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- PDB-7ora: Crystal structure of the T478K mutant receptor binding domain of ... -

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基本情報

登録情報
データベース: PDB / ID: 7ora
タイトルCrystal structure of the T478K mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-45 and COVOX-253 Fabs
要素
  • (COVOX-253 Fab ...) x 2
  • (COVOX-45 Fab ...) x 2
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 B.1.1.7 variant / B.1.351 variant / P.1 variant / B.1.617 variant / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN/IMMUNE SYSTEM
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Zhou, D. / Ren, J. / Stuart, D.I.
資金援助 英国, 中国, 2件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 中国
引用ジャーナル: Cell / 年: 2021
タイトル: Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.
著者: Liu, C. / Ginn, H.M. / Dejnirattisai, W. / Supasa, P. / Wang, B. / Tuekprakhon, A. / Nutalai, R. / Zhou, D. / Mentzer, A.J. / Zhao, Y. / Duyvesteyn, H.M.E. / Lopez-Camacho, C. / Slon-Campos, ...著者: Liu, C. / Ginn, H.M. / Dejnirattisai, W. / Supasa, P. / Wang, B. / Tuekprakhon, A. / Nutalai, R. / Zhou, D. / Mentzer, A.J. / Zhao, Y. / Duyvesteyn, H.M.E. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Johnson, S.A. / Ritter, T.G. / Mason, C. / Costa Clemens, S.A. / Gomes Naveca, F. / Nascimento, V. / Nascimento, F. / Fernandes da Costa, C. / Resende, P.C. / Pauvolid-Correa, A. / Siqueira, M.M. / Dold, C. / Temperton, N. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S.C. / Malik, T. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Baillie, V. / Serafin, N. / Ditse, Z. / Da Silva, K. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Madhi, S. / Nunes, M.C. / Goulder, P. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
履歴
登録2021年6月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年7月7日Provider: repository / タイプ: Initial release
改定 1.12021年7月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22021年8月18日Group: Database references / カテゴリ: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
R: Spike protein S1
A: COVOX-45 Fab heavy chain
B: COVOX-45 Fab light chain
F: COVOX-253 Fab heavy chain
G: COVOX-253 Fab light chain
C: Spike protein S1
D: COVOX-45 Fab heavy chain
E: COVOX-45 Fab light chain
H: COVOX-253 Fab heavy chain
L: COVOX-253 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)239,55226
ポリマ－236,70810
非ポリマー2,84416
水5,098283
1
R: Spike protein S1
A: COVOX-45 Fab heavy chain
B: COVOX-45 Fab light chain
F: COVOX-253 Fab heavy chain
G: COVOX-253 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,74515
ポリマ－118,3545
非ポリマー1,39110
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Spike protein S1
D: COVOX-45 Fab heavy chain
E: COVOX-45 Fab light chain
H: COVOX-253 Fab heavy chain
L: COVOX-253 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,80711
ポリマ－118,3545
非ポリマー1,4536
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)51.570, 182.385, 142.412
Angle α, β, γ (deg.)90.000, 93.038, 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 15 or resid 17 through 222 or resid 301))
d_2ens_1(chain "D" and (resid 1 through 15 or resid 17 through 222 or resid 301))
d_1ens_2chain "B"
d_2ens_2chain "E"
d_1ens_3(chain "C" and (resid 331 through 527 or resid 600 through 601))
d_2ens_3(chain "R" and (resid 331 through 527 or resid 600 through 601))
d_1ens_4(chain "F" and (resid 1 through 40 or resid 42...
d_2ens_4(chain "H" and (resid 1 through 40 or resid 42...
d_1ens_5(chain "G" and (resid 1 through 23 or resid 25 through 77 or resid 79 through 214))
d_2ens_5(chain "L" and (resid 1 through 23 or resid 25 through 77 or resid 79 through 214))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel seq-ID
d_11ens_1GLNGLYA1 - 15
d_12ens_1SERLYSA17 - 216
d_13ens_1GOLGOLA301
d_21ens_1GLNGLYD1 - 15
d_22ens_1SERLYSD17 - 216
d_23ens_1GOLGOLD301
d_11ens_2ASPARGB1 - 211
d_21ens_2ASPARGE1 - 211
d_11ens_3HISLYSC1 - 197
d_12ens_3FUCFUCK
d_13ens_3NAGNAGK
d_21ens_3HISLYSR1 - 197
d_22ens_3FUCFUCI
d_23ens_3NAGNAGI
d_11ens_4GLNALAF1 - 40
d_12ens_4GLYALAF42 - 61
d_13ens_4LYSCYSF63 - 224
d_14ens_4FUCFUCJ
d_15ens_4NAGNAGJ
d_16ens_4NAGNAGJ
d_21ens_4GLNALAH1 - 40
d_22ens_4GLYALAH42 - 61
d_23ens_4LYSCYSH63 - 224
d_24ens_4FUCFUCM
d_25ens_4NAGNAGM
d_26ens_4NAGNAGM
d_11ens_5ASPCYSG1 - 23
d_12ens_5ALASERG25 - 77
d_13ens_5LEUGLUG79 - 214
d_21ens_5ASPCYSL1 - 23
d_22ens_5ALASERL25 - 77
d_23ens_5LEUGLUL79 - 214

