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- PDB-8trv: Structure of the EphA2 LBDCRD bound to FabS1C_C1 -

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基本情報

登録情報
データベース: PDB / ID: 8trv
タイトルStructure of the EphA2 LBDCRD bound to FabS1C_C1
要素
  • (S1C variant of Fab_C1 ...) x 2
  • Ephrin type-A receptor 2
キーワードSIGNALING PROTEIN/IMMUNE SYSTEM / Cell signalling / antibody / agonist / high affinity / clustering / activation / SIGNALING PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / leading edge membrane ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / response to growth factor / bone remodeling / positive regulation of bicellular tight junction assembly / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / tight junction / RND1 GTPase cycle / RND2 GTPase cycle / neural tube development / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / transmembrane receptor protein tyrosine kinase activity / RAC1 GTPase cycle / osteoclast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / molecular function activator activity / protein localization to plasma membrane / skeletal system development / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / neuron differentiation / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / defense response to Gram-positive bacterium / cell adhesion / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
類似検索 - 分子機能
Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. ...Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
IODIDE ION / Ephrin type-A receptor 2
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: 3.25 Å
データ登録者Singer, A.U. / Bruce, H.A. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S.
資金援助 米国, 2件
組織認可番号国
Celgene CorporationOperating Contract 米国
Bristol-Myers Squibb (BMS) ResearchCollaboration and Option Agreement 米国
引用ジャーナル: Protein Sci. / 年: 2025
タイトル: Synthetic antibodies targeting EphA2 induce diverse signaling-competent clusters with differential activation.
著者: Adams, J.J. / Bruce, H.A. / Subramania, S. / Ploder, L. / Garcia, J. / Pot, I. / Blazer, L.L. / Singer, A.U. / Sidhu, S.S.
履歴
登録2023年8月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年7月17日Provider: repository / タイプ: Initial release
改定 1.12024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
改定 1.22025年5月7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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
改定 1.32025年6月4日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _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: Ephrin type-A receptor 2
C: S1C variant of Fab_C1 heavy chain
G: S1C variant of Fab_C1 light chain
D: S1C variant of Fab_C1 heavy chain
E: S1C variant of Fab_C1 light chain
B: Ephrin type-A receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)163,54326
ポリマ－162,4006
非ポリマー1,14320
水00
1
A: Ephrin type-A receptor 2
C: S1C variant of Fab_C1 heavy chain
G: S1C variant of Fab_C1 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)81,66412
ポリマ－81,2003
非ポリマー4659
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: S1C variant of Fab_C1 heavy chain
E: S1C variant of Fab_C1 light chain
B: Ephrin type-A receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)81,87814
ポリマ－81,2003
非ポリマー67811
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)73.933, 110.558, 263.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and ((resid 27 through 28 and (name N...
d_2ens_1(chain "B" and (resid 27 through 43 or (resid 44...
d_1ens_2(chain "C" and (resid 1 through 30 or (resid 31...
d_2ens_2(chain "D" and (resid 1 through 61 or (resid 62...
d_1ens_3(chain "E" and (resid 1 through 162 or (resid 163...
d_2ens_3(chain "G" and (resid 1 through 2 or (resid 3...

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_1LYSLYSMETMETAA27 - 595 - 37
d_12ens_1PROPROSERSERAA63 - 7441 - 52
d_13ens_1ASPASPPHEPHEAA78 - 10856 - 86
d_14ens_1CYSCYSLYSLYSAA115 - 11693 - 94
d_15ens_1THRTHRVALVALAA118 - 15296 - 130
d_16ens_1LEULEUALAALAAA163 - 216141 - 194
d_17ens_1SERSERPROPROAA218 - 329196 - 307
d_21ens_1LYSLYSMETMETBF27 - 595 - 37
d_22ens_1PROPROSERSERBF63 - 6841 - 46
d_23ens_1CYSCYSPHEPHEBF70 - 10848 - 86
d_24ens_1CYSCYSPROPROBF115 - 32993 - 307
d_11ens_2GLUGLUSERSERCB1 - 2391 - 217
d_21ens_2GLUGLUSERSERDD1 - 2391 - 217
d_11ens_3ASPASPCYSCYSEE1 - 2321 - 215
d_21ens_3ASPASPCYSCYSGC1 - 2321 - 215

