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- PDB-7si0: IgE-Fc in complex with 813 -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7si0
タイトルIgE-Fc in complex with 813
要素
  • (813 Variable fragment ...) x 2
  • IgE Fc
キーワードIMMUNE SYSTEM / IgE / omalizumab / xolair / inhibitor
機能・相同性
機能・相同性情報


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / type 2 immune response / immunoglobulin receptor binding / immunoglobulin complex, circulating / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / immune response / inflammatory response / extracellular space / extracellular region / plasma membrane
類似検索 - 分子機能
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Immunoglobulin heavy constant epsilon
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: 3 Å
データ登録者Pennington, L.F. / Jardetzky, T.J. / Kleinboelting, S.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115469 米国
引用ジャーナル: Nat Commun / 年: 2021
タイトル: Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex.
著者: Luke F Pennington / Pascal Gasser / Silke Kleinboelting / Chensong Zhang / Georgios Skiniotis / Alexander Eggel / Theodore S Jardetzky /
要旨: Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional ...Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional mechanism where antibody-mediated "disruption" of stable high-affinity macromolecular complexes can potentially enhance therapeutic efficacy. However, this mechanism is not well understood or utilized therapeutically. Here, we investigate and engineer the weak disruptive activity of an existing therapeutic antibody, omalizumab, which targets IgE antibodies to block the allergic response. We develop a yeast display approach to select for and engineer antibody disruptive efficiency and generate potent omalizumab variants that dissociate receptor-bound IgE. We determine a low resolution cryo-EM structure of a transient disruption intermediate containing the IgE-Fc, its partially dissociated receptor and an antibody inhibitor. Our results provide a conceptual framework for engineering disruptive inhibitors for other targets, insights into the failure in clinical trials of the previous high affinity omalizumab HAE variant and anti-IgE antibodies that safely and rapidly disarm allergic effector cells.
履歴
登録2021年10月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年12月15日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
B: IgE Fc
I: 813 Variable fragment Heavy chain
J: 813 Variable fragment Light chain
E: 813 Variable fragment Heavy chain
F: 813 Variable fragment Light chain
G: IgE Fc
H: IgE Fc
A: IgE Fc
C: 813 Variable fragment Heavy chain
D: 813 Variable fragment Light chain
K: 813 Variable fragment Heavy chain
L: 813 Variable fragment Light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)226,32821
ポリマ－222,41812
非ポリマー3,9109
水21612
1
B: IgE Fc
E: 813 Variable fragment Heavy chain
F: 813 Variable fragment Light chain
A: IgE Fc
C: 813 Variable fragment Heavy chain
D: 813 Variable fragment Light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)113,23410
ポリマ－111,2096
非ポリマー2,0254
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
I: 813 Variable fragment Heavy chain
J: 813 Variable fragment Light chain
G: IgE Fc
H: IgE Fc
K: 813 Variable fragment Heavy chain
L: 813 Variable fragment Light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)113,09411
ポリマ－111,2096
非ポリマー1,8865
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)98.958, 132.005, 177.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 1種, 4分子 BGHA

#1: タンパク質
IgE Fc / Immunoglobulin heavy constant epsilon / Ig epsilon chain C region / Ig epsilon chain C region ND


分子量: 27550.873 Da / 分子数: 4 / 断片: C3-4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IGHE / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01854

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抗体 , 2種, 8分子 IECKJFDL

#2: 抗体
813 Variable fragment Heavy chain


分子量: 13463.805 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体
813 Variable fragment Light chain


分子量: 14589.740 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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糖 , 3種, 6分子

#4: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


タイプ: oligosaccharide / 分子量: 342.297 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#6: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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非ポリマー , 2種, 15分子

#7: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Na
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 12 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
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: 2.61 Å3/Da / 溶媒含有率: 52.79 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M CAPS pH 10.5, 40%(v/v) MPD

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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: SSRL / ビームライン: BL12-1 / 波長: 1.19499 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年7月13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: 1.19499 Å / 相対比: 1
反射解像度: 3→39.59 Å / Num. obs: 47037 / % possible obs: 99.56 % / 冗長度: 6.8 % / CC1/2: 0.996 / Net I/σ(I): 11.4
反射 シェル解像度: 3→3.107 Å / Num. unique obs: 4623 / CC1/2: 0.671

