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- PDB-8eb2: Structure of HLA-A*02:01 in complex with NY-ESO-1 peptide and PA2... -

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基本情報

登録情報
データベース: PDB / ID: 8eb2
タイトルStructure of HLA-A*02:01 in complex with NY-ESO-1 peptide and PA2.1 Fab
要素
  • Beta-2-microglobulin
  • HLA-A*02:01 alpha chain
  • NY-ESO-1 peptide
  • PA2.1 Fab Heavy Chain
  • PA2.1 Fab Light Chain
キーワードIMMUNE SYSTEM / Complex / Fab / antibody / MHC class I
機能・相同性
機能・相同性情報


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
類似検索 - 分子機能
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
Beta-2-microglobulin / HLA class I antigen
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.9 Å
データ登録者Jette, C.A. / West, A.P.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Mol Ther Oncolytics / 年: 2022
タイトル: HLA-A∗02-gated safety switch for cancer therapy has exquisite specificity for its allelic target antigen.
著者: Mock, J.Y. / Winters, A. / Riley, T.P. / Bruno, R. / Naradikian, M.S. / Sharma, S. / Jette, C.A. / Elshimali, R. / Gahrs, C. / Toledo-Warshaviak, D. / West Jr., A.P. / Kamb, A. / Hamburger, A.E.
履歴
登録2022年8月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年11月30日Provider: repository / タイプ: Initial release
改定 1.12023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id
改定 1.22024年1月31日Group: Structure summary / カテゴリ: audit_author / Item: _audit_author.name

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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: HLA-A*02:01 alpha chain
B: Beta-2-microglobulin
C: NY-ESO-1 peptide
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
F: NY-ESO-1 peptide
G: HLA-A*02:01 alpha chain
H: Beta-2-microglobulin
I: NY-ESO-1 peptide
J: PA2.1 Fab Heavy Chain
L: PA2.1 Fab Light Chain
K: PA2.1 Fab Heavy Chain
M: PA2.1 Fab Light Chain
N: PA2.1 Fab Heavy Chain
O: PA2.1 Fab Light Chain


分子量 (理論値)分子数
合計 (水以外)277,75815
ポリマ－277,75815
非ポリマー00
水00
1
A: HLA-A*02:01 alpha chain
B: Beta-2-microglobulin
C: NY-ESO-1 peptide
K: PA2.1 Fab Heavy Chain
M: PA2.1 Fab Light Chain


分子量 (理論値)分子数
合計 (水以外)92,5865
ポリマ－92,5865
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
F: NY-ESO-1 peptide
J: PA2.1 Fab Heavy Chain
L: PA2.1 Fab Light Chain


分子量 (理論値)分子数
合計 (水以外)92,5865
ポリマ－92,5865
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: HLA-A*02:01 alpha chain
H: Beta-2-microglobulin
I: NY-ESO-1 peptide
N: PA2.1 Fab Heavy Chain
O: PA2.1 Fab Light Chain


分子量 (理論値)分子数
合計 (水以外)92,5865
ポリマ－92,5865
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)116.800, 148.790, 199.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#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 1 through 274)
d_2ens_1chain "D"
d_3ens_1(chain "G" and resid 1 through 274)
d_1ens_2(chain "B" and (resid 0 through 98 or (resid 99...
d_2ens_2chain "E"
d_3ens_2chain "H"
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"
d_1ens_4chain "J"
d_2ens_4chain "K"
d_3ens_4chain "N"
d_1ens_5(chain "L" and (resid 1 through 9 or (resid 10...
d_2ens_5(chain "M" and (resid 1 through 9 or (resid 10...
d_3ens_5(chain "O" and (resid 1 through 37 or resid 39 through 217))

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_1GLYGLYTRPTRPAA1 - 2741 - 274
d_21ens_1GLYGLYTRPTRPDD1 - 2741 - 274
d_31ens_1GLYGLYTRPTRPGG1 - 2741 - 274
d_11ens_2METMETMETMETBB0 - 991 - 100
d_21ens_2METMETMETMETEE0 - 991 - 100
d_31ens_2METMETMETMETHH0 - 991 - 100
d_11ens_3SERSERVALVALCC1 - 91 - 9
d_21ens_3SERSERVALVALFF1 - 91 - 9
d_31ens_3SERSERVALVALII1 - 91 - 9
d_11ens_4GLNGLNLYSLYSJJ1 - 2151 - 215
d_21ens_4GLNGLNLYSLYSKL1 - 2151 - 215
d_31ens_4GLNGLNLYSLYSNN1 - 2151 - 215
d_11ens_5ASPASPTYRTYRLK1 - 371 - 37
d_12ens_5GLUGLUGLYGLYLK39 - 21739 - 217
d_21ens_5ASPASPTYRTYRMM1 - 371 - 37
d_22ens_5GLUGLUGLYGLYMM39 - 21739 - 217
d_31ens_5ASPASPTYRTYROO1 - 371 - 37
d_32ens_5GLUGLUGLYGLYOO39 - 21739 - 217

