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- PDB-9i1q: HER3 receptor in complex with the Fab fragment of TK-hu A3 monocl... -

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基本情報

登録情報
データベース: PDB / ID: 9i1q
タイトルHER3 receptor in complex with the Fab fragment of TK-hu A3 monoclonal antibody
要素
  • Receptor tyrosine-protein kinase erbB-3
  • heavy chain hA3-Fab
  • light chain hA3-Fab
キーワードANTITUMOR PROTEIN / growth factor receptor / monoclonal antibody / cancer / complex
機能・相同性
機能・相同性情報


neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / negative regulation of cell adhesion / ErbB-3 class receptor binding / negative regulation of motor neuron apoptotic process / motor neuron apoptotic process / growth factor binding / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Signaling by ERBB4 / PI3K events in ERBB2 signaling / lateral plasma membrane / negative regulation of signal transduction / Schwann cell development / Signaling by ERBB2 / extrinsic apoptotic signaling pathway in absence of ligand / myelination / SHC1 events in ERBB2 signaling / cell surface receptor protein tyrosine kinase signaling pathway / Downregulation of ERBB2:ERBB3 signaling / basal plasma membrane / positive regulation of epithelial cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / regulation of cell population proliferation / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / neuron apoptotic process / basolateral plasma membrane / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / receptor complex / positive regulation of MAPK cascade / apical plasma membrane / protein heterodimerization activity / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane
類似検索 - 分子機能
Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats ...Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
THIOCYANATE ION / Receptor tyrosine-protein kinase erbB-3
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Bulfaro, G. / Savino, C. / Costanzo, A. / Fata, F. / Vallone, B. / Montemiglio, L.C.
資金援助 イタリア, 1件
組織認可番号国
Regione Lazio (Italy) イタリア
引用ジャーナル: Antibodies / 年: 2025
タイトル: Novel Humanized Anti-HER3 Antibodies: Structural Characterization and Therapeutic Activity.
著者: Muzi, A. / Arriga, R. / Bulfaro, G. / Fata, F. / Costanzo, A. / Chiarini, V. / Cappelletti, M. / Ferrara, F.F. / Bucci, F. / Montemiglio, L.C. / Savino, C. / Marra, E. / Ciliberto, G. / ...著者: Muzi, A. / Arriga, R. / Bulfaro, G. / Fata, F. / Costanzo, A. / Chiarini, V. / Cappelletti, M. / Ferrara, F.F. / Bucci, F. / Montemiglio, L.C. / Savino, C. / Marra, E. / Ciliberto, G. / Aurisicchio, L. / Vallone, B. / Roscilli, G.
履歴
登録2025年1月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年10月15日Provider: repository / タイプ: Initial release
改定 1.12025年11月5日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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: Receptor tyrosine-protein kinase erbB-3
B: Receptor tyrosine-protein kinase erbB-3
C: Receptor tyrosine-protein kinase erbB-3
D: Receptor tyrosine-protein kinase erbB-3
E: light chain hA3-Fab
F: light chain hA3-Fab
G: light chain hA3-Fab
H: light chain hA3-Fab
I: heavy chain hA3-Fab
J: heavy chain hA3-Fab
K: heavy chain hA3-Fab
L: heavy chain hA3-Fab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)480,99550
ポリマ－472,39312
非ポリマー8,60238
水1,892105
1
A: Receptor tyrosine-protein kinase erbB-3
C: Receptor tyrosine-protein kinase erbB-3
ヘテロ分子

E: light chain hA3-Fab
J: heavy chain hA3-Fab


分子量 (理論値)分子数
合計 (水以外)192,13519
ポリマ－187,8844
非ポリマー4,25115
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area15490 Å2
ΔGint5 kcal/mol
Surface area75900 Å2
手法PISA
2
D: Receptor tyrosine-protein kinase erbB-3
ヘテロ分子

B: Receptor tyrosine-protein kinase erbB-3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)143,63320
ポリマ－139,5722
非ポリマー4,06118
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area9010 Å2
ΔGint33 kcal/mol
Surface area60670 Å2
手法PISA
3
F: light chain hA3-Fab
I: heavy chain hA3-Fab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,4284
ポリマ－48,3122
非ポリマー1162
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-32 kcal/mol
Surface area19700 Å2
手法PISA
4
G: light chain hA3-Fab
K: heavy chain hA3-Fab