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(0.997649111589, -0.0249925068615, 0.0638092841636), (-0.0241427309553, -0.999609729938, -0.0140540511803), (0.0641356272809, 0.0124804812943, -0.997863146378)1.25054105275, -3.50151952174, 216.042173422
2given(0.999171222467, -0.00677034631122, 0.0401376457402), (-0.0061863452263, -0.99987345225, -0.0146563508126), (0.0402317949821, 0.0143958986252, -0.999086663296)2.94425370529, -3.70555741288, 216.256360807
3given(0.999234818549, -0.0240548611795, 0.0308405747836), (-0.0246262904951, -0.999529501331, 0.0182844684002), (0.0303862339851, -0.0190299664178, -0.999357061896)-10.6732903201, -7.27712309029, 215.739983727
4given(0.995466778144, 0.0365542858074, 0.0878047709447), (0.037484054195, -0.999257028183, -0.00896310814937), (0.0874118944575, 0.0122137551843, -0.996097377214)1.30053514125, -2.87311566386, 217.394273197
5given(0.996527119164, 0.0194024784955, 0.0809768151953), (0.0197923380523, -0.999796052835, -0.00401448494913), (0.0808824092455, 0.00560326362203, -0.996707900697)1.11183992971, -4.07815340179, 217.005274244

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要素

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タンパク質 , 1種, 2分子 RC

#1: タンパク質 Spike protein S1 / T478K mutant RBD


分子量: 23178.967 Da / 分子数: 2 / 変異: T478K / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2

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抗体 , 4種, 8分子 ADBEFHGL

#2: 抗体 COVOX-45 Fab heavy chain


分子量: 24187.152 Da / 分子数: 2 / 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)
#3: 抗体 COVOX-45 Fab light chain


分子量: 23359.775 Da / 分子数: 2 / 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)
#4: 抗体 COVOX-253 Fab heavy chain


分子量: 24371.400 Da / 分子数: 2 / 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 COVOX-253 Fab light chain


分子量: 23256.641 Da / 分子数: 2 / 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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糖 , 2種, 4分子

#6: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 367.349 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 570.542 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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非ポリマー , 3種, 295分子

#8: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C3H8O3
#9: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Cl
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 283 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.82 Å3/Da / 溶媒含有率: 56.43 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1 M BICINE pH 8.5 and 20% (w/v) PEG 10,000 / PH範囲: 8.5

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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: Diamond / ビームライン: I03 / 波長: 0.97626 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2021年5月17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: 0.97626 Å / 相対比: 1
反射解像度: 2.6→61 Å / Num. obs: 72862 / % possible obs: 90.5 % / 冗長度: 6.7 % / Biso Wilson estimate: 50.84 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.246 / Net I/σ(I): 7.3
反射 シェル解像度: 2.6→2.64 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1945 / CC1/2: 0.302

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解析

ソフトウェア
名称バージョン分類
GDA1.19_4092データ収集
PHENIX1.19_4092精密化
xia2データ削減
xia2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: 7BEL