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixベクター
1given(0.988779233665, 0.147693558135, -0.0224107107817), (-0.0842755299767, 0.675377464037, 0.732641055442), (0.123342053329, -0.722531586823, 0.680246164211)0.865216310745, -71.9869585355, 43.2444647056
2given(-0.999294353478, 0.0121628700616, 0.0355367373257), (-0.018733772247, 0.658642666115, -0.752222629379), (-0.0325551975157, -0.75235756324, -0.65795004077)-228.212716842, -19.0185655564, 66.5895966799
3given(0.988993870426, 0.147579185967, -0.0105597409587), (-0.0925871271434, 0.672976519209, 0.733846188572), (0.115406880849, -0.724791686254, 0.679233585293)0.70817554652, -73.1216883782, 42.0502464497
4given(-0.999011219965, 0.0154631464527, 0.0416830119512), (-0.0210719017158, 0.660881268631, -0.750194590577), (-0.0391478906408, -0.750331153474, -0.659901964525)-228.079829857, -19.4192197039, 65.4931859767
5given(0.992291021541, 0.120721595792, -0.0280147260862), (-0.0600898779512, 0.666382532411, 0.743184719343), (0.108386969401, -0.73577212288, 0.668499549781)1.6331202791, -68.5492486629, 41.2063188915
6given(-0.996537647779, 0.0693395500006, 0.0458774821138), (0.0089514748204, 0.63806325823, -0.769931912312), (-0.0826594680477, -0.766855465719, -0.636474749726)-228.578970549, -14.7357685252, 59.2273913773
7given(0.996318035668, 0.0088448209805, 0.085276848817), (0.0621794598453, 0.61025796979, -0.789758776514), (-0.0590261516252, 0.792153381265, 0.607461055521)-5.3558421452, 68.0656932755, 23.9426710308
8given(-0.998975843252, -0.04390095273, -0.0109531250141), (0.0178194867104, -0.159212673191, -0.987083477011), (0.0415900287515, -0.986267727873, 0.159831906901)-227.32220923, 3.22082604875, 11.1535880101
9given(0.996124188358, 0.000977983294363, 0.0879525151272), (0.0695294456527, 0.603688336275, -0.794182629395), (-0.0538726048726, 0.797219816734, 0.601280555357)-5.6823262091, 68.5391322519, 24.9265722714
10given(-0.999269272002, -0.0370406025902, -0.00942951703431), (0.0154868107172, -0.166824034723, -0.985865051684), (0.0349439655099, -0.985290685635, 0.167275772531)-227.160507169, 2.63244931076, 10.0284377712

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要素

#1: タンパク質 HLA-A*02:01 alpha chain / HLA class I antigen / HLA class I histocompatibility antigen / HLA class I histocompatibility ...HLA class I antigen / HLA class I histocompatibility antigen / HLA class I histocompatibility antigen A alpha chain / A alpha chain / MHC class I antigen / MHC class I protein / MHC class I protein (HLA-A)


分子量: 31854.203 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A, HLA / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q53Z42
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 3 / Fragment: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P61769
#3: タンパク質・ペプチド NY-ESO-1 peptide


分子量: 1090.335 Da / 分子数: 3 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#4: 抗体 PA2.1 Fab Heavy Chain


分子量: 23728.516 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 PA2.1 Fab Light Chain


分子量: 24033.703 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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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: 3.12 Å3/Da / 溶媒含有率: 60.6 %
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: 0.2M L-Proline, 0.1M HEPES pH 7.5, 13% PEG3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRL / ビームライン: BL12-2 / 波長: 0.98 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2022年4月1日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.98 Å / 相対比: 1
反射解像度: 2.9→49.6 Å / Num. obs: 145809 / % possible obs: 99.12 % / 冗長度: 6.7 % / Biso Wilson estimate: 76.85 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.19
反射 シェル解像度: 2.9→3.01 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7620 / CC1/2: 0.381 / % possible all: 95.2