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

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要素

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タンパク質 , 1種, 2分子 AB

#1: タンパク質 Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


分子量: 33952.336 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: residues 27-330 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EPHA2, ECK / プラスミド: pSCSTa
詳細 (発現宿主): expressed with a C-terminal thrombin cleavage site and 6-his sequence. The residues LTPR at the C-terminus are derived from the thrombin cleavage site
細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P29317, receptor protein-tyrosine kinase

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抗体 , 2種, 4分子 CDGE

#2: 抗体 S1C variant of Fab_C1 heavy chain


分子量: 23814.611 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. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering.
由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pSCSTa / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 S1C variant of Fab_C1 light chain


分子量: 23432.895 Da / 分子数: 2 / Mutation: SPHAGLSSP replaced by QGTTS; Q165S, K167Y / 由来タイプ: 組換発現
詳細: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering.
由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pSCSTa / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)

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非ポリマー , 4種, 20分子

#4: 化合物
ChemComp-IOD / IODIDE ION / ヨ-ジド


分子量: 126.904 Da / 分子数: 5 / 由来タイプ: 合成 / 式: I / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 10 / 由来タイプ: 合成 / 式: Cl / タイプ: SUBJECT OF INVESTIGATION
#6: 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: 4 / 由来タイプ: 合成 / 式: Na / タイプ: SUBJECT OF INVESTIGATION
#7: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6O2 / タイプ: SUBJECT OF INVESTIGATION

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詳細

研究の焦点であるリガンドがあるかY
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: 3.31 Å3/Da / 溶媒含有率: 62.89 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 20% PEG3350, 200 mM sodium iodide (PACT Premiere solution E3)
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: APS / ビームライン: 24-ID-E / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年4月5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: 0.97918 Å / 相対比: 1
反射解像度: 2.99→131.72 Å / Num. obs: 44485 / % possible obs: 99.6 % / 冗長度: 6.7 % / Biso Wilson estimate: 103.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Net I/σ(I): 12
反射 シェル解像度: 2.99→3.1 Å / 冗長度: 5.9 % / Rmerge(I) obs: 2.214 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4523 / CC1/2: 0.349 / Rpim(I) all: 0.975 / Rrim(I) all: 2.427 / % possible all: 98.6

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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
X-Area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
開始モデル: PDB entries 3FL7 & 8TRS

