[日本語] English
万見
- PDB-8t9b: Structure of the CK variant of Fab F1 (FabC-F1) in complex with t... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 8t9b
タイトルStructure of the CK variant of Fab F1 (FabC-F1) in complex with the C-terminal FN3 domain of EphA2
要素
  • CK variant of Fab F1 heavy chain
  • CK variant of Fab F1 light chain
  • Ephrin type-A receptor 2
キーワードIMMUNE SYSTEM / enhanced crystallization / EphA2 binding / expressed protein / Fab / Complex / receptor clustering
機能・相同性
機能・相同性情報


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / tight junction / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / negative regulation of angiogenesis / molecular function activator activity / skeletal system development / protein localization to plasma membrane / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / defense response to Gram-positive bacterium / 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
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: 4.2 Å
データ登録者Singer, A.U. / Bruce, H.A. / Enderle, L. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S.
資金援助1件
組織認可番号国
Other private
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.
#1: ジャーナル: PloS One / 年: 2020
タイトル: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing.
著者: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S.
#2: ジャーナル: Dev Comp Immunol / 年: 2003
タイトル: IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains.
著者: Lefranc, M.P. / Pommie, C. / Ruiz, M. / Giudicelli, V. / Foulquier, E. / Truong, L. / Thouvenin-Contet, V. / Lefranc, G.
履歴
登録2023年6月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年5月1日Provider: repository / タイプ: Initial release
改定 1.12024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
改定 1.22025年5月7日Group: Database references / カテゴリ: citation
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

-
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

-
集合体

登録構造単位
C: CK variant of Fab F1 heavy chain
G: CK variant of Fab F1 light chain
A: CK variant of Fab F1 heavy chain
B: CK variant of Fab F1 light chain
D: CK variant of Fab F1 heavy chain
E: CK variant of Fab F1 light chain
F: CK variant of Fab F1 heavy chain
H: CK variant of Fab F1 light chain
I: Ephrin type-A receptor 2
J: Ephrin type-A receptor 2
K: Ephrin type-A receptor 2
L: Ephrin type-A receptor 2


分子量 (理論値)分子数
合計 (水以外)238,49312
ポリマ－238,49312
非ポリマー00
水00
1
C: CK variant of Fab F1 heavy chain
G: CK variant of Fab F1 light chain
L: Ephrin type-A receptor 2


分子量 (理論値)分子数
合計 (水以外)59,6233
ポリマ－59,6233
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: CK variant of Fab F1 heavy chain
B: CK variant of Fab F1 light chain
K: Ephrin type-A receptor 2


分子量 (理論値)分子数
合計 (水以外)59,6233
ポリマ－59,6233
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
D: CK variant of Fab F1 heavy chain
E: CK variant of Fab F1 light chain
I: Ephrin type-A receptor 2


分子量 (理論値)分子数
合計 (水以外)59,6233
ポリマ－59,6233
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
F: CK variant of Fab F1 heavy chain
H: CK variant of Fab F1 light chain
J: Ephrin type-A receptor 2


分子量 (理論値)分子数
合計 (水以外)59,6233
ポリマ－59,6233
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)76.661, 130.650, 222.996
Angle α, β, γ (deg.)90.000, 89.760, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 through 47 or (resid 48...
d_2ens_1(chain "C" and (resid 1 through 47 or (resid 48...
d_3ens_1(chain "D" and (resid 1 through 153 or (resid 154...
d_4ens_1(chain "F" and (resid 1 through 47 or (resid 48...
d_1ens_2(chain "B" and (resid 5 or (resid 6 and (name...
d_2ens_2(chain "E" and (resid 5 through 50 or (resid 51...
d_3ens_2(chain "G" and (resid 5 or (resid 6 and (name...
d_4ens_2(chain "H" and (resid 5 through 66 or (resid 67...
d_1ens_3(chain "I" and (resid 438 through 461 or (resid 462...
d_2ens_3(chain "J" and (resid 438 through 462 or (resid 463...
d_3ens_3(chain "K" and (resid 438 through 461 or (resid 462...
d_4ens_3(chain "L" and (resid 438 through 461 or (resid 462...

