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- PDB-9z9f: Structure of FabS1CE2_ER-2a in complex with the extracellular reg... -

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基本情報

登録情報
データベース: PDB / ID: 9z9f
タイトルStructure of FabS1CE2_ER-2a in complex with the extracellular region of EGFR
要素
  • Epidermal growth factor receptor
  • heavy chain
  • light chain
キーワードSIGNALING PROTEIN / epidermal growth factor receptor / high-affinity antibody / dimerization arm / inhibition
機能・相同性
機能・相同性情報


multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor activity / epidermal growth factor binding / response to UV-A / regulation of peptidyl-tyrosine phosphorylation ...multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor activity / epidermal growth factor binding / response to UV-A / regulation of peptidyl-tyrosine phosphorylation / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / PTK6 promotes HIF1A stabilization / Signaling by EGFR / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / ERBB2 Regulates Cell Motility / Developmental Lineage of Mammary Gland Myoepithelial Cells / protein insertion into membrane / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / GAB1 signalosome / protein tyrosine kinase activator activity / ossification / positive regulation of G1/S transition of mitotic cell cycle / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / positive regulation of epithelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / positive regulation of fibroblast proliferation / cellular response to amino acid stimulus / SHC1 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / positive regulation of DNA replication / basal plasma membrane / positive regulation of DNA repair / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signal transduction by L1 / cellular response to estradiol stimulus / positive regulation of protein localization to plasma membrane / negative regulation of protein catabolic process / clathrin-coated endocytic vesicle membrane / cell-cell adhesion / NOTCH3 Activation and Transmission of Signal to the Nucleus / Signaling by ERBB2 TMD/JMD mutants / EGFR downregulation / Constitutive Signaling by EGFRvIII / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of miRNA transcription / positive regulation of protein phosphorylation / cell junction / epidermal growth factor receptor signaling pathway / kinase binding / ruffle membrane / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / HCMV Early Events / positive regulation of canonical Wnt signaling pathway / actin filament binding / neuron differentiation / transmembrane signaling receptor activity / PIP3 activates AKT signaling / positive regulation of cell growth / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / nuclear membrane / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / virus receptor activity / RAF/MAP kinase cascade / protein tyrosine kinase activity / double-stranded DNA binding / early endosome membrane / protein phosphatase binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / basolateral plasma membrane / positive regulation of MAPK cascade / learning or memory / positive regulation of ERK1 and ERK2 cascade / signaling receptor complex / cell surface receptor signaling pathway / Extra-nuclear estrogen signaling / endosome / endosome membrane / positive regulation of cell migration / cadherin binding / membrane raft
類似検索 - 分子機能
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / 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 ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / 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 / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / Epidermal growth factor receptor
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: 3.06 Å
データ登録者Mallette, E. / Singer, A.U. / Bruce, H.A. / Blazer, L.L. / Adams, J.J. / Suits, M.D.L. / Sidhu, S.S.
資金援助 カナダ, 2件
組織認可番号国
Canadian Institutes of Health Research (CIHR)MOP-93725 カナダ
Canadian Institutes of Health Research (CIHR)MOP-136944 カナダ
引用ジャーナル: Protein Sci. / 年: 2026
タイトル: Dual targeting of inhibitory EGFR epitopes with synthetic antibodies in therapeutic-resistant cancers.
著者: Adams, J.J. / Mallette, E. / London, M. / Liang, R.J. / van Dyk, D. / Pavlovic, Z. / Pot, I. / Geyer, C.R. / Bruce, H.A. / Blazer, L.L. / Hokanson, C.A. / Suits, M.D.L. / Singer, A.U. / Sidhu, S.S.
履歴
登録2025年11月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02026年6月3日Provider: repository / タイプ: Initial release