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10_2155精密化
PDB_EXTRACT3.27データ抽出
XDSデータ削減
XDSデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5hys

5hys


解像度: 3→39.59 Å / SU ML: 0.38 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 26.68 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2611 2291 4.87 %
Rwork0.2104 44746 -
obs0.2128 47037 99.63 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 177.01 Å2 / Biso mean: 65.0739 Å2 / Biso min: 28.18 Å2
精密化ステップサイクル: final / 解像度: 3→39.59 Å
タンパク質核酸リガンド溶媒全体
原子数13773 0 258 12 14043
Biso mean--83.82 37.06 -
残基数----1777
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00614408
X-RAY DIFFRACTIONf_angle_d0.72819646
X-RAY DIFFRACTIONf_chiral_restr0.0482205
X-RAY DIFFRACTIONf_plane_restr0.0052496
X-RAY DIFFRACTIONf_dihedral_angle_d14.3628579
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.06520.33351750.30782711100
3.0652-3.13650.3571360.29422741100
3.1365-3.21490.31241380.27352783100
3.2149-3.30180.29031560.26362788100
3.3018-3.39890.32191410.26292757100
3.3989-3.50850.34411390.25342783100
3.5085-3.63380.24941220.2331273399
3.6338-3.77920.26431380.22482823100
3.7792-3.95110.29781380.22582782100
3.9511-4.15920.2551510.2118276499
4.1592-4.41940.26571290.18692810100
4.4194-4.76010.21361530.1672797100
4.7601-5.23820.1981360.1696281499
5.2382-5.99390.26091430.1956280799
5.9939-7.54320.26581550.20242880100
7.5432-39.590.22051410.1885297399
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)
13.12010.47580.83122.16390.71792.21980.2055-0.1616-0.27840.1599-0.051-0.5140.20240.3974-0.15850.6840.01350.02840.8999-0.0370.6508-38.0569-42.9382-18.7148
21.6964-0.3024-0.68263.89120.06836.51210.087-0.19860.25410.1855-0.1963-0.66940.02980.70480.01130.5256-0.07140.04880.8355-0.01810.6653-35.6821-41.0662-21.6603
34.36990.5066-1.3995.40351.36224.3137-0.6121-0.3104-0.50630.34960.3088-0.12050.6325-0.47410.48010.52620.06110.15730.6122-0.03190.6026-60.3673-57.4472-6.1785
43.3316-1.06830.86365.9164-0.94298.71150.0215-0.0718-0.05940.5020.2453-0.1949-0.24720.1372-0.22770.4946-0.01660.05220.576-0.00930.4943-58.5886-52.1877-5.656
57.05170.20410.43476.1148-0.52854.4081-0.4834-0.8068-0.38150.8542-0.1791-0.140.02960.22560.73620.740.01260.01950.58850.1220.527725.4192-14.2698-7.5051
63.70830.23452.5115.65580.02516.93050.18280.3295-0.03950.06820.0009-0.3513-0.136-0.053-0.18120.3818-0.01220.01130.48910.05340.411520.6915-17.3607-17.8157
74.62891.5423-5.25433.1804-2.39078.0141-0.1741-0.0573-0.4588-0.0828-0.0707-0.55340.20980.25310.28830.43580.0123-0.02760.5908-0.04520.700123.8023-22.8237-14.0971
88.16551.38595.64241.8262-0.44575.31370.84060.0974-0.7986-0.0896-0.326-0.32720.76990.0809-0.55650.6329-0.0495-0.05740.6451-0.00160.462126.9595-14.2574-17.1099
96.04491.58393.21475.33020.07336.9718-0.63420.45780.5787-1.51380.70630.6706-0.18150.25410.22130.7463-0.0241-0.05110.57590.00590.517816.5171-12.5421-26.9538
