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- PDB-7eam: immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6 -

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基本情報

登録情報
データベース: PDB / ID: 7eam
タイトルimmune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
要素
  • Spike protein S1
  • the heavy chain of Fab fragment of antibody 7D6
  • the light chain of Fab fragment of antibody 7D6
キーワードVIRAL PROTEIN / IMMUNE SYSTEM / SARS-CoV-2 / Receptor binding domain / neutralizing antibody
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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.4 Å
データ登録者Li, T.T. / Gu, Y. / Li, S.W.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)82001756 中国
引用ジャーナル: Nat Commun / 年: 2021
タイトル: Cross-neutralizing antibodies bind a SARS-CoV-2 cryptic site and resist circulating variants.
著者: Li, T. / Xue, W. / Zheng, Q. / Song, S. / Yang, C. / Xiong, H. / Zhang, S. / Hong, M. / Zhang, Y. / Yu, H. / Zhang, Y. / Sun, H. / Huang, Y. / Deng, T. / Chi, X. / Li, J. / Wang, S. / Zhou, L. ...著者: Li, T. / Xue, W. / Zheng, Q. / Song, S. / Yang, C. / Xiong, H. / Zhang, S. / Hong, M. / Zhang, Y. / Yu, H. / Zhang, Y. / Sun, H. / Huang, Y. / Deng, T. / Chi, X. / Li, J. / Wang, S. / Zhou, L. / Chen, T. / Wang, Y. / Cheng, T. / Zhang, T. / Yuan, Q. / Zhao, Q. / Zhang, J. / McLellan, J.S. / Zhou, Z.H. / Zhang, Z. / Li, S. / Gu, Y. / Xia, N.
履歴
登録2021年3月7日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年3月17日Provider: repository / タイプ: Initial release
改定 1.12021年3月31日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
改定 2.02021年10月20日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / database_2 / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / software / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_entry_details.has_ligand_of_interest / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns.number_obs / _software.version / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle
解説: Sequence discrepancy / Provider: author / タイプ: Coordinate replacement
改定 3.02021年11月10日Group: Atomic model / Data collection / Derived calculations
カテゴリ: atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_gen.asym_id_list
改定 3.12023年11月29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

ダウンロードとリンク

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集合体

登録構造単位
A: Spike protein S1
H: the heavy chain of Fab fragment of antibody 7D6
L: the light chain of Fab fragment of antibody 7D6
B: Spike protein S1
C: the heavy chain of Fab fragment of antibody 7D6
D: the light chain of Fab fragment of antibody 7D6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,01910
ポリマ－147,7286
非ポリマー1,2914
水21,3661186
1
A: Spike protein S1
H: the heavy chain of Fab fragment of antibody 7D6
L: the light chain of Fab fragment of antibody 7D6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)74,5105
ポリマ－73,8643
非ポリマー6462
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Spike protein S1
C: the heavy chain of Fab fragment of antibody 7D6
D: the light chain of Fab fragment of antibody 7D6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)74,5105
ポリマ－73,8643
非ポリマー6462
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)37.440, 87.970, 102.720
Angle α, β, γ (deg.)89.960, 87.050, 89.980
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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要素

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抗体 , 2種, 4分子 HCLD

#2: 抗体 the heavy chain of Fab fragment of antibody 7D6


分子量: 23740.176 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#3: 抗体 the light chain of Fab fragment of antibody 7D6


分子量: 23619.990 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)

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タンパク質 / 非ポリマー , 2種, 1188分子 AB

#1: タンパク質 Spike protein S1


分子量: 26503.807 Da / 分子数: 2 / 断片: UNP residues 319-541 / 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: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P0DTC2
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1186 / 由来タイプ: 天然 / 式: H2O

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糖 , 2種, 4分子

#4: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 2 / 由来タイプ: 天然
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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詳細

研究の焦点であるリガンドがあるかN
配列の詳細Some disordered residues located at aa 135-139 of Chains H and C.