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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: heavy chain
B: light chain
C: heavy chain
D: light chain
G: Epidermal growth factor receptor
K: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)238,31430
ポリマ－235,6926
非ポリマー2,62324
水18010
1
A: heavy chain
B: light chain
K: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,63718
ポリマ－117,8463
非ポリマー1,79115
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: heavy chain
D: light chain
G: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,67712
ポリマ－117,8463
非ポリマー8319
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)66.533, 113.846, 118.767
Angle α, β, γ (deg.)114.160, 95.240, 104.880
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細 (eV)
d_1ens_1(chain "A" and (resid 2 through 42 or (resid 43...
d_2ens_1(chain "C" and (resid 2 through 104 or (resid 105...
d_1ens_2(chain "B" and (resid 2 through 99 or resid 101...
d_2ens_2(chain "D" and (resid 2 through 99 or resid 101 through 212))
d_1ens_3(chain "G" and (resid 3 through 292 or (resid 293...
d_2ens_3(chain "K" and ((resid 3 and (name N or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALHISHISAA2 - 1052 - 105
d_12ens_1SERSERLEULEUAA107 - 194107 - 194
d_13ens_1SERSERCYSCYSAA196 - 232196 - 232
d_21ens_1VALVALHISHISCC2 - 1052 - 105
d_22ens_1SERSERLEULEUCC107 - 194107 - 194
d_23ens_1SERSERCYSCYSCC196 - 232196 - 232
d_11ens_2ILEILEGLYGLYBB2 - 992 - 99
d_12ens_2GLYGLYCYSCYSBB101 - 212101 - 212
d_21ens_2ILEILEGLYGLYDD2 - 992 - 99
d_22ens_2GLYGLYCYSCYSDD101 - 212101 - 212
d_11ens_3GLUGLUGLYGLYGE3 - 4043 - 404
d_12ens_3THRTHRPROPROGE406 - 613406 - 613
d_13ens_3NAGNAGNAGNAGEG1
d_14ens_3NAGNAGNAGNAGEG2
d_15ens_3NAGNAGNAGNAGGW701
d_21ens_3GLUGLUGLNGLNKF3 - 3843 - 384
d_22ens_3TRPTRPGLYGLYKF386 - 404386 - 404
d_23ens_3THRTHRHISHISKF406 - 409406 - 409
d_24ens_3PHEPHEALAALAKF412 - 477412 - 477
d_25ens_3GLNGLNARGARGKF480 - 503480 - 503
d_26ens_3SERSERGLYGLYKF506 - 520506 - 520
d_27ens_3PROPROMETMETKF522 - 543522 - 543
d_28ens_3ILEILEPROPROKF545 - 572545 - 572
d_29ens_3GLYGLYHISHISKF574 - 591574 - 591
d_210ens_3CYSCYSPROPROKF593 - 613593 - 613
d_211ens_3NAGNAGNAGNAGKZ702
d_212ens_3NAGNAGNAGNAGKAA703
d_213ens_3NAGNAGNAGNAGKBA704

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.999047290226, -0.00118419046823, 0.0436246442348), (0.00270573735285, -0.99602784253, -0.0890012128637), (0.0435567546662, 0.0890344573678, -0.995075712961)2.54951666502, -64.9798562599, 62.546325105
2given(0.999952751964, 0.00902580842807, -0.00360951835492), (0.00873674298006, -0.997266933141, -0.0733643877197), (-0.00426182620893, 0.0733293859623, -0.997298670405)4.83950659771, -65.9148468332, 61.1532126303
3given(0.99990648431, -0.0132780262819, -0.00327363004365), (-0.0114413837891, -0.943351325617, 0.331598207465), (-0.00749115295501, -0.331529742972, -0.943415026461)-5.24822332502, -70.2469016309, 48.2492133513

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要素

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タンパク質 , 1種, 2分子 GK

#3: タンパク質 Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


分子量: 69133.773 Da / 分子数: 2 / 変異: residue 25-645 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EGFR, ERBB, ERBB1, HER1 / プラスミド: PSDCSTA
詳細 (発現宿主): N-terminal trypsinogen-2 signal peptide and a C-terminal thrombin cleavage site followed by a hexahistidine tag
細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P00533, receptor protein-tyrosine kinase

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抗体 , 2種, 4分子 ACBD

#1: 抗体 heavy chain


分子量: 25513.482 Da / 分子数: 2 / 変異: K133Q and E164G / 由来タイプ: 組換発現
詳細: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND SELECTED BY PHAGE DISPLAY.
由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PSDCSTA / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)
#2: 抗体 light chain


分子量: 23198.660 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND SELECTED BY PHAGE DISPLAY.
由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PSDCSTA / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)

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糖 , 2種, 8分子

#4: 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: 1 / 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
#9: 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: 7 / 由来タイプ: 合成 / 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 , 5種, 26分子

#5: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER


分子量: 106.120 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H10O3
#6: 化合物
ChemComp-NA / SODIUM ION