107.6313-1.35230.13741.5884-0.33162.644-0.79760.43221.21630.51040.2584-0.4548-0.98110.13070.41590.63-0.0219-0.13290.6636-0.07390.589231.8695-10.4714-7.5333
115.5694-3.4824-3.28943.07353.79165.6403-0.19550.0627-0.2541-2.28090.6604-1.6327-0.11070.6941-0.31840.5794-0.08810.20590.9393-0.01220.59633.2402-7.6052-32.1145
126.84180.3074-0.79042.68444.20667.3061-0.42580.5999-0.2365-1.00940.22950.61-0.86860.250.10410.79890.02350.05030.59480.14370.596327.41528.8391-30.7039
136.7232-0.129-2.95935.6843-1.04575.4963-0.21110.37340.2661-0.44710.31680.24150.1733-0.3108-0.12220.6325-0.0643-0.07840.61130.07750.460118.7413-3.0643-30.5934
141.52710.79840.74457.1023-1.68011.73420.09280.22290.0387-0.34710.0362-0.0728-0.1809-0.3151-0.0960.5551-0.06250.02970.74780.09230.531324.187-1.177-29.0709
157.83230.8548-0.57393.0806-0.15392.4231-0.2995-0.47970.60531.8128-0.6175-0.3133-0.72391.44250.93760.9316-0.04950.04970.4967-0.05870.481827.934610.5528-22.0221
164.36353.3569-4.63097.893-3.29014.86050.5478-1.01970.5619-0.3518-1.28851.14881.55510.7761.06210.76110.07130.17231.01950.08130.8744-55.0315-33.634-45.906
176.63074.0778-2.29084.2133-3.92514.40880.46110.03350.7422-2.0771-0.35521.2424-0.2539-0.0707-0.55452.08460.33790.32750.67230.16310.8676-48.0664-20.1442-65.4143
181.1876-0.09491.00862.9277-1.27597.9440.353-0.10630.1818-0.41060.05220.0277-1.441-0.0929-0.37850.95930.07690.29590.6155-0.05060.6983-43.6617-26.5141-47.8946
191.98562.5614-1.41745.4522-3.79978.2480.847-0.67970.5874-1.03640.24751.5428-0.2760.7563-0.73311.06540.2120.22590.67820.01820.8303-48.155-27.925-62.8903
206.3392.7351-1.73977.3549-4.72487.3818-0.1080.57080.17780.15150.29090.4844-1.4527-0.2666-0.25230.7721-0.05450.2380.91270.1090.6174-26.6903-36.976-53.7016
213.8449-3.8935-2.27075.6864-0.61989.02610.14220.19850.0064-0.34750.07850.35630.58640.524-0.19220.52120.0437-0.02760.5673-0.07750.6615-33.0585-53.6522-54.9167
224.51260.5658-1.12773.34360.51587.13080.3620.03360.39730.0815-0.09760.3862-0.09980.1612-0.22530.48440.00960.05480.5124-0.07580.6477-35.5468-41.5718-46.0808
238.58812.306-1.34623.50970.65176.51640.2795-1.0180.13540.2553-0.7684-0.01690.6791-0.12440.54750.45830.01760.13190.66640.03640.6591-39.8821-48.4429-40.0094
243.42344.48331.00486.53571.96784.83011.01990.8070.38041.0493-0.21230.42840.68850.3642-0.61560.65060.14120.01870.7299-0.03750.5404-35.899-52.3521-48.5336
251.4854-0.88131.01783.0093-0.18530.960.237-0.340.3677-0.4327-0.1098-0.6628-0.4703-0.0838-0.25430.66230.00680.1940.73970.03760.7435-33.2148-37.5626-50.0664
268.0967-0.1760.41783.7495-4.0756.51410.47921.67790.0279-2.7736-0.24050.6898-0.08240.4847-0.04690.92980.06710.04230.7133-0.06740.5115-40.3685-54.9738-62.0867
276.52442.1447-4.07814.9726-1.71093.2679-0.96351.53130.5606-0.72040.6549-0.0370.5753-0.81860.13271.0065-0.1997-0.45031.16430.19151.1494-4.4019-12.2947-40.6764
283.80910.53240.57992.78370.62481.7271-0.08140.69690.0862-0.7740.21980.2104-0.41290.303-0.09490.8152-0.1364-0.21670.86940.10130.70121.1724-13.247-38.6648
