620212
263.903125955722.1699515469-1.957228358314.921208130190.4758094626374.059099873530.147285084533-0.157110398942-0.1428367572130.924498283085-0.130498684766-0.529410355313-0.1702054380560.207152967707-0.004468417164720.712203787918-0.100154848804-0.09992531514750.5092458097-0.007974791421770.473951717615-99.453929577146.2810981135-21.9012231095
274.89569629353-1.59725276877-1.188175940536.55137540316-1.003873880196.102625669790.1721748336660.532131191141-0.8611277750820.300553658346-0.1097123029880.5239367379470.916822436564-0.239314604944-0.1301662657780.596029425095-0.0921882189129-0.2002616809910.665120883936-0.0559771202730.722262971825-119.32588754919.7992420733-27.8195420387
282.456102109611.73003187604-0.2125924133544.497268524690.4182921541483.251322819180.2023245807920.296264243985-0.596695533464-0.23002357078-0.306430517012-0.5154436151860.1423921773910.09263564162130.1636768393970.4298329601930.0686693681047-0.05851432881070.520696163708-0.06778433345450.700014074267-90.477873027139.7299071983-40.7706304928
293.16587633867-1.33059426581-0.6360079940461.933897741040.5159523721071.426164088120.0921374175384-0.118426888958-0.5225082740870.0058633369715-0.04813886351060.1215736316990.149666707549-0.129913782624-0.04720879288850.757295507756-0.0718766792156-0.1451992867560.753158750708-0.08242786359760.806319496767-123.55714135523.0090534396-43.0602506977
301.627118515160.116225827536-0.8420460612664.793393717480.2890084175196.2112521722-0.03089195201330.631879770377-0.492120664768-0.68414210416-0.183614001920.2702938308110.460229394173-0.6041810554060.2493547878850.786303738797-0.06539388395390.033582634970.974405203122-0.2676903433330.844118458864-109.28910590720.5378939134-68.0798991755
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 1:118AA1 - 1181 - 118
22chain A and resid 119:223AA119 - 223119 - 223
33chain B and resid 1:110BB1 - 1101 - 110
44chain B and resid 111:217BB111 - 217111 - 217
55chain CCC1 - 1201 - 120
66chain D and resid 1:118DD1 - 1181 - 118
77chain D and resid 119:223DD119 - 223119 - 223
88chain E and resid 1:110EE1 - 1101 - 110
99chain E and resid 111:217EE111 - 217111 - 217
1010chain FFF1 - 1201 - 120
1111chain G and resid 1:118GG1 - 1181 - 118
1212chain G and resid 119:223GG119 - 223119 - 223
1313chain H and resid 1:110HH1 - 1101 - 110
1414chain H and resid 111:217HH111 - 217111 - 217
1515chain III1 - 1201 - 120
1616chain J and resid 1:118JJ1 - 1181 - 118
1717chain J and resid 119:223JJ119 - 223119 - 223
1818chain K and resid 1:110KK1 - 1101 - 110
1919chain K and resid 111:217KK111 - 217111 - 217
2020chain LLL1 - 1201 - 120
2121chain M and resid 1:118MM1 - 1181 - 118
2222chain M and resid 119:223MM119 - 223119 - 223
2323chain N and resid 1:110NN1 - 1101 - 110
2424chain N and resid 111:217NN111 - 217111 - 217
2525chain OOO1 - 1201 - 120
2626chain P and resid 1:118PP1 - 1181 - 118
2727chain P and resid 119:223PP119 - 223119 - 223
2828chain Q and resid 1:110QQ1 - 1101 - 110
2929chain Q and resid 111:217QQ111 - 217111 - 217
3030chain RRR1 - 1201 - 120

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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