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解析

ソフトウェア
名称バージョン分類
Cootモデル構築
PHENIX1.19.1_4122精密化
PHASER位相決定
XDSデータ削減
Aimlessデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 1S9X, 3HC0

1s9x

3hc0


解像度: 2.9→49.59 Å / SU ML: 0.5886 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 33.5291
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2844 3749 2.57 %
Rwork0.2394 142060 -
obs0.2406 145809 98.2 %
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: 91.2 Å2
精密化ステップサイクル: LAST / 解像度: 2.9→49.59 Å
タンパク質核酸リガンド溶媒全体
原子数19374 0 0 0 19374
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.009419875
X-RAY DIFFRACTIONf_angle_d1.178626993
X-RAY DIFFRACTIONf_chiral_restr0.06222902
X-RAY DIFFRACTIONf_plane_restr0.00973472
X-RAY DIFFRACTIONf_dihedral_angle_d15.34257172
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.806417036139
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.694195936429
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.583890034758
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.700929502331
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.444967079366
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.565955606784
ens_4d_2JX-RAY DIFFRACTIONTorsion NCS0.770994661484
ens_4d_3JX-RAY DIFFRACTIONTorsion NCS1.043456766
ens_5d_2KX-RAY DIFFRACTIONTorsion NCS0.677249956591
ens_5d_3KX-RAY DIFFRACTIONTorsion NCS0.756939343847
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.51771120.54824103X-RAY DIFFRACTION77.03
2.94-2.980.53321340.49985112X-RAY DIFFRACTION94.49
2.98-3.020.52061360.44365157X-RAY DIFFRACTION97.05
3.02-3.060.42191400.41045295X-RAY DIFFRACTION98.16
3.06-3.110.39311370.40315225X-RAY DIFFRACTION98.24
3.11-3.160.36971410.36855385X-RAY DIFFRACTION99
3.16-3.210.41311370.35055228X-RAY DIFFRACTION98.82
3.21-3.260.3461450.3315323X-RAY DIFFRACTION99.02
3.26-3.320.35271370.3275318X-RAY DIFFRACTION98.84
3.32-3.390.33691360.3165289X-RAY DIFFRACTION98.76
3.39-3.460.34131400.31285271X-RAY DIFFRACTION98.42
3.46-3.530.38861430.30845324X-RAY DIFFRACTION99.65
3.53-3.610.33411380.31135364X-RAY DIFFRACTION99.85
3.61-3.70.29351460.26485366X-RAY DIFFRACTION99.78
3.7-3.80.34191400.24755317X-RAY DIFFRACTION99.85
3.8-3.920.31311380.24455361X-RAY DIFFRACTION99.82
3.92-4.040.31511430.22465366X-RAY DIFFRACTION99.93
4.04-4.190.24381450.22075317X-RAY DIFFRACTION99.76
4.19-4.350.2771390.20425325X-RAY DIFFRACTION99.73
4.35-4.550.23261430.19355286X-RAY DIFFRACTION98.66
4.55-4.790.23621390.1785357X-RAY DIFFRACTION99.76
4.79-5.090.23931480.17745371X-RAY DIFFRACTION99.96
5.09-5.480.25411410.1835303X-RAY DIFFRACTION99.67
5.48-6.030.20871340.19535366X-RAY DIFFRACTION99.82
6.03-6.910.25911400.21615315X-RAY DIFFRACTION99
6.91-8.690.22881360.1925339X-RAY DIFFRACTION99.93
8.69-49.590.19961410.16685277X-RAY DIFFRACTION98.29
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)
10.3608585738210.1629777627630.1758984383170.3710698439960.05349135898450.591527053196-0.0427151958092-0.02087785953440.029970298375-0.0516134093506-0.105729192423-0.0569444211301-0.0743049184547-0.0548639203225-4.09587682653E-60.600899239367-0.08157232467160.002178389845860.429099594839-0.0113606616340.494694387386-148.5484637882.216954693226.31772280352
20.1473572918310.0112757784461-0.03955407318510.274089529529-0.188715949560.2950005430110.112654566765-0.117567920711-0.135790953201-0.0777085948202-0.143584039904-0.4991467368640.04169207620690.06315545719240.001086181927850.5464442699860.03067783610450.04253627104580.536144221140.04026656690860.454242974922-141.7060014-31.786385681613.0810196818
30.6268619021-0.143987912159-0.3657259720140.2685802187420.07165004855320.256079675644-0.0952571960473-0.0459048173545-0.06387844903580.008652151909110.09968486632340.204134451284-0.0777279165351-0.1188322592580.0002475619094460.5460631832550.02602076577150.02770874325520.510257092341-0.0618040136410.477009872091-160.582288901-19.841261656516.8022029551