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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: 2.3 Å3/Da / 溶媒含有率: 46.55 %
結晶化温度: 293.15 K / 手法: 蒸発脱水法
詳細: PEG D5, 0.2M Potassium dihydrogen phosphate, 20% 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: SSRF / ビームライン: BL17U1 / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年1月2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: 0.9792 Å / 相対比: 1
反射解像度: 1.4→29.32 Å / Num. obs: 476102 / % possible obs: 94.7 % / 冗長度: 3.4 % / Biso Wilson estimate: 22.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Net I/σ(I): 8.8
反射 シェル解像度: 1.4→1.44 Å / 冗長度: 2.7 % / Rmerge(I) obs: 1.247 / Num. unique obs: 17141 / CC1/2: 0.331 / Rpim(I) all: 0.936 / % possible all: 89.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
Aimless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: 6M0J, 6RCO

6m0j

6rco


解像度: 1.4→22.32 Å / SU ML: 0.2 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 25.42 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1807 3906 0.82 %
Rwork0.174 472196 -
obs0.174 476102 92.32 %
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 max: 173.83 Å2 / Biso mean: 37.4867 Å2 / Biso min: 15.78 Å2
精密化ステップサイクル: final / 解像度: 1.4→22.32 Å
タンパク質核酸リガンド溶媒全体
原子数9836 0 84 1186 11106
Biso mean--102.05 42.65 -
残基数----1266
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.36291350.3854149381507382
1.42-1.440.38091020.3693152081531083
1.44-1.450.3521360.3608158091594587
1.45-1.470.41331240.3467159381606287
1.47-1.490.34481430.336162421638588
1.49-1.520.3511170.3133164301654791
1.52-1.540.31751450.2948167981694391
1.54-1.570.32671260.2768168511697792
1.57-1.590.2821620.2656171301729295
1.59-1.620.30791390.2566171811732093
1.62-1.650.27331380.2405172441738294
1.65-1.690.25941450.2326172751742095
1.69-1.720.21951430.2236172141735795
1.72-1.760.2161560.2111173231747995
1.76-1.810.20931670.2044173081747595
1.81-1.860.20691390.19173561749595
1.86-1.910.18251140.1964172671738195
1.91-1.970.20521530.1825170301718393
1.97-2.040.2191510.1761173481749995
2.04-2.130.2211350.1691171221725794
2.13-2.220.20731390.1746172311737093
2.22-2.340.16591440.1682172151735994
2.34-2.490.17411460.1761172141736095
2.49-2.680.19791260.1718173421746894
2.68-2.950.12641500.1713168211697192
2.95-3.370.16871340.1603173241745895
3.37-4.240.14191470.1367171691731694
4.24-22.320.13961500.1371168681701892
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)
10.17970.08130.19320.5428-0.22180.1854-0.02040.00570.0495-0.09440.06280.07230.0284-0.0174-00.24810.01020.01930.1995-0.00080.1925-29.902-3.57244.0132
20.32130.52280.14640.94-0.02420.7333-0.01460.0305-0.0121-0.06260.0008-0.07880.02750.056300.22320.03050.02950.1745-0.00390.2002-12.34928.08174.9547
30.0998-0.13590.11250.0628-0.15310.11780.10140.08240.2266-0.01430.0227-0.0374-0.1946-0.1412-00.2152-0.01710.01060.22490.00010.2339-20.323117.384538.5589