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_1GLUGLULYSLYSAC1 - 2381 - 230
d_21ens_1GLUGLULYSLYSCA1 - 2381 - 230
d_31ens_1GLUGLULYSLYSDE1 - 2381 - 230
d_41ens_1GLUGLULYSLYSFG1 - 2381 - 230
d_11ens_2THRTHRCYSCYSBD5 - 2325 - 214
d_21ens_2THRTHRCYSCYSEF5 - 2325 - 214
d_31ens_2THRTHRCYSCYSGB5 - 2325 - 214
d_41ens_2THRTHRCYSCYSHH5 - 2325 - 214
d_11ens_3GLUGLUGLNGLNII438 - 5123 - 77
d_12ens_3GLYGLYLEULEUII516 - 52781 - 92
d_21ens_3GLUGLULEULEUJJ438 - 5273 - 92
d_31ens_3GLUGLUGLNGLNKK438 - 5123 - 77
d_32ens_3GLYGLYLEULEUKK516 - 52781 - 92
d_41ens_3GLUGLULEULEULL438 - 5273 - 92

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.99842010676, 0.0560321329983, -0.00420600624384), (0.0560985071446, 0.998266522254, -0.0178019112162), (0.00320123616872, -0.0180097367683, -0.999832686737)-39.9525582904, 0.60214260181, -111.727568698
2given(-0.999945926993, 0.00139164151967, 0.0103056501162), (-0.00139105668448, -0.999999030437, 6.39168327534E-5), (0.0103057290735, 4.95776330959E-5, 0.999946893335)-38.2520901348, 9.33371414912, 0.128966078114
3given(0.998909216798, -0.0465969302567, 0.003017065958), (-0.0466370397879, -0.998799706948, 0.0149710360667), (0.00231584027122, -0.0150954129372, -0.999883375895)1.08642413504, 8.72569042699, -111.787721708
4given(-0.999900922159, -0.0138470260496, 0.00253095553959), (0.0138632457583, -0.999882724844, 0.00650745544828), (0.00244054981627, 0.00654189796229, 0.999975623347)-38.8384583439, 9.6940034049, 0.372976270828
5given(-0.998250206466, 0.0591284930608, -0.000588726866659), (0.0591312759022, 0.998220505049, -0.0077016562933), (0.000132291899478, -0.00772299215569, -0.999970168501)-40.0125743942, 1.03899766636, -111.451347926
6given(0.999138510258, -0.0410624128265, -0.00600962329286), (-0.0410404993201, -0.999150538437, 0.00372544718143), (-0.00615749419899, -0.00347559980623, -0.999975002423)1.2579680814, 8.61885907881, -111.643845526
7given(-0.992950741028, 0.118124365111, 0.00977037661506), (0.118138331547, 0.99299677244, 0.000862868622276), (-0.0096000266361, 0.00201104202979, -0.999951896442)-38.8807642053, 2.84922848592, -111.838095307
8given(-0.999704605855, 0.00779062719244, 0.0230218843649), (-0.00808703376138, -0.999885244538, -0.0128100601529), (0.022919444075, -0.0129924548922, 0.999652887356)-37.4888172449, 8.38412798953, 0.979067715776
9given(0.9914242527, -0.129286018547, -0.0190545681056), (-0.12926045017, -0.991607340506, 0.00257260105387), (-0.0192272509513, -8.75370261922E-5, -0.999815135492)-0.329794613231, 6.47618625026, -111.992905659

-
要素

#1: 抗体
CK variant of Fab F1 heavy chain / FabC-F1 heavy chain


分子量: 25332.188 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: engineered Fab from phage display / 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)
#2: 抗体
CK variant of Fab F1 light chain / FabC-F1 light chain


分子量: 23267.811 Da / 分子数: 4 / Mutation: HAGLSSP replaced by QGTTS / 由来タイプ: 組換発現 / 詳細: Fab selected/engineered by phage display / 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: タンパク質
Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


分子量: 11023.206 Da / 分子数: 4 / Fragment: C-termimal FN3 domain (UNP residues 436-529) / 由来タイプ: 組換発現 / 詳細: residues 438-531 / 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
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 4.86 Å3/Da / 溶媒含有率: 74.72 % / 解説: thin hexagonal plates
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 / pH: 8 / 詳細: 1.5 M sodium formate, 100 mM Tris-HCl, pH 8.0

-
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: 2021年10月20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: 4.2→131.33 Å / Num. obs: 31847 / % possible obs: 97.3 % / 冗長度: 3 % / Biso Wilson estimate: 101.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.119 / Rrim(I) all: 0.211 / Net I/σ(I): 4.2
反射 シェル解像度: 4.2→4.43 Å / 冗長度: 3 % / Rmerge(I) obs: 1.185 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4648 / CC1/2: 0.602 / Rpim(I) all: 0.813 / % possible all: 97.8

-
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
XDS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 entry 8T7F