40.619094030101-0.0233990022975-0.1969741228680.2867461939840.1613498132760.516363856963-0.0619607934727-0.0980975450351-0.006743111221070.0158254245556-0.05867750445760.08398645884830.04506894182630.016848307094-0.0002128477917510.496025407089-0.00714334516768-0.01514183940250.478771737507-0.009595529446950.385676943332-145.483858503-53.248155937828.413748428
50.136204700986-0.0289369411815-0.1106662494320.1373375217110.103900315420.1770359404050.115862021766-0.645095641836-0.712435918647-0.150270584494-0.164210823155-0.1120066597440.6138656235150.0270993670802-0.06564042836751.060052668450.06807133217640.01655318317311.143292845160.4403430038550.899402501142-144.889470767-73.155747819457.6527364593
60.194115038468-0.00570788689312-0.102735806060.304837480571-0.05004243756790.2031252644690.0323168788891-0.277447138315-0.00202223657229-0.00841066382582-0.07754518934340.2851644034580.194350623522-0.462804626221-6.59271617818E-50.585867785397-0.09389922432330.130394009940.8700914699470.04085419548590.644193137783-161.217501638-59.260122095749.3035436452
70.442242687185-0.1929698482510.3046640935680.3933826266180.1107905588090.468981048298-0.1336305788570.4392330856070.500168913569-0.05653117524270.00600995808823-0.0558099749633-0.2722815652130.41416591145-0.000637319339420.685271915855-0.0529212244285-0.1163251313250.658325673001-0.04735258933190.784836964432-79.5617946291-19.629341180765.6084107222
80.205166295547-0.10926783132-0.009576579760110.366111960488-0.4382977115330.9826357041740.184484305394-0.00545301724252-0.1524691981370.1622094163630.08892439293270.620266832656-0.2868336216530.02847351959520.06176566925710.761313802025-0.0518877317342-0.05033492600080.415603145316-0.0247585742740.699724027086-86.4758187983-46.93968343486.4789038523
90.152046479218-0.00108950030603-0.1175728163030.04258011710470.03874242991020.3113936619950.09852356144270.348920631282-0.186019233574-0.315344888935-0.108209278441-0.04880051157430.0815685226510.2598553039-0.0005804624886710.7054233653190.0527782793637-0.1045997160430.723364144544-0.1584701522810.875512400165-67.2483430376-41.741835105775.5688472349
100.322284126241-0.00495309954868-0.2194961209220.43005166288-0.07031573304420.335788085062-0.0126016469656-0.4280182355660.0243964446874-0.05048521737840.08121073144560.260689991465-0.0836757990118-0.004047712006220.006680493786910.531710129921-0.0267440595659-0.05125973887750.612693308266-0.04766397433830.33022151236-108.800432254-46.711280579637.4945813322
110.257038802154-0.0951817403390.0135102115804-0.006674192213820.01121761206590.184394825546-0.208319868528-0.2600645952970.813936197572-0.163377855238-0.1880906018830.0363842230496-0.336071798027-0.270138317844-0.001293269947370.551212582398-0.0408631600037-0.1003603836860.659685435795-0.1441437702720.70911634947-79.3466266237-33.667350485122.0112834347
120.223034708127-0.217989292496-0.2428757190910.8242022715460.6872873949960.941927660505-0.0779339296447-0.278527060277-0.534411533132-0.0941602623157-0.476042030845-0.2767697014270.1102839617460.130359057722-0.2751246185190.622841765672-0.0456047661561-0.0136503071160.6250971273950.3295224179880.747860865028-110.966310823.1895973657416.123854164
130.0650739646258-0.055073452353-0.04974293963650.06755439573390.0461987061430.09380276233340.204484148094-1.253596188440.0672819729337-0.02520933121560.0646199457101-0.471980734349-0.09323054232550.08315340928670.007925630220830.811941581064-0.15949534497-0.2292495681951.299799854860.1679814454481.12853709696-82.835343587425.197490266515.3428720946