分子量 (理論値)分子数
合計 (水以外)48,3122
ポリマ－48,3122
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-28 kcal/mol
Surface area19780 Å2
手法PISA
5
H: light chain hA3-Fab
L: heavy chain hA3-Fab
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,4865
ポリマ－48,3122
非ポリマー1743
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-28 kcal/mol
Surface area20110 Å2
手法PISA
単位格子
Length a, b, c (Å)98.030, 98.810, 270.380
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Receptor tyrosine-protein kinase erbB-3 / Proto-oncogene-like protein c-ErbB-3 / Tyrosine kinase-type cell surface receptor HER3


分子量: 69786.086 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: Extracellular domain / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ERBB3, HER3 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P21860, receptor protein-tyrosine kinase

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抗体 , 2種, 8分子 EFGHIJKL

#2: 抗体
light chain hA3-Fab


分子量: 24244.043 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: Cricetulus griseus (モンゴルキヌゲネズミ)
#3: 抗体
heavy chain hA3-Fab


分子量: 24068.160 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: Cricetulus griseus (モンゴルキヌゲネズミ)

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糖 , 4種, 29分子

#4: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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: 586.542 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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 多糖 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 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
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 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
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 糖...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 24 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 2種, 114分子

#8: 化合物
ChemComp-SCN / THIOCYANATE ION


分子量: 58.082 Da / 分子数: 9 / 由来タイプ: 合成 / 式: CNS
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 105 / 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: 2.78 Å3/Da / 溶媒含有率: 55.81 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.2 M KSCN, 0.1 M BIS-TRIS propane pH 8.5, 14% PEG 3350

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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: ELETTRA / ビームライン: 11.2C / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2023年11月29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: 2.55→96.76 Å / Num. obs: 82868 / % possible obs: 87.6 % / 冗長度: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.3
反射 シェル解像度: 2.551→2.94 Å / 冗長度: 6.4 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4143 / CC1/2: 0.649 / % possible all: 63.7