7bel


解像度: 2.6→51.5 Å / SU ML: 0.3817 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.5435
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2448 3634 5.01 %
Rwork0.204 68969 -
obs0.206 72603 90.18 %
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: 66.02 Å2
精密化ステップサイクル: LAST / 解像度: 2.6→51.5 Å
タンパク質核酸リガンド溶媒全体
原子数16248 0 180 283 16711
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002116813
X-RAY DIFFRACTIONf_angle_d0.530522864
X-RAY DIFFRACTIONf_chiral_restr0.04282578
X-RAY DIFFRACTIONf_plane_restr0.00412919
X-RAY DIFFRACTIONf_dihedral_angle_d11.67096017
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONTorsion NCS0.59046800905
ens_2d_2EX-RAY DIFFRACTIONTorsion NCS0.502630553378
ens_3d_2RX-RAY DIFFRACTIONTorsion NCS0.448329328249
ens_4d_2HX-RAY DIFFRACTIONTorsion NCS0.44940940193
ens_5d_2LX-RAY DIFFRACTIONTorsion NCS0.565874067116
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.386730.39761328X-RAY DIFFRACTION45.98
2.63-2.670.4021800.3481502X-RAY DIFFRACTION51.2
2.67-2.710.3365760.35411642X-RAY DIFFRACTION54.8
2.71-2.750.37531050.331868X-RAY DIFFRACTION64.31
2.75-2.790.38431050.31492053X-RAY DIFFRACTION71.06
2.79-2.840.3741450.30282400X-RAY DIFFRACTION81.23
2.84-2.890.32081640.26322710X-RAY DIFFRACTION93.19
2.89-2.940.29851560.25952784X-RAY DIFFRACTION96.74
2.94-30.27361530.2522898X-RAY DIFFRACTION97.73
3-3.060.29131520.25322939X-RAY DIFFRACTION99.01
3.06-3.120.29661450.25572864X-RAY DIFFRACTION98.98
3.12-3.20.30941460.26432928X-RAY DIFFRACTION98.68
3.2-3.280.29321560.26762924X-RAY DIFFRACTION99.19
3.28-3.360.30621690.26022873X-RAY DIFFRACTION98.89
3.36-3.460.27821500.23112944X-RAY DIFFRACTION99.17
3.46-3.580.22211580.20842879X-RAY DIFFRACTION99.12
3.58-3.70.24831550.20332949X-RAY DIFFRACTION99.33
3.7-3.850.2451380.1992908X-RAY DIFFRACTION99.25
3.85-4.030.2251480.19222933X-RAY DIFFRACTION99.58
4.03-4.240.24151510.16732920X-RAY DIFFRACTION99.13
4.24-4.50.17351630.14352930X-RAY DIFFRACTION99.68
4.5-4.850.17811370.14032945X-RAY DIFFRACTION99.55
4.85-5.340.18111340.14962966X-RAY DIFFRACTION99.55
5.34-6.110.22971560.16882952X-RAY DIFFRACTION99.62
6.11-7.690.22661700.18882932X-RAY DIFFRACTION99.65
7.69-51.50.19881490.18172998X-RAY DIFFRACTION99.18
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)
19.12732371782-0.290707657264.266543556545.231854154331.042078535586.66261121736-0.280045474776-1.31125737554-0.34099764380.7192525314560.0535975193011-0.346145053373-0.5715129241080.87746347780.2969170480640.389226013445-0.08237926514280.02937319775510.7354705000110.1322289961540.428096665682-12.956-21.31894.235
21.13027273779-0.729241248814-0.8568171175153.30649880854-1.530475305072.238268194550.520517369929-0.928146855367-0.7036948338280.330113228390.120837343286-0.2420918378880.379179829537-0.519999887366-0.4571165127180.311454128419-0.0979152979093-0.1163273889850.36266075780.1080070386220.317110675471-9.502-19.88187.576
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN R AND RESID 331:349 )R331 - 349