8t7f


解像度: 4.2→66.12 Å / SU ML: 0.5627 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 40.3085
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.315 1713 5.51 %
Rwork0.2957 29395 -
obs0.2968 31108 96.25 %
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: 156.28 Å2
精密化ステップサイクル: LAST / 解像度: 4.2→66.12 Å
タンパク質核酸リガンド溶媒全体
原子数15657 0 0 0 15657
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004916048
X-RAY DIFFRACTIONf_angle_d1.006221967
X-RAY DIFFRACTIONf_chiral_restr0.05682506
X-RAY DIFFRACTIONf_plane_restr0.02022820
X-RAY DIFFRACTIONf_dihedral_angle_d17.07885439
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS1.27511466564
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS1.05600153551
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS1.26981567014
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS1.85389334328
ens_2d_3DBX-RAY DIFFRACTIONTorsion NCS1.41475831148
ens_2d_4DBX-RAY DIFFRACTIONTorsion NCS1.95312198724
ens_3d_2IIX-RAY DIFFRACTIONTorsion NCS1.71164158135
ens_3d_3IIX-RAY DIFFRACTIONTorsion NCS1.53224374605
ens_3d_4IIX-RAY DIFFRACTIONTorsion NCS1.69206863884
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.320.40081400.37162474X-RAY DIFFRACTION97.65
4.32-4.460.36841450.3472465X-RAY DIFFRACTION97.1
4.46-4.620.35381410.32072387X-RAY DIFFRACTION95.54
4.62-4.810.33621320.30762288X-RAY DIFFRACTION89.2
4.81-5.030.33481350.28772418X-RAY DIFFRACTION95.47
5.03-5.290.29771420.28622458X-RAY DIFFRACTION97.71
5.29-5.620.35191480.29872513X-RAY DIFFRACTION98.37
5.62-6.060.35371470.3332482X-RAY DIFFRACTION98.35
6.06-6.670.39711500.33322503X-RAY DIFFRACTION98.85
6.67-7.630.32371470.31982522X-RAY DIFFRACTION98.34
7.63-9.60.24331450.26772437X-RAY DIFFRACTION94.75
9.61-66.120.24441410.22552448X-RAY DIFFRACTION93.8
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)
14.71915725414-2.42110505357-0.8932216210485.687285470831.812398401870.8439286626741.12444098102-0.251945466208-0.266250464677-3.79181328789-1.150529006841.19435306067-0.110674460226-1.670019070610.0198225231744-0.2921024901370.0494479481731-0.5221857686522.84816054208-0.4242883107791.36795292297-46.3834695549-7.8107037145-81.4996442256
23.29607462866-1.152198112323.129117774585.169162365340.3387963999033.800171635480.700792884556-0.24765367753-0.760918189582-0.07259540412390.0235321286162-0.03835878809311.32576693515-0.268396667709-0.558560058440.739276013967-0.129980486755-0.08955138843812.41303464163-0.1018287972081.20803800032-41.16994812-8.61568531637-77.7742517101
33.99138501633-0.3442883908024.531163496166.05407321525-0.3223468533066.488958436880.103535580254-0.369539425334-0.330916613829-1.79974493165-0.540772905350.608412598666-0.233130054547-1.274846958740.4022670696321.813440028720.0516978276296-0.2367793491122.30880188757-0.3703850454251.1577027743-36.250105229-30.7563048385-107.804857674
48.68541611988-5.20928635361-1.353686960248.630886869084.282908639996.322003547090.9349552440470.3452739193670.106823261638-0.7485189761960.520739429433-1.04844067091-0.6526586090310.50945884116-1.227294237321.125067010820.1563186344910.1316397626951.80083585107-0.1659921617351.05184853514-22.9340625696-13.9742970357-79.3436884397
58.108600326-4.66363078047-0.5261386390587.487637136942.751978057685.61510676370.785212862512-2.656924670530.3189250956511.444578633860.22683651081-0.7183924194320.2794092712070.608898672033-1.16855243507-0.8286103984580.309604931415-0.8718237427333.28640367086-0.01592924192250.964890947475-22.7716313194-18.0911520651-71.3140546629
62.30107805248-0.0287141231611-1.021809077151.454306205970.02477462194530.7875510069030.0615926895798-0.09724936219040.188864732513-0.2509357314670.172766070966-0.5033280488760.262296357331-0.178726656632-0.2307433946441.16078698930.0867451367043-0.08060791592361.25202651586-0.1330781356830.875542459597-25.2178454068-18.3948458398-99.5130111122
74.53781318902-0.9677373682722.482305713471.95544146867-2.154755233554.068481159380.2268876136230.758466090362-0.0999050275924-0.873094356544-0.8236114722490.01664769872680.3637441589190.1718186253450.3611093553721.605063675870.336265788532-0.03766644342191.99004287435-0.3247933429041.59628545995-23.3483167746-22.4314602179-112.259335592