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487: ???)精密化
autoPROCデータ削減
autoPROC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: 2.8→49 Å / SU ML: 0.36 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 30.09 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2634 4076 5.01 %
Rwork0.2091 --
obs0.2118 81346 64.61 %
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
精密化ステップサイクル: LAST / 解像度: 2.8→49 Å
タンパク質核酸リガンド溶媒全体
原子数31206 0 547 105 31858
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00732521
X-RAY DIFFRACTIONf_angle_d1.1344194
X-RAY DIFFRACTIONf_dihedral_angle_d6.5274601
X-RAY DIFFRACTIONf_chiral_restr0.0734983
X-RAY DIFFRACTIONf_plane_restr0.0095704
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.4611290.4179515X-RAY DIFFRACTION13
2.83-2.870.7386240.4072576X-RAY DIFFRACTION14
2.87-2.90.5061410.3616661X-RAY DIFFRACTION16
2.9-2.940.338460.3374775X-RAY DIFFRACTION19
2.94-2.980.6239460.3479920X-RAY DIFFRACTION22
2.98-3.020.3746460.31931105X-RAY DIFFRACTION27
3.03-3.070.4048710.32391262X-RAY DIFFRACTION31
3.07-3.120.4476870.30811485X-RAY DIFFRACTION37
3.12-3.170.33271080.29141646X-RAY DIFFRACTION40
3.17-3.220.3261810.28861867X-RAY DIFFRACTION46
3.22-3.280.29121290.28562166X-RAY DIFFRACTION53
3.28-3.350.35241060.28542379X-RAY DIFFRACTION58
3.35-3.410.36371460.27572497X-RAY DIFFRACTION61
3.43-3.490.33991130.27041956X-RAY DIFFRACTION66
3.49-3.570.33621820.26973091X-RAY DIFFRACTION76
3.57-3.660.341520.25782298X-RAY DIFFRACTION56
3.66-3.760.33862440.24493804X-RAY DIFFRACTION95
3.76-3.860.28972000.22753750X-RAY DIFFRACTION96
3.89-3.990.30911480.22173129X-RAY DIFFRACTION96
3.99-4.140.26522310.1994089X-RAY DIFFRACTION99
4.14-4.30.25662070.18024115X-RAY DIFFRACTION100
4.3-4.50.22311880.16474150X-RAY DIFFRACTION99
4.5-4.730.21371930.1544105X-RAY DIFFRACTION99
4.73-5.030.20832210.15514087X-RAY DIFFRACTION99
5.03-5.420.2162150.16824147X-RAY DIFFRACTION100
5.42-5.960.22182100.19174112X-RAY DIFFRACTION99
5.96-6.820.24141910.20884177X-RAY DIFFRACTION99
6.82-8.590.23451990.21154191X-RAY DIFFRACTION99
8.59-490.2082220.19194215X-RAY DIFFRACTION98
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)
11.2349-0.35831.22421.9604-0.17971.235-0.11470.1913-0.00630.41040.1314-0.62640.27370.8996-0.43180.5055-0.0875-0.21032.21280.09780.535344.7914-18.8631106.213
20.0748-0.1921-0.06410.38410.08170.00520.1215-0.0946-0.1271-0.0179-0.1839-0.2113-0.38160.97960.03630.4442-0.28070.05611.84380.05870.441534.0835-16.664394.2604
30.77090.6248-0.53210.9377-1.09874.9177-0.0796-0.09320.038-0.03560.1358-0.04490.0515-0.0426-0.01120.22850.12440.10190.1975-0.00270.1522-11.8249-26.0664108.4143
41.73630.2018-0.31372.0107-0.21742.25370.23420.5051-0.3322-0.58840.12270.19280.85750.0681-0.00180.44070.1048-0.06070.31930.02910.14610.9086-47.86820.8422
50.6543-0.0787-0.18140.94240.17230.9388-0.27430.1744-0.1636-0.5260.1413-0.5885-0.24850.3545-0.05990.3166-0.11060.21350.4996-0.02020.351628.9141-33.616726.2184
60.9316-0.0621-1.6880.0354-0.09883.911-0.2053-0.0849-0.0614-0.0467-0.0596-0.05540.53630.14460.2120.51960.0440.3080.55590.11790.637955.673-14.11731.1029
70.4515-0.2626-0.82250.8782-0.09161.9558-0.0915-0.15060.08860.20370.22290.65670.1044-0.94570.06890.52120.10860.32150.92580.08830.74423.3035-10.409740.7998
82.67751.9045-0.04724.8228-0.70624.0785-0.0275-0.5396-0.54630.4663-0.6483-0.18491.0790.39710.52980.64520.03820.16410.66110.09430.3608-22.6247-39.7042150.0763
91.68340.3214-2.07870.0259-0.3632.35070.1042-0.58510.00110.1367-0.0354-0.1556-0.44161.3242-0.06010.5667-0.18660.03681.39140.17750.52230.3155-24.2168156.5723