3fl7

8trs


解像度: 3.25→131.72 Å / SU ML: 0.4573 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 29.7391
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.272 1683 4.84 %
Rwork0.217 33088 -
obs0.2197 34771 99.57 %
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 mean: 123.87 Å2
精密化ステップサイクル: LAST / 解像度: 3.25→131.72 Å
タンパク質核酸リガンド溶媒全体
原子数10669 0 23 0 10692
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.010110933
X-RAY DIFFRACTIONf_angle_d1.161414926
X-RAY DIFFRACTIONf_chiral_restr0.06271678
X-RAY DIFFRACTIONf_plane_restr0.01331934
X-RAY DIFFRACTIONf_dihedral_angle_d16.52833744
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS3.06500889003
ens_2d_2BCX-RAY DIFFRACTIONTorsion NCS0.960819593314
ens_3d_2EEX-RAY DIFFRACTIONTorsion NCS0.745157911437
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.350.33021350.30652694X-RAY DIFFRACTION99.51
3.35-3.450.36831430.30112682X-RAY DIFFRACTION99.72
3.45-3.580.30431420.28652726X-RAY DIFFRACTION99.55
3.58-3.720.37451450.27722720X-RAY DIFFRACTION99.72
3.72-3.890.33881510.27042725X-RAY DIFFRACTION99.79
3.89-4.090.33711410.23912744X-RAY DIFFRACTION100
4.09-4.350.24411240.21342755X-RAY DIFFRACTION99.79
4.35-4.690.27471390.20262744X-RAY DIFFRACTION99.9
4.69-5.160.24071390.18942769X-RAY DIFFRACTION99.86
5.16-5.910.24941250.20592771X-RAY DIFFRACTION98.97
5.91-7.440.3011450.22532810X-RAY DIFFRACTION98.83
7.44-131.720.21731540.17322948X-RAY DIFFRACTION99.3
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)
14.47638614222-1.12944522740.2629403140224.055007670780.5125051759023.424837400240.5106051209850.4866482955872.85690946801-0.266636284538-0.071311077072-0.447366955925-0.6594031880980.266114796523-0.2630796149591.22068294384-0.1318885989160.1745577763550.9543888536360.3077757754182.2503341959213.1570507812-23.18074019-6.24560772419
24.37960885195-0.8625692075150.6824563014573.93093855327-1.036860230772.973259074920.337207038360.3996305330280.042029607072-0.2372854335540.1749246149170.05590253240770.5499174590720.121019604064-0.5315963127770.8959694766780.120071823242-0.1771826387240.851290190815-0.1256282628940.75379414528410.8498130544-50.2617497824-2.47305097787
31.30029222479-2.271815197490.01019052222974.72380852346-3.198828005273.700495996690.4396881711510.127607766977-0.609357027817-0.785564083779-0.002045634523840.8587238427541.09069290606-0.224695489643-0.482911841391.509871656330.186851970161-0.5960685943520.94005467321-0.187987846951.1550682754519.746898926-84.484897670316.0673377508
46.13846163721-0.238932580997-5.102269291445.16918747056-0.2285814937856.527784734130.311661263152-0.147207201519-0.329827958984-0.753805654371-0.08335189865051.784432382890.0699060807108-0.796687438698-0.1149585125880.798513407346-0.00634620435228-0.3468426212310.871210562286-0.2569665375281.270300735114.6133277172-75.196370775938.8490458989
54.83611329502-2.63032154156-0.6561140047363.24210664082-1.33114354635.71362284764-0.1266452890590.277915879431-0.249351496707-0.80353057125-0.09408206995931.449455447981.18730684572-0.7272560139110.3751100829881.01056898108-0.14373180485-0.3334476035550.913066181199-0.1153476804721.6694835443911.0379096314-82.211410479540.1336042881
62.57689704373-0.3572455712430.7209869946414.210093791272.320884274114.321138206440.117124314388-0.287427718456-0.617351125057-0.349415422898-0.01956530996510.140530849745-0.4100877199720.0974749337835-0.1281591197230.5897296373140.0538816429712-0.03847043838641.01681202254-0.1853453591920.75857711288922.4609582099-65.37889820350.7936627809
75.369442870780.167777667889-1.184083261946.797403423990.04904833277912.93894328938-0.3179096186190.3925465128480.4446264155670.240100504030.2596565602360.0997377582989-0.105007790434-0.399055801063-0.04400883271350.578858560542-0.0969765987243-0.0161745238891.34130251952-0.2695330716970.67969295637225.6305918059-53.497239942860.8458067654