40.03640.04040.00680.0410.04820.06380.03060.0152-0.0134-0.107-0.02710.0861-0.2193-0.002300.23650.0010.02770.22360.00130.2234-18.30716.532825.3201
50.0545-0.0854-0.04760.26530.02850.05230.0938-0.09350.0111-0.08570.07090.06450.55410.06010.00030.2104-0.0244-0.00850.209-0.00020.1717-21.5935.613136.5079
60.0634-0.1124-0.04760.18470.12860.07080.05090.14710.0217-0.19080.06920.09270.2997-0.275700.2475-0.0415-0.02180.27990.02640.2117-27.06197.837625.7013
70.1671-0.04830.11940.05740.0420.2585-0.02790.14130.1005-0.08190.10970.0436-0.033-0.33120.00030.2297-0.02270.01780.2590.00080.2373-27.687414.142529.92
80.1926-0.16790.1180.155-0.0770.04560.0718-0.079-0.0079-0.0156-0.0413-0.00710.0568-0.11990.00010.1945-0.01980.01780.2378-0.02110.1833-24.6879.994639.2575
90.0578-0.01490.02440.0157-0.03090.04750.1379-0.01690.0525-0.1769-0.0974-0.17980.0201-0.0653-0.00010.2990.00530.01580.1916-0.00920.1976-15.56984.292424.5961
10-0.00880.0122-0.01140.0638-0.00580.005-0.12190.0589-0.01970.0080.0435-0.0339-0.0363-0.19210.00010.22560.02750.00530.2663-0.02560.2227-23.624518.09153.0596
110.05580.1132-0.05930.1591-0.1580.1115-0.1107-0.2553-0.17070.0480.16690.0523-0.0532-0.06150.00150.13740.0507-0.01040.2766-0.02760.2137-6.685911.811169.9639
120.1504-0.031-0.14520.5993-0.00440.18110.08990.1242-0.1121-0.0658-0.05920.02560.08050.087-00.15060.046-0.01020.2724-0.0320.2312-8.647712.227560.9368
130.21640.0258-0.22690.1514-0.03010.1849-0.1271-0.12710.25440.05430.0431-0.1493-0.07370.0658-0.00030.16610.0598-0.02270.2673-0.02580.2504-0.804717.86366.6693
140.07110.11660.02220.36930.23770.21880.0832-0.27030.0915-0.14780.1430.0467-0.0498-0.00850.00740.1910.0595-0.03670.3062-0.02580.2624-5.484520.905569.5098
150.1764-0.14330.1770.35990.33260.36310.055-0.1876-0.20750.29540.03890.22960.446-0.19140.00560.30580.008-0.00370.20280.01020.2511-12.7242-11.255740.387
160.5237-0.17220.20810.97070.23460.5102-0.11760.1266-0.00020.0650.07410.0543-0.02480.1207-0.00010.2032-0.0486-0.00530.2068-0.01020.2167-11.7912-7.126631.9568
170.37820.3684-0.10690.3043-0.08890.0317-0.2422-0.04890.0145-0.01770.2047-0.02790.25450.03950.00070.40610.1144-0.03230.2867-0.01650.239-3.6201-8.41153.4516
18-0.1088-0.14950.07230.1945-0.24650.3480.0279-0.05510.0650.00030.09630.03010.06730.0776-00.21470.0624-0.02640.2148-0.03120.2211-9.73114.702670.1637
190.0504-0.02180.01090.0713-0.01620.00410.2533-0.0621-0.19410.2597-0.31920.13650.23230.024-0.00050.3208-0.05350.00190.2587-0.03140.2818-17.42-4.035276.395
200.1223-0.0949-0.05490.0824-0.06310.23760.2550.11720.0356-0.1952-0.09940.02240.2035-0.16420.01330.24530.0552-0.00990.2605-0.02910.23-9.2296-0.292459.9267
210.0284-0.0886-0.06640.14370.06360.36110.05620.1425-0.11630.1683-0.03150.04780.396-0.43520.00010.26070.06590.00650.2868-0.00460.2213-16.93163.942877.6845