295.0892-0.57331.41846.9941.1563.84030.00390.0049-0.0950.72380.10140.24610.2554-0.1674-0.13930.767-0.01430.13030.75780.04030.6728-27.4054-4.1587-32.7244
301.09022.1459-0.0434.43010.15940.9141-0.7128-0.43420.04530.09940.38951.56061.6561.69720.23861.22930.2230.00721.26770.14160.2546-14.662119.24-50.1985
310.62731.35830.01863.9185-0.05381.71-0.0591-0.86160.4331.11170.1664-0.7302-0.16441.075-0.08511.10650.187-0.19711.46210.13150.6964-4.120922.8582-50.5706
329.0535-2.59980.15459.4259-0.08487.93230.0844-0.39090.71530.45490.2011-0.9882-1.25420.7394-0.24620.58890.0298-0.02150.8753-0.01440.5574-9.31728.7224-61.4471
333.8583-1.28171.42238.2798-2.58775.79790.3491-0.1141-1.22891.40110.1252-1.25080.96382.0954-0.7311.31350.1418-0.32381.6254-0.06081.30943.706923.2378-45.0585
343.5990.7359-2.57154.061-1.41413.3725-0.0073-0.41170.36790.16780.1533-0.17640.40890.5315-0.24230.78290.1303-0.02930.88170.00240.4638-10.887820.2271-58.0218
354.30221.794-1.20864.86520.41787.4936-0.4575-0.58890.37361.4288-0.8592-0.06591.1350.57720.99071.0470.1120.19780.80490.11140.7963-29.51577.1915-24.2497
363.820.0590.24477.6134-1.49315.68170.0239-0.45640.34680.81770.34840.0446-0.5425-0.122-0.29350.65790.05980.12660.744-0.00420.5654-26.265813.8311-34.6979
372.95152.2245-2.94234.4372-2.61572.78330.0390.09680.4632-0.18870.2070.92490.1643-0.9303-0.27710.74780.10920.03770.9066-0.03030.8299-33.473817.254-40.5138
382.20380.0431-1.02135.14871.99833.8826-0.39660.89540.3698-0.7009-0.23140.3716-0.1269-0.2730.52620.6384-0.0237-0.17120.95960.00040.9644-36.427-81.1977-15.9528
393.1343-1.03851.69735.6311-0.32197.6573-0.14970.99330.262-0.5607-0.07940.0828-0.2598-0.10950.15730.523-0.102-0.04120.9603-0.04180.8004-31.8223-82.9615-16.1736
409.5049-3.90963.3835.7045-0.16072.5932-0.3371-0.00041.33480.373-0.1205-0.64330.11490.12250.3960.7071-0.02890.07560.70110.08080.5925-59.0263-67.3812-4.858
417.06511.25632.86617.23891.09664.0606-0.07770.043-0.4890.48960.2886-0.09150.10710.1343-0.20150.61480.02870.06180.6483-0.09630.5528-58.8068-72.4361-6.8959
429.8955-2.7480.8234.8375-0.99963.6017-0.11781.02630.81281.1789-0.1388-0.48510.68130.39910.28931.09410.06510.03940.6232-0.10480.5808-11.3287-94.861616.4448
436.1303-0.41834.75294.1190.45067.16280.36380.232-0.22890.11140.0605-0.13850.91540.1601-0.42010.7020.0386-0.00370.52880.01890.4702-14.9125-94.89335.1747
445.4935-0.17320.48455.49881.69366.7787-0.61260.121-1.2907-0.25380.53060.22191.6890.6693-0.25291.23320.0907-0.21510.5788-0.10.7954-12.567-103.2786.3683
458.379-0.4322.86173.31422.92544.4838-0.19520.7011-1.4070.30710.34920.40680.94590.4132-0.1420.9531-0.0533-0.07660.63070.10710.8551-11.1103-100.116311.6356
466.2964-0.25475.32643.2595-0.70956.5192-0.0003-0.1876-0.40110.47380.34370.37540.327-0.2575-0.43970.59570.05780.06020.5581-0.02470.579-13.7564-89.19985.4272