82.028991831040.226213950320.772306157475.35786964185-0.05934700064483.533776526160.285333223651-0.305118411187-0.3292907473320.1102159347340.06413965615180.2918209338460.695581965931.04269547725-0.3837245946650.9286508189470.341757330724-0.1678585323021.09031280489-0.179572840130.72881484745738.162437662-78.812243384235.811226542
92.57952772806-1.058175964720.2003869442685.556289640450.6637814722944.957456187260.655004339045-0.0417667001227-0.372443881161-1.22481476825-0.5989898760270.8724995549810.07647693421280.4835722530260.0129180361250.9400284711370.187864948498-0.2026227030090.962340621652-0.05967906184170.71795649400534.9763274297-73.321138136529.0963324754
103.138750596891.883044181010.3013234683149.303397814412.237662747084.305279757930.1252189205780.09434285018730.306678868816-1.74873629773-0.01584328482131.112159987520.3037844578720.536955698559-0.06156778153330.9860460232990.263050403605-0.2567331731850.848273094434-0.1763708110130.86245962049934.0888586446-73.680674241933.7418962786
117.875342484187.290517622854.489965933549.132614907354.476026586253.9089475840.879092548483-0.1798184788450.04043265951520.0658030791055-0.518380407476-0.2638137285140.5601102022190.0993990871057-0.4232710090870.902319803141-0.002712699791130.02116313943921.36991120259-0.3326134417970.80525412932338.1741725741-72.335117388943.5362718462
125.050289186430.9804610678962.465002781596.80526947903-0.3864132642627.901129303840.235866795444-0.635732920338-0.113333976737-0.009027963143290.389696831626-0.197092605534-0.0921862194165-0.53177036552-0.8370678737350.644279308689-0.0263397728816-0.04440979126081.32642525259-0.1682613425920.63173353975335.554210436-58.760826058966.5210045629
139.825251551034.130372478880.9211198165898.95440629493-5.127734616554.3957226905-0.0919274653764-1.28665185705-1.91087184770.500605648933-0.0940628035226-1.38751690179-1.79535044013-1.741514106850.5677831571160.7859067290550.0874632796862-0.00254880754741.15472558903-0.137268015880.71797180813342.2230217068-67.429120099774.4396219706
144.914206094831.84231899578-1.620474391224.98503487648-3.075132972398.51383623435-0.8389179696021.23016948174-0.465930173473-0.726343623661.08766729685-0.1284622123810.810929720024-1.26238292810.1469916203940.687093601601-0.1683015380820.04336644605531.38388234271-0.2134142315410.95240511347737.7269203479-62.790203948355.9662861122
158.26582920305-0.565977682831-0.6304519006982.71789930399-0.5718277935596.469475457920.0846726022135-1.81924286833-0.6529084167140.7533194843560.0103453539140.340464139907-0.2602599912240.638969792225-0.1889148058060.789928815607-0.01039387463560.08700967967521.65941050744-0.1522001774620.77492275300739.4289339316-61.382098199774.0892589896
165.594880780660.920025864951-0.4170182670514.739985077411.178145154172.392629445050.3918515433910.203244768881-0.481046977018-1.259354562-0.3594051221280.7142210479470.0737584053915-0.271754154415-0.02771821494491.028313225980.203905639499-0.2162936319590.804654801896-0.02859548180890.7492801896447.8896428522-107.73769472333.0574928469
177.770484666463.0775584522-1.022631188737.169950606543.91830310047.551346329990.0747510162779-0.684794400497-0.01504440175930.282827377060.0681418208284-0.1261101605180.0748831992026-0.342533184715-0.1956667527720.648378367942-0.0475036175281-0.04266783364131.0227345160.289681627350.73978367967860.5100189396-106.18518281664.5682539727
184.708940398051.37249944601-0.9372088147258.868175459131.443760154054.459609688960.434118950836-0.125413966960.0211634189042-0.945855004302-1.06935967307-0.00671681404228-0.03642131061650.7394396800210.4056461416991.056054792650.1233451980470.1197397661871.110398004090.2256323045940.87929066706474.9324848997-104.81966449932.1385308112