220.13180.1675-0.19410.1382-0.1430.1515-0.0536-0.1432-0.02560.20560.02520.05220.52420.1697-0.00030.39560.0984-0.02180.2335-0.01660.2095-7.7199-4.375476.5554
230.0475-0.06020.0354-0.0340.00050.08720.04220.08540.0314-0.08180.02110.0159-0.01320.00960.00040.2054-0.04520.02420.2172-0.03480.19120.6151-43.397493.5485
240.2052-0.22080.0750.33450.17730.1944-0.0688-0.0364-0.01310.1032-0.0275-0.1143-0.03140.0769-0.00010.28460.00310.03580.20280.02020.1954-6.9063-47.4602101.8749
250.1337-0.1123-0.06040.07110.03390.01660.2339-0.06340.33230.0637-0.0437-0.5228-0.0024-0.0660.01160.3981-0.0766-0.10260.24210.00180.3649-7.3979-57.8758101.647
260.05310.0595-0.1180.1309-0.13320.1106-0.1172-0.0394-0.02610.09440.0607-0.00990.3291-0.0475-00.2616-0.03370.02880.2059-0.00740.1904-17.4936-39.8614100.5495
270.2398-0.2875-0.09970.20310.15050.2305-0.01870.0224-0.02790.27940.04780.0640.17240.048300.2693-0.0420.03380.18020.01550.2128-19.9956-41.2625101.2414
280.0671-0.05930.08440.0315-0.00920.0536-0.08290.09270.01250.06660.07550.0936-0.283-0.1235-00.253-0.016-0.00040.2327-0.01240.2425-22.35-26.995997.4352
290.1965-0.06960.07660.2386-0.19380.01640.1003-0.00860.0355-0.2702-0.019-0.00590.004-0.033700.2462-0.0011-0.01990.20530.0070.2337-31.1832-28.507288.8026
300.1841-0.21530.23920.2315-0.250.2726-0.0195-0.02780.02950.20910.00850.00510.12210.0052-0.00010.2882-0.02570.01850.1647-0.01360.1868-13.0187-41.4539100.7757
310.08590.1160.07030.05540.09210.06940.0631-0.13790.16510.0133-0.02840.0506-0.16530.1727-0.00010.22750.0140.02360.22760.00840.2289-13.2996-26.581463.6503
320.024-0.0173-0.01030.0091-0.01530.03580.0081-0.003-0.03740.0971-0.0176-0.106-0.1819-0.0676-00.25210.00920.03020.22710.00390.2218-15.324-27.414676.9066
330.08520.1356-0.05070.1844-0.04060.03970.04470.06690.04690.08510.1754-0.08070.4871-0.01870.00010.20780.0159-0.00670.2023-0.00740.1717-12.0147-38.345165.6988
340.08530.1255-0.0590.1751-0.13340.0880.0249-0.063-0.02380.1270.0616-0.0840.3110.3474-0.00010.23930.0434-0.02460.2596-0.02620.2004-6.5527-36.103776.5217
350.1021-0.00740.04360.0456-0.11610.2693-0.0058-0.06260.03530.09570.01330.0292-0.05260.31490.00020.21960.02140.01940.26480.00310.2367-5.9406-29.796772.3002
360.19210.15440.12940.1120.05030.07470.01140.1171-0.03340.0014-0.07610.00060.06870.14230.00010.17760.01620.01060.24190.01860.1884-8.9406-33.965862.9651
370.1528-0.0135-0.03030.030.0330.03040.1109-0.00150.08520.1962-0.09760.25980.0285-0.0675-0.00020.2951-0.02070.0220.19160.00360.1919-18.0498-39.664277.6316
380.0032-0.0575-0.02420.04380.00820.0021-0.1699-0.04950.01670.012-0.0046-0.0301-0.0020.25690.00020.2385-0.0311-0.00250.28590.04660.2356-10.0014-25.891149.1617
390.0402-0.05060.03860.08520.07260.1185-0.16190.1198-0.1222-0.11280.1679-0.0873-0.0889-0.01690.00470.1582-0.0558-0.0150.27770.0270.2153-26.9304-32.215632.2615