81.975605417471.82518206556-0.1757566590513.96594088151-2.047907169941.436181854351.96437678878-0.758322755018-0.3753739985980.157707863314-1.01533392008-1.01498488074-0.2050109320851.430473741330.1387775576750.993017835777-0.0125969110305-0.6641150606052.298622833070.4358764818891.592899778799.49726901391-14.0162810212-24.9543786912
92.47258858441.547841233340.2053193337724.8331155491-1.824929539743.266725096640.5866174305660.5504242384890.2402411509540.475251472097-0.250694647194-1.046214891090.4184666462120.668749195175-0.09301167186530.6918077418880.0150135642402-0.1833123174892.282807355240.1332403451450.9966630921244.84104988194-7.94772194792-33.5727790081
102.196112270111.119514273161.092039451025.77474494307-1.770994894482.967372584430.599993351249-0.3226731252720.006769505812422.07911069651-0.51573209394-0.452688415151-0.9576217707720.7492079842510.08682022014991.281437601770.024203695642-0.3619639701912.148208889310.2979453379341.070879254157.68557097765-5.90604098088-22.5099099174
113.297463194051.30228559782-0.6802338427594.3099712694-2.454386471524.51621101789-0.319122327550.866651976943-0.3407682282560.5217334457330.705042994914-0.124924230725-0.900519097425-0.183605895323-0.3676402833570.7181562683770.151807000025-0.00129590663382.436145196650.07653379137931.006928215-0.669413221641-6.4388492562-41.4188470541
123.316762727971.0527661828-0.8066653005344.80420195501-2.462466660274.578874755240.775993277735-0.833792750628-0.610934813971.60561005381-0.934390345428-0.3511197636720.9923112327840.132698873982-0.2527645044841.70655432992-0.1653347726-0.1021607956252.33722735490.1645510212940.977836779678-1.93382939307-21.0688940143-13.803402599
134.20034020331.39561343540.812013736459.05201389463-1.143010110186.617093319441.24383949253-1.72168283306-1.694198486742.08944222166-0.430757651491.146800686150.0476233632987-0.366599120988-0.5649600909352.37921436358-0.134572069163-1.042990037832.881973282982.563933313820.626860701186-12.2653319413-33.0893537049-0.742539529828
145.39062373650.8396606130780.5359592287789.15336026258-1.323747354812.65765085735-0.7463282280031.30278826231-1.02422611841.245010147250.4798241331570.779084164684-0.8736017716431.66157355727-0.5198033803191.91720662674-0.557449497522-0.6128448222722.625367248640.1872188903540.854804866149-0.493933126632-28.9464122721-8.77704380623
156.20422854538-0.0710380464912.51962199362.018049649772.44988886895.64716247757-1.241869934770.1953123050881.074532828932.116019932090.9405495729221.06925247478-0.9508424106771.04259052916-0.3128908033691.90465362251-0.122148911114-0.5430218160712.606046479080.7152930506231.63554170103-7.71059897035-25.4949595983-6.74782032605
161.88839188793-1.70483977852.397681450026.941914199661.358380077826.61632999428-1.1126675528-0.93598879421-1.50590472795-0.5986897297090.5488648800390.643515635080.6925159815742.080318960280.4969264447741.827313133890.20493322301-0.3415072275451.661229737910.5814043774121.52388085686-2.68205536116-36.1878521804-0.927001104672
177.908512069984.83052647979-1.885332782195.23884139621-4.170899776524.956942019550.4464172862871.250103336910.02296386210340.4198901710940.05553720470330.492761918716-0.0549271605744-0.364085785007-0.4078182045220.848976903114-0.07777017818430.07254240365252.318830482240.4076361356960.999428096669-18.0508488718-16.0823863043-35.8463936618
181.904535159831.23635146728-0.9465561068442.5902089233-2.490516124926.526395215910.415793158779-1.15285019725-0.03740707695311.16462695396-0.3423738368670.03817773196990.2710945202460.133394329952-0.3146865973681.61624309044-0.05791072307710.0403699659382.073793312570.3132907113721.17287362539-16.7261541661-20.0409442411-6.69000403409
194.419239504521.246618722872.678511627293.703591311621.432755195162.877884269630.8641770201030.1518900250540.1841645813290.4295306101-0.4289812295430.8640784504270.0173877465346-0.355323476976-0.2918383641480.8845027861220.02036651286940.4321169105851.62904056368-0.1409076228641.28406706787-44.627696231618.8534605673-29.5782851979