197.93126550676-3.70854195264-2.011607338482.459436356721.777432217681.851077207020.4667294632721.01299989513-1.27842881116-0.713136522161-0.618903221369-0.153473280058-0.2004553098710.6716850771220.5194026990811.318245658860.2713080511450.09461202796411.200957656840.1741898781591.0113496000569.0599520584-103.98345192724.5082457149
205.998224459840.540468198122.710966863435.0563914543-2.357139721354.928690804410.001203617849420.1285863144360.514589525381-0.830087580299-0.735264484547-1.14570877852-1.037402192110.3865473931041.200913829441.31768235410.1529636351280.1201527142310.7648439264360.1892776394970.80199257641964.6005715463-93.856695161730.6093406466
219.170712188141.938728400484.87284739144.48930638551-3.675617401598.340617494710.02665480755621.727205763780.203528967005-0.322041886756-0.855973668776-1.136815091570.1581783795292.388720407090.3811670805571.391293646180.4028879251230.2611058417541.316110498990.2671145374411.3261940123273.8026639752-99.50585643723.016465976
226.922511932143.085335171071.777638804015.18717734879-2.392575368515.680044160310.09050972961470.244635525816-0.396388547888-1.21303997153-0.206027673265-0.191441803417-0.5657976590951.041548310070.3375581720931.100160698030.2650346878730.08656457713950.9156353112880.01425431432190.62812834671467.4482897643-99.654515756330.3988132836
236.912857287632.176485283645.776146016412.757596155831.95734572295.34500172498-0.5615652037971.00338707916-0.241990619317-0.8471475355680.0746160266049-0.377518204507-0.6995856016811.82205056760.7205570723131.179493192410.06047715909170.07732369895461.203999450670.172145960040.82849593354371.7917842902-106.11927863137.8349538025
247.217759586924.7691102674-1.828692246157.90289931609-1.749573945257.983628923180.155409122035-1.136175859270.3902755300020.237458802997-0.1762372724950.6942803186531.272590746270.632633500695-0.2180142498040.8881624587010.09130196904660.08970620954611.537773924430.6798657930051.1346739125564.735660646-115.70806609870.4626602973
257.61044490264-2.07096946417-5.937222593072.385909288393.284828487878.858519438890.9536347016150.2777380223420.202943447274-0.6027938290920.429542708412-0.0650756972501-0.2511715205230.408211140612-1.726338518040.806306999925-0.0341078093848-0.01311152649311.110896104880.3998545080350.88160556741673.6839743537-111.66475689458.0991468568
262.19294954688-0.9307337695211.246165994325.164940777142.16630703435.33410749510.0259305596694-0.663931565625-2.616793567692.105921209390.856451114989-1.001513350881.393085612641.04282291547-0.8151228740011.288542521070.2581796607550.05378654390171.134853349560.2154994625751.209792269176.3431132515-125.06859236263.2091271845
275.352497129715.98684320189-2.228509501549.79019372625-2.881784131175.01990241617-0.6981037395120.7841063743011.32914533672-1.343035811271.669571251522.306387246920.190086169417-0.333202789267-1.208639850620.688531487689-0.0628961178848-0.1176808450141.252601369770.2953628536911.0741366968271.5968443657-109.02961401453.4763078971
289.91339094303-5.67623431206-1.96796652065.447320768025.122586326087.60975931294-0.442303455218-0.438777427967-3.004512320390.742173539828-0.967773848930.7567456647650.7349342652590.4585783614691.709441921120.657883363777-0.188538081373-0.00331943606651.315317608590.342196862741.274615048665.7086679077-123.70491385266.7954481096
292.15512000624-5.37309403568-3.155851108195.166064137874.979212395135.829060558310.200508501033-1.23922576757-0.28128689390.03014178759580.8436181001620.16917352511.58089816385-0.100263348776-1.360000792740.765369622909-0.192746309534-0.1080885029881.216211772040.4091950534551.1886491951377.0217642246-120.89568409865.6207285702