476.45163.9161.8639.80343.72593.8014-0.0679-0.1048-0.80280.62290.4889-1.09590.56880.8342-0.33930.4501-0.0661-0.02180.8297-0.06850.5518-0.4326-85.5381-6.5093
484.67680.353-0.27234.053-0.53963.9963-0.10130.28220.45410.46530.0780.7976-0.28490.28140.10260.4199-0.03670.04260.57940.09520.6219-2.8771-64.60822.0471
497.59750.9159-0.25065.90146.46618.84720.13420.87110.323-1.7030.7099-1.4182-1.30320.9198-0.73790.4677-0.01110.18890.59580.02210.4757-3.3345-74.0174-6.9314
505.2951-1.1057-1.26364.12211.51742.3929-0.09220.85510.0591-0.57660.2782-0.1914-0.09670.1244-0.29140.71860.01640.04470.70610.0190.4985-11.159-82.4503-8.7884
518.78890.1631-2.35725.4562-3.61067.19530.172-1.1280.07360.6117-0.4648-0.016-1.1161-0.29260.02320.5992-0.04490.0080.67950.05220.4906-13.1524-77.64557.002
522.98580.7167-2.46883.75290.37733.01810.46940.41320.88380.0473-0.00470.0781-0.1111-0.7725-0.54670.4582-0.00630.00990.73380.03330.7313-17.3791-73.6577-4.956
532.53471.52021.54672.23990.99332.8946-0.04230.1106-0.1048-0.02110.14620.197-0.27530.2476-0.06410.53580.00180.05480.68140.07990.5409-8.6828-72.593-0.8209
545.2691-0.01920.82055.1012-1.12933.56320.44180.2074-0.0919-0.33370.28410.26260.73720.783-0.72910.52380.12230.10710.8335-0.03150.475-6.9555-87.4238-4.6896
556.5188-0.1031-5.24912.6725-2.54266.74381.2969-1.0531-0.34181.2082-0.6878-2.2066-1.12591.6649-0.53470.701-0.0108-0.05610.86120.0890.707-0.8296-66.78678.3259
561.7229-1.6694-1.26474.59923.11782.1299-0.47-0.49360.56640.72520.4844-0.34281.7267-1.66110.02530.6148-0.04850.14790.8892-0.08850.5261-26.945618.9854-79.1441
574.29941.5962-3.12633.4649-2.51976.491-0.23220.80050.1013-0.57930.16150.41460.0114-1.52880.10180.6653-0.00050.02810.7366-0.02820.5603-25.875825.7067-94.4369
583.4962-0.68582.32663.747-0.83162.47620.0464-0.2306-0.3394-0.4222-0.0737-0.47710.11250.35480.10750.50860.08160.10860.51590.0120.4539-17.115923.4811-82.9736
596.65821.36660.08787.25785.56797.3385-0.02670.25130.3512-1.09310.4343-0.153-1.30320.9843-0.11810.49780.00230.04120.55220.02960.5563-13.267232.7126-85.2024
609.5010.44032.97077.2789-2.98749.3911-0.22670.20340.4448-0.54810.00060.1488-0.1823-0.83060.1590.60710.0517-0.0090.5966-0.00860.4961-24.960931.3206-84.4796
612.67350.10920.74012.140.72082.8391-0.07580.14820.0428-0.3343-0.0331-0.2496-0.09490.0650.15580.53370.00760.04320.6497-0.03040.6116-14.694722.4288-83.9555
626.85970.834-4.35174.6698-3.15464.52310.21150.7354-0.0527-0.73250.54410.84290.6637-0.5432-0.46960.5114-0.0186-0.04310.71420.00940.3617-23.056318.3284-96.3635
631.04940.6349-0.54793.66070.59982.69690.02370.28730.1886-1.0426-0.0606-0.00410.26650.38890.04330.33090.03430.01440.69990.05480.6275-2.476.3533-86.4735
640.6279-2.22780.50387.7205-1.79934.1435-0.4715-0.45750.02570.45260.4273-0.91890.13870.7602-0.10660.386-0.09580.13210.7818-0.00160.6241.21587.3834-82.7594
652.38090.27252.0276.00341.81276.7736-0.18730.2646-0.2746-0.33410.0914-1.4146-0.4989-0.36750.22340.50440.07520.16630.8523-0.02170.74052.935921.2255-75.1635