203.031494414831.836751263371.282642543882.056073285291.902700341995.39049155682-0.2085069833080.5581520694810.3868579023370.179898780675-0.2907799135420.165709223807-0.2264636568960.0899589541794-0.1242417857980.7549983608270.1976683966120.02622809941461.77924909420.2687930991031.12780090581-38.640218485821.3622137573-29.5348183444
216.99854343504-0.561106060262-2.102602043020.710690261788-1.942130199917.153624399050.336895166862-0.7408091596241.013631356250.536968546718-0.3242564983930.138106617070.333519351573-0.3567595525350.1235066616752.22452866642-0.2369580115890.2317898264171.39676322689-0.4661619545021.43596893899-32.907359030740.3924935818-4.05302870545
225.034929605410.975091913959-1.120683647290.971615646623-0.2388146087963.169591878960.707479243735-1.38817390644-0.1614367485811.046615386460.497018290223-0.2657532462160.2467658652850.474011137718-0.6683516852480.956206752355-0.2242210587650.02850519113852.66117144466-0.3382549430591.43001638156-21.574131046123.4668300848-31.0121355606
235.535364535022.432460494740.6357405293492.51899360829-0.1144259442411.13449972892-0.03573760713490.6166141200170.292828285654-0.1335913306120.376067695709-0.355489693284-1.24700875870.0960036219575-0.5445611189870.734470135102-0.1517064166610.1354350315482.08832828934-0.176188344381.16575251681-21.976099617126.250155647-34.0097994736
243.140152104010.7604972212441.895537402672.112328656220.6462881961843.24072335814-0.110091388224-1.51603295738-0.3045553969441.543796238940.129651108189-0.352357344692-0.313586423725-0.313635650926-0.1954661703722.345965843390.103163647362-0.1230606623852.02229071273-0.4023097798211.10028143491-22.378631349630.48481840260.94033274173
253.741048197711.491767739461.359404223441.8403045072-0.1369393756564.376056963960.874692541631-1.735816936330.2872590457041.32267728878-0.4774053173490.291378653196-0.2245631538150.212162632967-0.2004893781342.34675947723-0.3101113220670.00321689520762.07332120636-0.07852900970061.29300848225-20.196939629432.22782285391.67034790022
263.82855693344-0.564133369672-0.1987174014344.77817591263-2.030993871922.962154956660.688091915744-0.7590917719760.535004231142-0.472531805337-0.40440739264-0.4859564272360.2011826839020.913679818254-0.4088274394350.7325682815740.04363457563370.1511353933112.163373384120.15235618941.236889912525.9978526221317.5384570705-80.4608738487
274.608489163221.33907524955-1.093177321792.423282829911.079459838498.51735644937-0.1834925424960.5701197767030.881312438732-0.46632653887-0.203107545153-0.2844491372990.2100500193111.550966802820.6107432944311.66292378978-0.1329006007960.1058040452761.805253182770.537590747511.24081020607-2.8169667424839.9464428548-107.918665125
287.25953663477-5.416532564382.124896035494.53835418701-0.7083632223983.475593848810.392764263104-0.09795208978090.201869159760.1227391527850.3101136959570.416786108164-0.1136607267190.511482226015-0.8113011460510.7305928759420.01448811162440.1369310967672.154093650220.1967049729651.1623741158-14.218589761624.326467542-77.0316297653
295.2626791132-2.30951998717-0.8179378383942.357929415360.9563543676571.88281087796-0.0349743248851.10466185258-0.0899579777643-0.701871810575-0.7859310077510.0870220290934-0.849874098172-0.1873794914020.8572930919881.450510260420.1233912835120.02151076498031.971781365730.2430141397711.06493898515-15.690192847531.5688301009-111.679386663
308.220464261310.37171305467-0.3514020808616.9444213603-1.374609143552.94469799311-0.207720687073-0.0844627152879-0.672410938624-0.4716873940630.02525434342340.731549702876-0.464628148102-0.3046096368970.064672696265-0.7954600982470.5171237213750.3050053436772.37624365218-0.1703458214611.5140646898-43.345783782311.0337701363-64.6080364857
312.01569818213.28263913292-1.539617452191.5143472347-1.867754194413.81625505884-0.3529842786860.608499146533-0.872817963752-0.598930096932-0.0356973221838-0.627200976918-0.1124417763020.1072611158660.1606711491670.4382648438880.08457800516880.2058737861751.541599502650.1678045469761.48015364282-30.763756261423.4426136349-66.3223535453