306.0695712442.8289313408-4.890912033688.96400476809-4.327343911254.193343851080.18400173702-0.555687804748-2.354245010911.31670672019-0.4862765739210.03774381716630.071004248269-0.505423210941-0.03082444105660.927625576103-0.0941109099871-0.1320704418791.763497805680.4729805658960.92280344988978.1274264851-117.49363845369.9997862089
311.259091240081.52456774053-0.7331382229483.11849477103-1.136017639681.536012763890.57770849904-0.9416696917521.58485027085-0.159097566483-0.1398639175311.0087201804-0.686817227560.468526389835-0.4973618840491.678395704140.1471636001080.2466071198931.57715022088-0.6373741243052.1604598883542.9572471993-30.340942589428.7306559423
324.49550705525-2.32960218707-0.6940366300496.6864163650.7320980098431.669908698581.554540892-1.171002190920.474435850714-2.06390030795-0.0962588640557-0.631985732627-1.828980269940.623763458623-1.423309357921.877420875620.04305833219270.3595366276491.26037955779-0.4715397707211.7064613532234.6869209714-26.243647921225.5404004078
334.61789548247-0.3392783580192.494078279249.613757165620.9809204057963.303474468511.76556053817-0.4865753760250.2938446623290.3788993079380.9192584728210.809962579587-0.5607344103410.24820475737-1.616521939851.68760548489-0.05199216161810.4209982166861.4971082943-0.3185364558731.7864151803231.5457209611-32.918912631530.8412237842
342.46614552069-1.79033118832-0.7718377967586.059388085360.2217804828380.5497716749890.086489841345-0.2829390504080.0552812552157-0.8816143554020.1653359892890.3754930087290.0600031409250.153934466082-0.2955659019641.548059028430.210775995664-0.1784205660061.10011123492-0.1091966898520.66885607258545.7957164707-71.77473302114.9376951129
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 27 through 178 )AA27 - 1781 - 143
22chain 'A' and (resid 179 through 259 )AA179 - 259144 - 224
33chain 'A' and (resid 260 through 329 )AA260 - 329225 - 294
44chain 'C' and (resid 1 through 57 )CB1 - 571 - 52
55chain 'C' and (resid 58 through 99 )CB58 - 9953 - 91
66chain 'C' and (resid 100 through 158 )CB100 - 15892 - 136
77chain 'C' and (resid 159 through 239 )CB159 - 239137 - 217
88chain 'G' and (resid 1 through 44 )GC1 - 441 - 38
99chain 'G' and (resid 45 through 91 )GC45 - 9139 - 75
1010chain 'G' and (resid 92 through 111 )GC92 - 11176 - 95
1111chain 'G' and (resid 112 through 131 )GC112 - 13196 - 116
1212chain 'G' and (resid 132 through 162 )GC132 - 162117 - 147
1313chain 'G' and (resid 163 through 173 )GC163 - 173148 - 158
1414chain 'G' and (resid 174 through 192 )GC174 - 192159 - 177
1515chain 'G' and (resid 193 through 232 )GC193 - 232178 - 215
1616chain 'D' and (resid 1 through 143 )DD1 - 1431 - 121
1717chain 'D' and (resid 144 through 239 )DD144 - 239122 - 217
1818chain 'E' and (resid 1 through 18 )EF1 - 181 - 18
1919chain 'E' and (resid 19 through 44 )EF19 - 4419 - 38
2020chain 'E' and (resid 45 through 75 )EF45 - 7539 - 61
2121chain 'E' and (resid 76 through 91 )EF76 - 9162 - 75
2222chain 'E' and (resid 92 through 111 )EF92 - 11176 - 95
2323chain 'E' and (resid 112 through 131 )EF112 - 13196 - 116
2424chain 'E' and (resid 132 through 146 )EF132 - 146117 - 131
2525chain 'E' and (resid 147 through 162 )EF147 - 162132 - 147
2626chain 'E' and (resid 163 through 173 )EF163 - 173148 - 158
2727chain 'E' and (resid 174 through 192 )EF174 - 192159 - 177
2828chain 'E' and (resid 193 through 206 )EF193 - 206178 - 191
2929chain 'E' and (resid 207 through 216 )EF207 - 216192 - 201
3030chain 'E' and (resid 217 through 232 )EF217 - 232202 - 215
3131chain 'B' and (resid 27 through 102 )BG27 - 1021 - 72
3232chain 'B' and (resid 103 through 134 )BG103 - 13473 - 100
3333chain 'B' and (resid 135 through 169 )BG135 - 169101 - 125
3434chain 'B' and (resid 170 through 329 )BG170 - 329126 - 284

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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