101.5191-0.9693-1.0451.55330.31012.5549-0.28550.41910.35750.26670.0323-0.1566-0.2130.61970.07590.4529-0.2507-0.09221.39030.06840.478636.5265-9.6124127.9632
110.00220.0042-0.0085-0.0035-0.00160.0065-0.2254-0.69540.36330.12680.32440.0309-0.05980.61360.02131.47390.0463-0.25121.893-0.27291.063226.27642.8013159.6052
121.30760.13840.63191.1342-0.90543.2536-0.2819-0.6507-0.438-0.12120.00890.13670.45860.4160.16320.32470.25740.14650.81710.2970.631630.705925.687136.8282
131.84890.58410.22180.42710.14520.2260.0701-0.0138-0.2717-0.03480.23940.1928-0.0941-0.91130.02750.18250.07410.21760.77830.39830.541759.784819.618848.9865
144.438-0.7584-4.0050.37450.59833.62490.03590.7317-0.1322-0.31040.52920.31070.1985-0.2573-0.45920.4861-0.02030.02021.1504-0.02940.526769.941510.4920.2801
150.1775-0.26070.09850.7620.88922.54930.2860.4674-0.2213-0.15720.1771-0.04510.3877-0.0878-0.23910.4235-0.1060.06770.7912-0.21220.256794.646312.600113.5928
161.65870.571.41791.59710.29541.4282-0.0607-0.04490.38310.23480.13450.9114-0.3115-0.54440.06910.23460.03980.31340.31460.09850.555775.680334.753852.1807
171.1317-0.7222-0.20862.20760.39630.92440.3776-0.3928-0.13460.7321-0.1943-0.43670.7929-0.1581-0.0510.6335-0.0632-0.04810.39030.16550.2178-11.4554-3.054179.0698
181.65960.3272-0.10213.54910.98741.0912-0.116-0.1335-0.03090.0858-0.09150.04380.9274-0.66840.09520.4431-0.1182-0.0410.3054-0.01560.1668-19.67222.376279.891
191.9272-0.04250.74552.86261.68564.54460.1137-0.04620.06980.1284-0.25550.68510.4026-0.67460.37370.3812-0.28660.02860.5663-0.09720.3465-29.473.395879.143
201.5976-0.0987-0.47812.77411.19532.4007-0.106-0.1615-0.07990.0779-0.28480.24050.9754-0.48390.16190.535-0.1889-0.08230.15590.04790.2859-19.1684-3.25475.043
215.9763-1.2064-0.12864.9888-0.62845.37730.54880.011-0.41580.28370.1578-0.4850.37750.8017-0.2010.25640.0585-0.12870.1536-0.09380.3697-7.8934-11.031944.158
221.9716-0.34190.1714.31091.74263.63760.43160.0523-0.38910.6901-0.0909-0.50790.61010.5775-0.41110.5698-0.0833-0.33760.4731-0.02350.4703-9.166-11.541852.423
234.5710.7982-1.06785.11821.22264.0425-0.02450.6248-0.7236-0.23330.3422-1.1420.87290.8493-0.22490.57440.1835-0.03130.5226-0.36270.5303-4.6189-15.655939.9627
241.2332-0.4328-0.1811.92350.04921.19230.02150.03070.08350.42420.0651-0.0319-0.03060.1176-0.01430.21890.07350.06080.0427-0.01230.12063.876642.918957.6655
250.3495-0.1245-0.45660.07130.36432.0898-0.1924-0.098-0.05230.52450.1805-0.04480.19650.2173-0.03310.6244-0.02120.00710.09720.0570.0595-0.671142.424176.6762
260.350.1867-0.39850.4089-0.07110.4674-0.3-0.2586-0.3080.8588-0.07260.09160.5606-0.0803-0.04331.682-0.05870.26450.17120.06910.4531-7.819537.113195.8644
271.84510.9505-1.22411.21990.34282.1343-0.01770.0062-0.3678-0.0329-0.2855-0.40060.56320.68550.31090.29160.30310.14241.03760.18470.340823.046815.271971.3151
281.41271.26980.52455.56380.68764.5095-0.0169-0.07920.22120.9119-0.07960.71120.17540.02510.20180.38730.01970.15860.68760.0540.43138.400915.4753106.3823
293.02620.7277-0.50210.618-0.11310.6704-0.1438-0.5075-0.25980.1004-0.1246-0.18510.01730.02340.1370.3058-0.0751-0.01311.58470.18640.458660.259672.546369.1106
303.93980.44330.43892.0664-1.84262.8569-0.2723-0.5146-0.66-0.0433-0.11760.02560.5460.60120.3540.40370.05380.08941.18860.3710.640650.959168.85962.2342
311.91240.202-1.60410.4914-0.96193.139-0.3809-0.4378-0.7762-0.1097-0.4112-0.23850.97261.00430.51230.38020.25490.14231.16490.19440.71159.935866.807960.7466