322.413960773331.11637503279-3.882912238314.75255833871-0.5354028707076.71716529829-0.8424097616910.615983979450.846816008311-0.0592953579513-0.1937448147171.217280760080.412881804756-2.380933893270.3955892986090.272746709702-0.351402786365-0.479366051122.20927162976-0.1382002019831.52212134052-49.695079164316.1523802497-64.6484616915
332.774712722531.88294724503-3.040040616884.38829115934-0.9951856560515.64472925209-0.177028506712-0.3370031818060.2674095819390.6257861986040.143389171316-0.529961103830.2289745118510.1575065779490.6063741445510.6315791478990.2345014283920.1019447479622.10775916349-0.1862550314981.14404133414-32.633527534818.1165685513-52.6428709308
341.625998593511.56176324395-2.354709698322.89478403759-1.428637695773.97868913525-0.305975118324-0.01187931344070.1956774221740.1021715604310.08191692194560.915628782311-0.275555872748-1.274788565860.05521128483240.6659287131640.02894544988930.09838179694121.37275775884-0.02356638008941.46142063742-41.706128831424.0171819804-60.2824907439
353.242392432953.85110527201-2.214649300294.60393937395-2.208078620648.27757133721-0.225628041704-0.7068663169430.106769353287-0.403970926879-0.486971406601-0.177188362852-0.4610611075680.6222287796560.324893325160.953023395028-0.0461967712178-0.05964288072041.29906934680.06223214648541.58708462592-24.694885196625.4919968952-58.5464834396
360.3662698652541.193707274120.6687528396475.13475263531-0.5433544063986.75714460891-0.234401058368-0.3115071890011.8926129421.2482275153-0.2301400632761.570512633511.88136919915-1.194973223050.393476708208-0.6618318997030.01636187581130.05669726546442.66439489036-0.05588322068431.19858935382-40.079683830213.4945873067-57.305910524
379.97878808036.04399084045-0.1857209039517.821182515042.475787514531.54746324471-0.1353601174030.232573518244-0.672373873949-0.825908635471-0.6360063629460.3963187866281.272379843880.6459913864710.680606474750.866105456650.1301068916290.1988205773442.530210413750.3641079825340.824705614009-27.382032464417.2535791278-63.7482579804
388.3014487906-7.861058061531.187549361318.70866399476-0.6786269806212.92892169802-0.863323756432-1.071937693870.5309174187791.963730559620.356074749872-0.569765147057-0.134868274993-0.5286098235060.2789021776590.659357433723-0.192200564013-0.4068331296332.135949365270.8203594344861.46937452322-3.3295104560418.0216268063-45.3615301808
393.51358344749-1.14995884425-0.3020286931916.58651816197-0.05909286711491.11713768957-0.548976835386-1.056953067390.792552008787-0.109423553361-0.0560188790188-2.446539552360.6219929455481.908375953920.5784769280810.813572414527-0.427053106722-0.09937633643093.86203199491-0.2282537786971.363100869579.0489886692814.9682239083-46.6257925535
400.7324185622411.17007826419-0.894678703422.78341264898-0.2257484250652.106681177530.04610066105820.2521536700710.724121695894-0.1680890094480.326015917257-0.00622292879503-0.3945574400650.813536457124-0.401141092492-0.950335208981-0.4602506246670.3324910310122.2431024889-0.3437142441381.20251649576-2.0840089295516.3630105724-56.3338354019
418.29657053070.944468671324-0.1695765358556.05699682856-0.1687790499091.813719269041.057865667272.16380374470.708691054456-1.862954070760.1257417456590.17905154078-0.472606394791-0.891674949296-0.8034442354861.00679018149-0.101522979050.3248702579043.115102628160.8534537216581.70721082822-3.1020675003319.4796259217-59.9252800415
422.58073244454-3.49268403966-3.10238789767.302140322731.08208621337.697903504780.887932482934-0.8477846265450.7598469566151.12481690531-1.18291915429-1.1020869698-0.3832029377910.5436574605350.4645929248970.690262968182-0.325394602023-0.03903632914481.43415177286-0.05779137276011.16857482953-3.2030290644316.9827925474-51.3564399293