分子量: 22.990 Da / 分子数: 9 / 由来タイプ: 合成 / 式: Na
#7: 化合物 ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Cl
#8: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


分子量: 62.068 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H6O2
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 10 / 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: 3.28 Å3/Da / 溶媒含有率: 62.51 %
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
詳細: 0.1 M ammonium citrate, 0.1 M bis-tris propane pH 6.5, cryoprotected with this buffer plus 30% ethylene glycol
PH範囲: 6.5 / Temp details: room temperature

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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: NSLS-II / ビームライン: 17-ID-1 / 波長: 0.919716 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2025年7月18日 / 詳細: mirrors
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: 0.919716 Å / 相対比: 1
反射解像度: 3.06→34.66 Å / Num. obs: 55114 / % possible obs: 99.2 % / 冗長度: 3.6 % / Biso Wilson estimate: 43.7 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.148 / Rrim(I) all: 0.284 / Net I/σ(I): 4.4
反射 シェル解像度: 3.06→3.25 Å / 冗長度: 3.7 % / Rmerge(I) obs: 1.468 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 8023 / CC1/2: 0.409 / Rpim(I) all: 0.891 / Rrim(I) all: 1.721 / % possible all: 98.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
PHENIX1.20.1_4487精密化
autoPROCデータ削減
Aimless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: 3.06→34.42 Å / SU ML: 0.4002 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 24.6901
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2487 2483 4.81 %
Rwork0.2127 49149 -
obs0.2144 51632 91.4 %
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: 64.34 Å2
精密化ステップサイクル: LAST / 解像度: 3.06→34.42 Å
タンパク質核酸リガンド溶媒全体
原子数15593 0 160 10 15763
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003316142
X-RAY DIFFRACTIONf_angle_d0.677421969
X-RAY DIFFRACTIONf_chiral_restr0.04932493
X-RAY DIFFRACTIONf_plane_restr0.00662864
X-RAY DIFFRACTIONf_dihedral_angle_d16.72455686
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.37719664665
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.966271527388
ens_3d_2EGX-RAY DIFFRACTIONTorsion NCS4.11028494091
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.120.3602670.28341485X-RAY DIFFRACTION49.63
3.12-3.180.3047930.27041800X-RAY DIFFRACTION60.08
3.18-3.250.3136990.27072004X-RAY DIFFRACTION67.49
3.25-3.330.29381250.27132511X-RAY DIFFRACTION82.38
3.33-3.410.32451720.26712747X-RAY DIFFRACTION94.37
3.41-3.50.30041440.24912980X-RAY DIFFRACTION98.77
3.5-3.610.29721620.24932914X-RAY DIFFRACTION99.1
3.61-3.720.28391510.2423012X-RAY DIFFRACTION99.22
3.72-3.850.25321440.22692936X-RAY DIFFRACTION99.16
3.85-4.010.26141570.21342941X-RAY DIFFRACTION99.23
4.01-4.190.23751550.20632984X-RAY DIFFRACTION99.27
4.19-4.410.23081630.18762955X-RAY DIFFRACTION99.36
4.41-4.690.20611770.16942926X-RAY DIFFRACTION99.36
4.69-5.050.19681380.17283019X-RAY DIFFRACTION99.43
5.05-5.550.191220.18552985X-RAY DIFFRACTION99.55
5.55-6.350.2581330.20972971X-RAY DIFFRACTION99.61
6.35-7.990.25731350.21482997X-RAY DIFFRACTION99.75
7.99-34.420.19321460.17352982X-RAY DIFFRACTION99.49
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)
11.541891048-0.3900929457950.07463380728983.165535099070.8139510121040.602424941671-0.06429356189290.00960746697641-0.3608355451440.164022054509-0.0334888882450.516204982959-0.230896894856-0.2516585587630.07413475100330.298574240970.131171121267-0.002523463052430.03986655451230.03884285663040.42076048241-19.0247253304-51.914413166135.3911438537
22.83898663904-0.396429281774-3.132878459187.89133418978-1.234532638643.811008067590.0146256488077-0.768414525517-0.1197680554051.885640170420.0892759916714-0.958504927118-0.35981668080.549204960732-0.03948421154870.5305354550690.157538078989-0.1429664162080.0175106719710.1347420817580.506675372512-5.96499029832-45.700649176544.8608192867