323.27911.1215-2.86741.9456-1.06617.62-0.17470.0527-0.1822-0.04090.0341-0.55380.65370.10390.30390.52620.17270.2110.7631-0.01070.945769.801165.176629.7645
330.3578-0.7163-0.68741.43561.39221.368-0.1745-0.08120.246-0.5001-0.4774-0.4040.71090.74570.55290.81930.32940.09040.97630.33781.104272.509763.646836.4099
341.46660.42880.93420.88170.31272.2836-0.5371-0.1067-0.2963-0.5939-0.0904-0.24152.47940.39780.41291.37440.44080.59031.21080.30161.006976.239962.114526.1852
352.59060.123-0.82892.43270.31222.82150.0284-0.16920.35020.33160.06710.0296-0.4155-0.26970.01150.20390.02930.07350.1171-0.03490.1974-5.007864.821163.024
360.57880.2982-0.3191.16020.47462.74530.065-0.1852-0.05790.2437-0.14650.16430.0985-0.43050.02930.30220.06530.11320.1613-0.04610.3073-6.155758.592568.2953
370.2692-0.1088-0.16621.21610.71040.5495-0.0421-0.23880.15890.35950.1717-0.2507-0.03860.1519-0.3451.0668-0.0150.1266-0.0037-0.33570.1607-1.656652.978694.2193
382.8213-0.2870.38521.9227-0.26442.591-0.05590.04270.38610.05330.03120.0015-0.55750.02670.08990.2942-0.01250.05460.11680.03360.362-12.916121.398369.8065
390.4759-0.112-0.50961.08951.16133.61370.10240.25260.11360.0807-0.1376-0.2222-0.092-0.03770.06510.1130.03120.02250.15550.09880.3454-10.983513.981165.7826
401.00340.0285-1.50730.1717-0.25412.5233-0.19051.6281-1.0761-0.5240.5617-0.61890.9697-0.4266-0.36460.4973-0.0737-0.05640.5927-0.22490.6001-13.9711-9.573535.6606
410.1814-0.6367-0.27192.24690.8612.9475-0.06530.3710.5061-0.1023-0.13060.29770.10650.21520.17420.13080.07380.00460.21930.06240.4167-10.96061.745547.7156
422.3389-1.1738-0.05111.6444-1.80655.2447-0.05530.6249-0.1186-0.6685-0.12760.98990.417-0.9222-0.00480.2269-0.0917-0.19540.3849-0.07740.5316-22.5871-4.355239.206
434.48935.13365.83216.64095.59179.40940.05950.71760.2558-0.39210.2740.5484-0.15110.0635-0.28720.34980.1295-0.01370.36760.02320.4776-13.80376.271739.2429
440.51680.18240.40570.24570.17740.9338-0.26070.17820.30010.1356-0.1159-0.3662-0.40510.83470.19070.788-0.3955-0.38141.52270.1660.563435.788235.832782.1836
451.9633-0.25622.77561.89210.78145.4128-0.17680.20630.376-0.0188-0.2418-0.0167-0.35780.38380.29480.4621-0.2866-0.17971.01360.01390.353826.922531.594476.5609
460.2964-0.25150.62380.78250.00121.7201-0.3064-0.13080.45240.2212-0.2598-0.49-0.76551.03460.35680.624-0.3579-0.33381.21680.11310.491329.935235.464378.9159
477.4295-1.70551.32982.9867-2.5475.4148-0.3641-1.7576-1.84741.19310.32390.44550.95220.40070.09231.07120.43370.15241.39170.24210.839417.795813.1925114.0675
485.2527-0.15683.0476.5306-0.5346.2275-0.084-0.4244-0.27060.6022-0.2385-0.7855-0.13621.12290.24680.56370.0763-0.10420.87190.07320.308122.80321.2742104.8002
491.5989-1.67273.19076.1514-3.13776.3805-0.5103-0.078-0.14420.82080.8593-0.1125-0.5871-0.2371-0.31450.6720.1952-0.27051.33140.00690.602925.803126.0091112.1196
508.88744.5903-5.24287.1457-3.11476.30150.53060.02960.45760.00030.3534-0.4894-0.68940.5659-0.61460.2865-0.04390.03110.5681-0.09920.360750.219987.989144.5181
517.16790.2401-1.66792.2531-0.48711.55180.2424-1.04750.9230.06650.0697-0.0283-0.73130.4368-0.29240.2936-0.08640.06630.7814-0.19720.493347.835789.864155.1107
525.0432-0.8891-2.82691.79260.41516.7390.4089-0.3762-0.1127-0.09290.0191-0.3207-0.33-0.064-0.33970.0988-0.0403-0.04210.57830.04350.347350.992282.046451.0851
532.2046-1.45850.22962.37212.27124.1886-0.79910.3616-2.2139-0.71210.3745-1.03791.73520.05510.41711.2812-0.13570.76910.9858-0.32961.936962.728160.197923.7923
544.25621.37350.29130.9-0.16562.7501-0.60740.0644-0.9276-0.0162-0.42770.44240.7931-0.16380.12290.4394-0.06450.39850.8116-0.14010.817759.728772.25133.2178