432.116569392954.12865841777-0.9124982290342.131734963061.422178455766.85989361737-0.6762387130651.55483482954-0.400767686537-0.9929706751240.399815813557-0.7005820713840.2844051824950.2756970436120.3149982112370.5906242855240.1565275395230.09795812568772.032533949570.2299309794021.16695550189-3.98805333209-10.3992258995-65.9274929009
444.63794490642-3.714250586521.772961292632.97494243585-1.98870242118.95384358733-1.051058737391.57461916618-1.64612085957-0.09773660962891.10883663686-1.77406000047-0.353248511005-0.400147284128-0.2736607094861.39244205726-0.666625822847-0.04981371499552.63939009214-0.03362708264531.9095746014112.9875270653-6.71730455505-64.6250131985
455.92273776662-0.6576700699051.995150915694.504877829230.1113045467624.897477089140.792689322696-1.51131694696-2.389802416540.992459609186-0.1569927129180.262657797414-0.302547022533-1.02321604214-1.355698594680.8025704240020.0965424908266-0.2448135002841.792617568890.1373668124361.58713123308-5.89489811123-8.37673620424-53.3286435699
465.43322911730.4126276356951.386524812022.981636462930.1409001446413.965110355061.25093397025-0.923224385905-2.24775072596-0.479457185309-0.307671083785-0.437853976397-0.304101456986-0.264698238641-1.479775342910.679389044301-0.0261504739224-0.1831438371871.584159901870.08481263917131.83873456345-4.18305229952-14.4129791621-58.1006432205
472.055722652622.055582980571.970182070136.194840452383.169887166475.800315798550.708991824111-0.531675243279-0.192533232793-1.034186087090.126570188757-1.43294797197-0.429409247247-0.5727969524080.0801924696080.882582751508-0.1007657095020.23644265441.103406784760.1415355957151.46880310376-1.59002106643-4.99448399432-58.951706095
486.90224023664-1.87020148857-3.130750917511.969237456161.47732065911.670411332280.234185533224-2.339945021140.6109291092750.9158256496370.05911293889341.28203593588-0.5714548941640.553148343394-0.1416057232810.734535243693-0.3204708373610.004119761664192.19122110281-0.4252942016781.02171809003-41.2396922964-1.27848953263-45.4034240888
493.80943649278-3.76639238121-3.257786010785.38393182461.825571730514.06521975794-0.686427997287-2.41381009713-1.181352702811.43862378636-0.03963529711870.7056720167410.3937581333321.220847037490.4927704118740.850783396962-0.4624056733330.09266795898412.544600468940.08044893489961.21975209206-29.8918080356-15.6424484397-44.7077317135
507.63123804076-0.727344643853-0.5844767424214.63597159055-1.693681527233.73698735045-0.541946144378-2.4156540693-0.7463321274170.895608515523-0.279777779111.31718151466-0.1647428765650.4745457866160.1981488663550.39351368932-0.6512171474650.05599857579563.098132708450.07050217510111.06907260082-38.3784785098-9.96678214333-46.3076298476
516.45663601850.672720805030.06026528378211.670491665080.2892740589940.5171755658140.689872131397-1.993335023960.9303866853220.8409520754170.007587685836492.02112489191-0.953943794546-1.372649226810.05545923599450.7522856727220.12848436967-0.006564039104632.97481555597-0.3061097579072.07498434349-50.8408814595-3.98624754136-48.3070699219
522.01675289673.695575888453.89348027541.024752795520.9613883970283.21865631918-0.1480702272721.62655819821-1.02447064176-1.71872873183-0.8295317479220.6769023166610.3068832446360.41474915019-0.147429298136-0.629063921857-0.104808497609-0.6144908218352.99066318816-0.04593336290271.23001556585-31.1750716318-7.89306634433-60.1523100769
535.58415465690.3657036416512.034215898262.042390028490.2574283407783.252767518180.1230134772610.695194974171-2.236837354241.26829098795-0.48887116241.14172549450.580190439823-1.171743253140.2200891571730.0162325223628-0.266198708428-0.2034096571812.778074533960.1752441711241.80530352387-43.4569655689-11.9892813134-50.8028722682
544.76093179822-0.2327996834352.211191184272.079543692241.654002348763.529559519650.4340835989621.42341543509-2.892933272580.133243252585-0.4880615998090.8782423563961.67890750489-0.111703397344-0.3191829526790.5214432936930.539680358812-0.05147355567521.53287818360.7013813600011.47462749048-32.0272884798-9.29131223636-53.4411694612