665.8141-1.27551.60185.49530.51635.0841-0.1211-0.6622-0.47630.26480.22590.2498-0.0508-0.3625-0.05710.4880.02630.04960.6430.07660.5822-9.88429.4346-76.0393
675.7681-0.6413-0.40184.3525-1.00866.29970.2576-0.6558-0.65860.45570.3218-0.8319-0.17250.5758-0.65390.4934-0.01880.07490.7486-0.09880.45881.12098.4578-78.3554
688.3581-2.33871.40285.42560.38888.80870.2279-1.00210.17561.21820.16881.40010.6783-0.3468-0.4630.4638-0.03090.07060.82450.15320.818-12.2769-2.8201-79.4068
694.75442.90381.77495.28123.29272.56220.1255-0.4765-0.12160.47720.20530.16970.22810.4756-0.30920.50680.06470.09990.7598-0.02330.4609-7.374212.363-83.5746
701.0551-1.0085-0.52645.70094.65054.2060.4661-0.3474-0.1402-0.21360.1004-1.267-0.493-0.4478-0.54630.55430.1270.05890.75780.04920.742-4.411820.225-84.1174
710.9186-2.04682.0324.7775-4.81994.8640.00650.0417-0.0476-1.44820.40710.3322-0.1003-0.8207-0.57040.5220.06730.02960.6923-0.08530.7593-10.1261-3.6369-89.5872
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 336 through 376 )B336 - 376
2X-RAY DIFFRACTION2chain 'B' and (resid 377 through 434 )B377 - 434
3X-RAY DIFFRACTION3chain 'B' and (resid 435 through 458 )B435 - 458
4X-RAY DIFFRACTION4chain 'B' and (resid 459 through 544 )B459 - 544
5X-RAY DIFFRACTION5chain 'I' and (resid 1 through 17 )I1 - 17
6X-RAY DIFFRACTION6chain 'I' and (resid 18 through 60 )I18 - 60
7X-RAY DIFFRACTION7chain 'I' and (resid 61 through 83 )I61 - 83
8X-RAY DIFFRACTION8chain 'I' and (resid 84 through 102 )I84 - 102
9X-RAY DIFFRACTION9chain 'I' and (resid 103 through 111 )I103 - 111
10X-RAY DIFFRACTION10chain 'I' and (resid 112 through 122 )I112 - 122
11X-RAY DIFFRACTION11chain 'J' and (resid 0 through 7 )J0 - 7
12X-RAY DIFFRACTION12chain 'J' and (resid 8 through 25 )J8 - 25
13X-RAY DIFFRACTION13chain 'J' and (resid 26 through 71 )J26 - 71
14X-RAY DIFFRACTION14chain 'J' and (resid 72 through 105 )J72 - 105
15X-RAY DIFFRACTION15chain 'J' and (resid 106 through 111 )J106 - 111
16X-RAY DIFFRACTION16chain 'E' and (resid 0 through 7 )E0 - 7
17X-RAY DIFFRACTION17chain 'E' and (resid 8 through 16 )E8 - 16
18X-RAY DIFFRACTION18chain 'E' and (resid 17 through 111 )E17 - 111
19X-RAY DIFFRACTION19chain 'E' and (resid 112 through 122 )E112 - 122
20X-RAY DIFFRACTION20chain 'F' and (resid -1 through 7 )F-1 - 7
21X-RAY DIFFRACTION21chain 'F' and (resid 8 through 25 )F8 - 25
22X-RAY DIFFRACTION22chain 'F' and (resid 26 through 52 )F26 - 52
23X-RAY DIFFRACTION23chain 'F' and (resid 53 through 65 )F53 - 65
24X-RAY DIFFRACTION24chain 'F' and (resid 66 through 88 )F66 - 88
25X-RAY DIFFRACTION25chain 'F' and (resid 89 through 106 )F89 - 106
26X-RAY DIFFRACTION26chain 'F' and (resid 107 through 112 )F107 - 112
27X-RAY DIFFRACTION27chain 'G' and (resid 336 through 370 )G336 - 370
28X-RAY DIFFRACTION28chain 'G' and (resid 371 through 443 )G371 - 443
29X-RAY DIFFRACTION29chain 'G' and (resid 444 through 544 )G444 - 544
30X-RAY DIFFRACTION30chain 'H' and (resid 336 through 349 )H336 - 349