552.72890.218-1.02220.2805-1.22785.3866-0.57250.6963-0.9784-0.533-0.35680.71251.1402-1.58530.89870.6268-0.25640.20481.4224-0.52031.212154.684268.565527.3589
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 318 )
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 611 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 193 )
5X-RAY DIFFRACTION5chain 'B' and (resid 194 through 323 )
6X-RAY DIFFRACTION6chain 'B' and (resid 324 through 567 )
7X-RAY DIFFRACTION7chain 'B' and (resid 568 through 613 )
8X-RAY DIFFRACTION8chain 'C' and (resid 8 through 178 )
9X-RAY DIFFRACTION9chain 'C' and (resid 179 through 332 )
10X-RAY DIFFRACTION10chain 'C' and (resid 333 through 497 )
11X-RAY DIFFRACTION11chain 'C' and (resid 498 through 586 )
12X-RAY DIFFRACTION12chain 'D' and (resid 7 through 221 )
13X-RAY DIFFRACTION13chain 'D' and (resid 222 through 260 )
14X-RAY DIFFRACTION14chain 'D' and (resid 261 through 349 )
15X-RAY DIFFRACTION15chain 'D' and (resid 350 through 542 )
16X-RAY DIFFRACTION16chain 'D' and (resid 543 through 611 )
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 13 )
18X-RAY DIFFRACTION18chain 'E' and (resid 14 through 53 )
19X-RAY DIFFRACTION19chain 'E' and (resid 54 through 66 )
20X-RAY DIFFRACTION20chain 'E' and (resid 67 through 119 )
21X-RAY DIFFRACTION21chain 'E' and (resid 120 through 156 )
22X-RAY DIFFRACTION22chain 'E' and (resid 157 through 180 )
23X-RAY DIFFRACTION23chain 'E' and (resid 181 through 220 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 80 )
25X-RAY DIFFRACTION25chain 'F' and (resid 81 through 134 )
26X-RAY DIFFRACTION26chain 'F' and (resid 135 through 220 )
27X-RAY DIFFRACTION27chain 'G' and (resid 1 through 112 )
28X-RAY DIFFRACTION28chain 'G' and (resid 113 through 220 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 37 )
30X-RAY DIFFRACTION30chain 'H' and (resid 38 through 66 )
31X-RAY DIFFRACTION31chain 'H' and (resid 67 through 121 )
32X-RAY DIFFRACTION32chain 'H' and (resid 122 through 151 )
33X-RAY DIFFRACTION33chain 'H' and (resid 152 through 180 )
34X-RAY DIFFRACTION34chain 'H' and (resid 181 through 218 )
35X-RAY DIFFRACTION35chain 'I' and (resid 221 through 304 )
36X-RAY DIFFRACTION36chain 'I' and (resid 305 through 346 )
37X-RAY DIFFRACTION37chain 'I' and (resid 347 through 443 )
38X-RAY DIFFRACTION38chain 'J' and (resid 221 through 304 )
39X-RAY DIFFRACTION39chain 'J' and (resid 305 through 347 )
40X-RAY DIFFRACTION40chain 'J' and (resid 348 through 361 )
41X-RAY DIFFRACTION41chain 'J' and (resid 362 through 404 )
42X-RAY DIFFRACTION42chain 'J' and (resid 405 through 421 )
43X-RAY DIFFRACTION43chain 'J' and (resid 422 through 443 )
44X-RAY DIFFRACTION44chain 'K' and (resid 221 through 254 )
45X-RAY DIFFRACTION45chain 'K' and (resid 255 through 274 )
46X-RAY DIFFRACTION46chain 'K' and (resid 275 through 347 )
47X-RAY DIFFRACTION47chain 'K' and (resid 348 through 361 )
48X-RAY DIFFRACTION48chain 'K' and (resid 362 through 427 )
49X-RAY DIFFRACTION49chain 'K' and (resid 428 through 443 )
50X-RAY DIFFRACTION50chain 'L' and (resid 221 through 237 )
51X-RAY DIFFRACTION51chain 'L' and (resid 238 through 312 )
52X-RAY DIFFRACTION52chain 'L' and (resid 313 through 346 )
53X-RAY DIFFRACTION53chain 'L' and (resid 347 through 362 )
54X-RAY DIFFRACTION54chain 'L' and (resid 363 through 402 )
55X-RAY DIFFRACTION55chain 'L' and (resid 403 through 439 )

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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