31.032190170090.50864928798-0.2173063814270.6589036113660.1562152996841.84311755169-0.121980945389-0.1201899913690.423588067795-0.137933457567-0.00391650000507-0.1313647105540.357567690756-0.1306925863450.0722675510008-0.1629953970640.166747326481-0.1785703310570.0534497616330.01196207000140.485451676879-7.73145698195-83.263397228630.2434434613
44.79325073174-2.03480621072-0.5734827200283.37115025520.3270794630162.53787000195-0.781796591583-0.160734923856-0.3770162388010.2906526449130.2402002579310.3635362896710.3410038875580.2652912443850.2532191399810.03883297965950.02595810120160.1007640792280.156663021005-0.009437832288350.548594214871-10.353627199-91.366793317535.3226053326
51.39607995033-0.829893683053-0.0931790310172.340399523391.153076814631.18364512222-0.01336899888090.170903328737-0.1507234541650.0145370275870.140675257885-0.730789680753-0.09414538462630.244682935591-0.05590471624840.196810424148-0.0258099805636-0.09406963245620.1217013994830.02646098349640.4290362028845.47439249145-53.302978466535.2001013507
62.49470088440.720842054768-1.357350237521.88927243936-1.413379873471.36604221653-0.2458979775820.6757064441540.487032364214-0.3313278396980.201941526142-0.001829220848370.229366419455-0.0862979841948-0.1041597917360.01065059797590.163051882869-0.1495814109470.06791216733750.06043878977460.5299546436170.625502608581-85.022643767519.5678502786
74.35552477490.05519955878140.8972323686790.727993682325-0.4049404338021.772703848320.003764301003370.295177491479-0.4095337482570.0242159085031-0.0603562354677-0.3396596371920.254993458133-0.108236171693-0.03818616389960.01203860222260.0610275565166-0.06786339333560.1997813863860.04860549337760.5812426795953.00955754021-86.846569450920.0371834893
80.90993067467-0.01958243623420.24098335832.513995047350.8524891501291.734554559780.1851997274510.1120760660890.1444963928420.04209572890090.02288277294440.2318508535790.400570991127-0.104654304694-0.1014588244040.195879337408-0.06056702051240.06226969582570.1099349598820.04856299258750.324570293407-13.2743941783-17.110444723321.0776729785
92.117888529750.636765833402-0.2573246822343.979924433130.3655325742283.50279872296-0.365476113721-0.179511005942-0.00702853570508-0.1000436483290.0727748251707-0.2161259116550.5713111845830.04637230528060.1849031672170.290392771839-0.06648766850340.0543913334747-0.0136387703120.1221980777090.45825304636-11.3447452344-19.011052242618.5332363788
100.523945070182-0.3199991667540.08856470502760.775541032382-0.6204019549040.859713499339-0.141987729635-0.07151878555840.1613686033520.01390113307280.07473541132580.2408340350250.105071473764-0.05388833511930.0495633513105-0.0696338735379-0.0218379717259-0.04643578303680.1689647433510.02795237841810.340301618549-4.452056689835.0256382566923.7308342686
111.88263461022-0.1385582685940.8395329849181.156950672960.4520536295611.26834772145-0.1929070977580.278292012406-0.0161594756666-0.1517136377610.0718952523412-0.0121580692357-0.238900689798-0.0124689010556-0.05741719963770.04686900260680.1110624433450.06675242987110.133124553637-0.02914544582050.561146022502-3.8292464430518.255848860121.2387404539
121.230489419230.547728336308-0.2500056969672.024169265930.6044581006321.17142176841-0.036064379277-0.1317627150450.1896132253720.01189902020610.0585136694367-0.6260074020160.3046413862020.118922886592-0.01011698045990.2680097437410.1209978999890.01531235683350.06514789305530.04813345252510.4320524236519.51686039761-15.059258624122.4762211543
131.44358891802-0.06325314412850.2457587452391.84636976467-0.2079996675752.83182214917-0.0893929476957-0.259893021388-0.2298083695250.1561417830870.054466429578-0.138560545464-0.003656065389270.08000844150430.03532138408480.1164847721590.001628064283660.0245247701670.1554856574650.03474779901830.3896203700374.3857011246616.373120532933.884901878
145.22983960607-3.30297042138-2.525825377082.115556716961.271698237785.06846422633-0.123660629531-0.2373858943510.414405606360.345073912793-0.104289197348-0.520008608711-0.5579029085060.1224148240140.1863889451560.2189579498220.000608927931047-0.1064954988540.1738342853460.0394883891350.60974246216910.396088393323.171827331238.2611997231