554.447067208740.01348826571122.057934514064.414574459422.366280434453.18822831746-0.205406669399-0.28225595475-2.02585157602-0.421230522746-1.375704160190.694058463536-1.08757061444-0.3926851002511.622136295961.526331626990.0709411672882-0.6410408661711.76612235777-0.292463431331.58977422421-45.18458233080.499735324007-54.7952502856
563.581004809871.70305980697-1.674808120256.101745872063.095027694745.0808250472-0.310860526248-0.545038741090.3226544146170.178919785009-1.273043781130.2094220639240.1864617503950.9722126632950.746869874971.10433724792-0.757365719532-0.3077122394471.986973190010.6635219675660.820753601428-27.9752525344-7.01153691803-47.7552499634
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 'C' and (resid 1 through 106 )CA1 - 1061 - 98
22chain 'C' and (resid 107 through 143 )CA107 - 14399 - 135
33chain 'C' and (resid 144 through 238 )CA144 - 238136 - 230
44chain 'G' and (resid 5 through 49 )GB5 - 491 - 39
55chain 'G' and (resid 50 through 95 )GB50 - 9540 - 75
66chain 'G' and (resid 96 through 176 )GB96 - 17676 - 156
77chain 'G' and (resid 177 through 232 )GB177 - 232157 - 210
88chain 'A' and (resid 1 through 24 )AC1 - 241 - 23
99chain 'A' and (resid 25 through 85 )AC25 - 8524 - 77
1010chain 'A' and (resid 86 through 99 )AC86 - 9978 - 91
1111chain 'A' and (resid 100 through 120 )AC100 - 12092 - 112
1212chain 'A' and (resid 121 through 155 )AC121 - 155113 - 147
1313chain 'A' and (resid 156 through 167 )AC156 - 167148 - 159
1414chain 'A' and (resid 168 through 183 )AC168 - 183160 - 175
1515chain 'A' and (resid 184 through 209 )AC184 - 209176 - 201
1616chain 'A' and (resid 210 through 240 )AC210 - 240202 - 232
1717chain 'B' and (resid 5 through 95 )BD5 - 951 - 75
1818chain 'B' and (resid 96 through 232 )BD96 - 23276 - 210
1919chain 'D' and (resid 1 through 106 )DE1 - 1061 - 98
2020chain 'D' and (resid 107 through 148 )DE107 - 14899 - 140
2121chain 'D' and (resid 149 through 238 )DE149 - 238141 - 230
2222chain 'E' and (resid 4 through 49 )EF4 - 491 - 40
2323chain 'E' and (resid 50 through 131 )EF50 - 13141 - 112
2424chain 'E' and (resid 132 through 181 )EF132 - 181113 - 162
2525chain 'E' and (resid 182 through 232 )EF182 - 232163 - 211
2626chain 'F' and (resid 1 through 143 )FG1 - 1431 - 135
2727chain 'F' and (resid 144 through 238 )FG144 - 238136 - 230
2828chain 'H' and (resid 5 through 124 )HH5 - 1241 - 104
2929chain 'H' and (resid 125 through 232 )HH125 - 232105 - 210
3030chain 'I' and (resid 438 through 442 )II438 - 4421 - 5
3131chain 'I' and (resid 443 through 455 )II443 - 4556 - 18
3232chain 'I' and (resid 456 through 468 )II456 - 46819 - 31
3333chain 'I' and (resid 469 through 484 )II469 - 48432 - 47
3434chain 'I' and (resid 485 through 494 )II485 - 49448 - 57
3535chain 'I' and (resid 495 through 501 )II495 - 50158 - 64
3636chain 'I' and (resid 502 through 521 )II502 - 52165 - 83
3737chain 'I' and (resid 522 through 527 )II522 - 52784 - 89
3838chain 'J' and (resid 438 through 451 )JJ438 - 4511 - 14
3939chain 'J' and (resid 452 through 467 )JJ452 - 46715 - 30
4040chain 'J' and (resid 468 through 477 )JJ468 - 47731 - 40
4141chain 'J' and (resid 478 through 487 )JJ478 - 48741 - 50
4242chain 'J' and (resid 488 through 527 )JJ488 - 52751 - 87
4343chain 'K' and (resid 438 through 456 )KK438 - 4561 - 19
4444chain 'K' and (resid 457 through 467 )KK457 - 46720 - 30
4545chain 'K' and (resid 468 through 481 )KK468 - 48131 - 44
4646chain 'K' and (resid 482 through 501 )KK482 - 50145 - 64
4747chain 'K' and (resid 502 through 527 )KK502 - 52765 - 90
4848chain 'L' and (resid 438 through 444 )LL438 - 4441 - 7
4949chain 'L' and (resid 445 through 451 )LL445 - 4518 - 14
5050chain 'L' and (resid 452 through 456 )LL452 - 45615 - 19
5151chain 'L' and (resid 457 through 471 )LL457 - 47120 - 34
5252chain 'L' and (resid 472 through 484 )LL472 - 48435 - 47
5353chain 'L' and (resid 485 through 494 )LL485 - 49448 - 57
5454chain 'L' and (resid 495 through 509 )LL495 - 50958 - 72
5555chain 'L' and (resid 510 through 521 )LL510 - 52173 - 81
5656chain 'L' and (resid 522 through 527 )LL522 - 52782 - 87

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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