140.2496309908720.0558740143-0.03009627096980.2111401408240.3292242296870.5713510690420.0394972266998-0.206713489823-0.3595207738860.07890492911710.04555141915330.151115494460.056483884941-0.0816158411007-0.0007065971710430.4320526491730.01616029341740.001033270248360.4356691098150.007247258957340.460361111532-109.849923071-57.071704565418.2239569383
150.222804332041-0.1055290327170.06991639331580.1939277936980.1775028501180.1910597165180.08778264236280.011389812914-0.05118836642250.03051846668930.00197106653317-0.04382518999680.06018590540630.213393592741-4.95879005938E-50.449121823698-0.0362325004395-0.007225469283530.633690709716-0.04044914369480.555188735396-74.010255793-48.590267134317.2708304493
160.405792558897-0.0985702825796-0.08222650366660.193538181118-0.2293913941870.4529574813660.01388984824420.160893300142-0.5852452704060.115882293309-0.166794573817-0.02767072786260.264321543756-0.105494211349-0.009518147675270.550859960908-0.03948848490830.05819741321610.5324644294850.1236103946120.686367986031-113.57214981712.0247256163-3.67028331666
170.1620310425910.105251168514-0.001036459523880.09646964992170.02585460579080.1725611294180.111654116765-0.105668573706-0.140977265556-0.062097519289-0.113145797208-0.607974857467-0.03540465003090.386624139364-0.0002976538021180.695294389001-0.0661974854332-0.1098085267411.00979053930.2145674659131.2413128298-77.905280849920.31663358980.543994118079
180.1548792934670.136719893551-0.06574434737810.575114089266-0.245749972340.126974691104-0.12295816359-0.0570295667058-0.1756463832310.536578377259-0.3941930049271.443964455520.0834968014367-0.204782724712-0.2707997747560.307273171404-0.331172978913-0.4104489700020.200930239509-1.038315694371.83765055343-116.960663099-28.303810473358.6954199392
190.1775725210920.0620692518437-0.1934510061840.063737153196-0.0499772544110.287621913895-0.6968694826310.268775148561-0.789853554288-0.5090775765440.00445612595475-0.004453389829430.275730414271-0.0445008087109-0.2733204008530.789131918055-0.54103045387-0.3251625707051.95847107349-0.8658724210641.49667949478-146.850733207-14.551956647144.5568840968
200.8233223018820.693480267593-0.810982402581.380211744960.1863939922182.091774983010.0309417000332-0.00888022382162-0.2499970204950.363100477151-0.5741770658070.521042672060.128215562257-0.148754006559-1.110439326770.6957811805470.076648368192-0.2090585741460.51051835955-0.3399956120331.13396379894-115.46734346-7.4560982051665.3475786712
210.0405243153784-0.02143699393310.01394885701970.05416443119810.02882315886270.01830699049630.1177506569870.261977196786-0.2066735639060.640159018778-0.04772651580590.185548719979-0.0441495185086-0.6057778472630.002206886972561.027317409560.244905391701-0.08106867455761.84208543725-0.7095582001911.55997236644-151.552206872-7.4993567007158.3418201392
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 1:176AA1 - 1761 - 176
22chain A and resid 177:275AA177 - 275177 - 275
33chain B and resid 0:99BB0 - 991 - 100
44chain D and resid 1: 181DD1 - 1811 - 181
55chain D and resid 182:274DD182 - 274182 - 274
66chain E and resid 0:99EE0 - 991 - 100
77chain G and resid 1:176GG1 - 1761 - 176
88chain G and resid 177:275GG177 - 275177 - 275
99chain H and resid 0:99HH0 - 991 - 100
1010chain J and resid 1:118JJ1 - 1181 - 118
1111chain J and resid 119:219JJ119 - 219119 - 215
1212chain K and resid 1:118KL1 - 1181 - 118
1313chain K and resid 119:219KL119 - 219119 - 215
1414chain L and resid 1:112LK1 - 1121 - 112
1515chain L and resid 113:217LK113 - 217113 - 217
1616chain M and resid 1:112MM1 - 1121 - 112
1717chain M and resid 113:217MM113 - 217113 - 217
1818chain N and resid 1:118NN1 - 1181 - 118
1919chain N and resid 119:219NN119 - 219119 - 215
2020chain O and resid 1:112OO1 - 1121 - 112
2121chain O and resid 113:217OO113 - 217113 - 217

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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://pdbjlvh1.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