152.33973404662-0.0118891495622-0.1481145980722.08436187201-0.7132135589653.67094288928-0.05820451680820.919231704495-0.148984082751-1.01466339260.1281057691270.2432682609410.369449272303-0.562296179625-0.06054802893961.0274978461-0.230352089835-0.07337151591640.9048583533260.006606930071950.28991332243-12.0012411587-29.6615563804-24.3732534648
167.43504829651-1.52438792030.6665286499633.01227362605-0.8715037751832.189986791250.05295459333161.46783970326-0.423707231544-0.609938518066-0.499536101687-0.07201456423480.3122956880810.03741324238290.0185179048160.721389593157-0.1194331220150.04376009292610.07587535297560.04299111524720.265354462355-6.54202693867-36.31997884274.03338679564
172.46287873011-0.2041197654960.4985013005342.60106143683-0.4768699530182.927731671450.466548683153-0.228189394557-0.2258263417810.002250241201320.00887940923924-0.0875258134430.4071173157940.377922491985-0.4774891420270.727195706395-0.02852308069390.009891456171841.26755852530.1331017770850.82254657506925.6519367648-61.2850539251-2.74304197351
180.699721844506-0.1665861385030.6554658508990.612335909799-0.2818472343461.329431387320.3861917227490.873855240713-0.010262795191-0.668913911158-0.460960226971-0.3775111754740.3268049653681.368869130350.04031568853221.266226317230.02889336913310.2461488327441.80631054647-0.01956482068330.84885066161330.8203547465-46.645052961-29.2286323409
190.6209689794760.0734208268326-0.0938635593191.96761555863-2.217912952553.803577387380.0203124419336-0.491034630317-0.03146756093130.678365619815-0.002027076671920.155622270001-0.361226565879-0.304373361155-0.03463539472560.701881447183-0.02679954921490.02481390964160.5727597897620.01558433670770.270797222771-16.3958628788-47.798681507976.7628238
207.881310955225.043443962313.033387412393.363427198452.206110920541.617992686160.121306455136-0.190906134865-0.2148766129650.431759915982-0.137100279142-0.6813493118720.03234595124070.4051397020660.01712918501580.887655166822-0.0624173785249-0.3269131947730.901232454889-0.03256209462890.7212418330419.07439418231-23.207839459566.9694109585
211.362770828780.3172252550030.3880464315043.30547469652-2.568404823233.02857247330.11062401418-0.1586697183510.2028241420770.24892786203-0.694916408081-0.490820889008-0.1559011749320.7836413632220.5684142048670.7127349790310.0430972460252-0.02584046586150.948930666098-0.04676509762540.3620823141826.4523367302-27.488940486785.4327824874
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 2 through 91 )AA2 - 911 - 90
22chain 'A' and (resid 92 through 123 )AA92 - 12391 - 122
33chain 'A' and (resid 124 through 204 )AA124 - 204123 - 203
44chain 'A' and (resid 205 through 232 )AA205 - 232204 - 231
55chain 'B' and (resid 1 through 113 )BD1 - 1131 - 113
66chain 'B' and (resid 114 through 163 )BD114 - 163114 - 163
77chain 'B' and (resid 164 through 212 )BD164 - 212164 - 212
88chain 'C' and (resid 1 through 67 )CG1 - 671 - 67
99chain 'C' and (resid 68 through 109 )CG68 - 10968 - 109
1010chain 'C' and (resid 110 through 161 )CG110 - 161110 - 161
1111chain 'C' and (resid 162 through 232 )CG162 - 232162 - 232
1212chain 'D' and (resid 1 through 113 )DH1 - 1131 - 113
1313chain 'D' and (resid 114 through 188 )DH114 - 188114 - 188
1414chain 'D' and (resid 189 through 212 )DH189 - 212189 - 212
1515chain 'G' and (resid 3 through 227 )GI3 - 2271 - 225
1616chain 'G' and (resid 228 through 288 )GI228 - 288226 - 286
1717chain 'G' and (resid 289 through 432 )GI289 - 432287 - 427
1818chain 'G' and (resid 433 through 614 )GI433 - 614428 - 601
1919chain 'K' and (resid 1 through 268 )KM1 - 2681 - 268
2020chain 'K' and (resid 269 through 344 )KM269 - 344269 - 344
2121chain 'K' and (resid 345 through 613 )KM345 - 613345 - 613

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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