31X-RAY DIFFRACTION31chain 'H' and (resid 350 through 370 )H350 - 370
32X-RAY DIFFRACTION32chain 'H' and (resid 371 through 384 )H371 - 384
33X-RAY DIFFRACTION33chain 'H' and (resid 385 through 396 )H385 - 396
34X-RAY DIFFRACTION34chain 'H' and (resid 397 through 443 )H397 - 443
35X-RAY DIFFRACTION35chain 'H' and (resid 444 through 458 )H444 - 458
36X-RAY DIFFRACTION36chain 'H' and (resid 459 through 527 )H459 - 527
37X-RAY DIFFRACTION37chain 'H' and (resid 528 through 544 )H528 - 544
38X-RAY DIFFRACTION38chain 'A' and (resid 336 through 376 )A336 - 376
39X-RAY DIFFRACTION39chain 'A' and (resid 377 through 434 )A377 - 434
40X-RAY DIFFRACTION40chain 'A' and (resid 435 through 458 )A435 - 458
41X-RAY DIFFRACTION41chain 'A' and (resid 459 through 544 )A459 - 544
42X-RAY DIFFRACTION42chain 'C' and (resid 1 through 17 )C1 - 17
43X-RAY DIFFRACTION43chain 'C' and (resid 18 through 64 )C18 - 64
44X-RAY DIFFRACTION44chain 'C' and (resid 65 through 73 )C65 - 73
45X-RAY DIFFRACTION45chain 'C' and (resid 74 through 91 )C74 - 91
46X-RAY DIFFRACTION46chain 'C' and (resid 92 through 121 )C92 - 121
47X-RAY DIFFRACTION47chain 'D' and (resid -1 through 7 )D-1 - 7
48X-RAY DIFFRACTION48chain 'D' and (resid 8 through 18 )D8 - 18
49X-RAY DIFFRACTION49chain 'D' and (resid 19 through 25 )D19 - 25
50X-RAY DIFFRACTION50chain 'D' and (resid 26 through 42 )D26 - 42
51X-RAY DIFFRACTION51chain 'D' and (resid 43 through 52 )D43 - 52
52X-RAY DIFFRACTION52chain 'D' and (resid 53 through 71 )D53 - 71
53X-RAY DIFFRACTION53chain 'D' and (resid 72 through 94 )D72 - 94
54X-RAY DIFFRACTION54chain 'D' and (resid 95 through 106 )D95 - 106
55X-RAY DIFFRACTION55chain 'D' and (resid 107 through 112 )D107 - 112
56X-RAY DIFFRACTION56chain 'K' and (resid 1 through 7 )K1 - 7
57X-RAY DIFFRACTION57chain 'K' and (resid 8 through 25 )K8 - 25
58X-RAY DIFFRACTION58chain 'K' and (resid 26 through 52 )K26 - 52
59X-RAY DIFFRACTION59chain 'K' and (resid 53 through 67 )K53 - 67
60X-RAY DIFFRACTION60chain 'K' and (resid 68 through 83 )K68 - 83
61X-RAY DIFFRACTION61chain 'K' and (resid 84 through 111 )K84 - 111
62X-RAY DIFFRACTION62chain 'K' and (resid 112 through 121 )K112 - 121
63X-RAY DIFFRACTION63chain 'L' and (resid -1 through 18 )L-1 - 18
64X-RAY DIFFRACTION64chain 'L' and (resid 19 through 25 )L19 - 25
65X-RAY DIFFRACTION65chain 'L' and (resid 26 through 36 )L26 - 36
66X-RAY DIFFRACTION66chain 'L' and (resid 37 through 71 )L37 - 71
67X-RAY DIFFRACTION67chain 'L' and (resid 72 through 79 )L72 - 79
68X-RAY DIFFRACTION68chain 'L' and (resid 80 through 88 )L80 - 88
69X-RAY DIFFRACTION69chain 'L' and (resid 89 through 94 )L89 - 94
70X-RAY DIFFRACTION70chain 'L' and (resid 95 through 106 )L95 - 106
71X-RAY DIFFRACTION71chain 'L' and (resid 107 through 112 )L107 - 112

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万見について

-
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