2X-RAY DIFFRACTION2( CHAIN R AND RESID 350:364 )R350 - 364
3X-RAY DIFFRACTION3( CHAIN R AND RESID 365:421 )R365 - 421
4X-RAY DIFFRACTION4( CHAIN R AND RESID 422:459 )R422 - 459
5X-RAY DIFFRACTION5( CHAIN R AND RESID 460:494 )R460 - 494
6X-RAY DIFFRACTION6( CHAIN R AND RESID 495:527 )R495 - 527
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1:108 )A1 - 108
8X-RAY DIFFRACTION8( CHAIN A AND RESID 109:165 )A109 - 165
9X-RAY DIFFRACTION9( CHAIN A AND RESID 166:222 )A166 - 222
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1:18 )B1 - 18
11X-RAY DIFFRACTION11( CHAIN B AND RESID 19:102 )B19 - 102
12X-RAY DIFFRACTION12( CHAIN B AND RESID 103:128 )B103 - 128
13X-RAY DIFFRACTION13( CHAIN B AND RESID 129:150 )B129 - 150
14X-RAY DIFFRACTION14( CHAIN B AND RESID 151:163 )B151 - 163
15X-RAY DIFFRACTION15( CHAIN B AND RESID 164:211 )B164 - 211
16X-RAY DIFFRACTION16( CHAIN F AND RESID 1:39 )F1 - 39
17X-RAY DIFFRACTION17( CHAIN F AND RESID 40:52 )F40 - 52
18X-RAY DIFFRACTION18( CHAIN F AND RESID 53:121 )F53 - 121
19X-RAY DIFFRACTION19( CHAIN F AND RESID 122:144 )F122 - 144
20X-RAY DIFFRACTION20( CHAIN F AND RESID 145:213 )F145 - 213
21X-RAY DIFFRACTION21( CHAIN F AND RESID 214:226 )F214 - 226
22X-RAY DIFFRACTION22( CHAIN G AND RESID 1:18 )G1 - 18
23X-RAY DIFFRACTION23( CHAIN G AND RESID 19:30 )G19 - 30
24X-RAY DIFFRACTION24( CHAIN G AND RESID 31:49 )G31 - 49
25X-RAY DIFFRACTION25( CHAIN G AND RESID 50:76 )G50 - 76
26X-RAY DIFFRACTION26( CHAIN G AND RESID 77:91 )G77 - 91
27X-RAY DIFFRACTION27( CHAIN G AND RESID 92:114 )G92 - 114
28X-RAY DIFFRACTION28( CHAIN G AND RESID 115:151 )G115 - 151
29X-RAY DIFFRACTION29( CHAIN G AND RESID 152:164 )G152 - 164
30X-RAY DIFFRACTION30( CHAIN G AND RESID 165:214 )G165 - 214
31X-RAY DIFFRACTION31( CHAIN C AND RESID 331:349 )C331 - 349
32X-RAY DIFFRACTION32( CHAIN C AND RESID 350:375 )C350 - 375
33X-RAY DIFFRACTION33( CHAIN C AND RESID 376:421 )C376 - 421
34X-RAY DIFFRACTION34( CHAIN C AND RESID 422:459 )C422 - 459
35X-RAY DIFFRACTION35( CHAIN C AND RESID 460:494 )C460 - 494
36X-RAY DIFFRACTION36( CHAIN C AND RESID 495:527 )C495 - 527
37X-RAY DIFFRACTION37( CHAIN D AND RESID 1:127 )D1 - 127
38X-RAY DIFFRACTION38( CHAIN D AND RESID 128:165 )D128 - 165
39X-RAY DIFFRACTION39( CHAIN D AND RESID 166:222 )D166 - 222
40X-RAY DIFFRACTION40( CHAIN E AND RESID 1:113 )E1 - 113
41X-RAY DIFFRACTION41( CHAIN E AND RESID 114:128 )E114 - 128
42X-RAY DIFFRACTION42( CHAIN E AND RESID 129:150 )E129 - 150
43X-RAY DIFFRACTION43( CHAIN E AND RESID 151:211 )E151 - 211
44X-RAY DIFFRACTION44( CHAIN H AND RESID 1:121 )H1 - 121
45X-RAY DIFFRACTION45( CHAIN H AND RESID 122:226 )H122 - 226
46X-RAY DIFFRACTION46( CHAIN L AND RESID 1:76 )L1 - 76
47X-RAY DIFFRACTION47( CHAIN L AND RESID 77:114 )L77 - 114
48X-RAY DIFFRACTION48( CHAIN L AND RESID 115:164 )L115 - 164
49X-RAY DIFFRACTION49( CHAIN L AND RESID 165:214 )L165 - 214

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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