400.18710.0397-0.16410.5495-0.24770.21660.1019-0.1291-0.07620.0808-0.0673-0.03480.0407-0.1168-00.1584-0.0447-0.01390.26970.03230.2271-24.9736-31.780641.2836
410.13040.0293-0.12030.1323-0.00560.0979-0.1250.17370.1322-0.06960.12980.0589-0.13740.0038-0.00010.1817-0.0574-0.02290.29080.03610.2535-32.8188-26.160235.5454
420.0375-0.0349-0.00790.1707-0.12930.11690.04060.2460.10910.23110.08210.0424-0.01620.2007-0.00270.2201-0.0613-0.0310.30080.04970.2889-28.1392-23.081432.705
430.18970.250.09660.4098-0.33530.2660.11960.0641-0.2377-0.43510.0109-0.28590.45380.1020.0020.3048-0.0228-0.00730.21410.01490.2544-20.9172-55.225361.8435
440.23570.1093-0.11570.1565-0.10570.0798-0.0673-0.0811-0.0403-0.10840.0451-0.13240.11180.0031-0.00010.22320.0466-0.01010.17770.00470.2352-17.9853-54.312970.9775
450.22150.12630.06160.11490.10460.162-0.1581-0.20610.1410.00590.1220.1464-0.2485-0.25110.00010.19980.0821-0.01210.27370.00880.2437-27.156-46.44671.463
460.33150.11410.18970.4886-0.3760.2821-0.1385-0.11930.0116-0.14820.0761-0.10880.0139-0.1358-0.00070.18940.0402-0.01050.2083-0.00120.2337-20.9479-51.898169.2654
470.0863-0.0956-0.07780.03730.0470.0532-0.13750.05690.08290.06490.12330.07270.4935-0.06860.00020.398-0.111-0.03190.27820.02050.2247-30.0206-52.404848.7708
48-0.10470.14720.07060.11380.11340.28450.00560.04560.0411-0.04450.0621-0.0480.102-0.066900.2399-0.0652-0.02430.22430.0340.2359-23.8946-39.323932.0585
490.0029-0.00440.00260.06510.02270.00480.24890.0827-0.0819-0.1429-0.1459-0.19340.2149-0.03330.00030.33640.0467-0.00370.27680.03290.3078-16.2097-48.066125.8159
500.18590.1548-0.14590.1557-0.08880.14410.3799-0.03420.03460.2694-0.1444-0.00910.20310.0850.0360.2536-0.0506-0.0160.24770.02070.2092-24.396-44.308142.2952
510.04240.0539-0.08780.1713-0.0680.43390.0366-0.1446-0.1464-0.1999-0.0702-0.08140.42110.46340.00140.2468-0.06320.01850.28580.00410.224-16.6864-40.097824.5256
520.0825-0.0981-0.11020.11920.1510.1594-0.04990.1158-0.0475-0.1273-0.0823-0.17650.3927-0.0919-0.00030.3891-0.0981-0.02180.23710.02310.2174-25.9147-48.40925.6604
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 324 through 393 )A324 - 393
2X-RAY DIFFRACTION2chain 'A' and (resid 394 through 527 )A394 - 527
3X-RAY DIFFRACTION3chain 'H' and (resid 1 through 17 )H1 - 17
4X-RAY DIFFRACTION4chain 'H' and (resid 18 through 32 )H18 - 32
5X-RAY DIFFRACTION5chain 'H' and (resid 33 through 44 )H33 - 44
6X-RAY DIFFRACTION6chain 'H' and (resid 45 through 60 )H45 - 60
7X-RAY DIFFRACTION7chain 'H' and (resid 61 through 83 )H61 - 83
8X-RAY DIFFRACTION8chain 'H' and (resid 84 through 98 )H84 - 98
9X-RAY DIFFRACTION9chain 'H' and (resid 99 through 113 )H99 - 113
10X-RAY DIFFRACTION10chain 'H' and (resid 114 through 126 )H114 - 126
11X-RAY DIFFRACTION11chain 'H' and (resid 127 through 152 )H127 - 152
12X-RAY DIFFRACTION12chain 'H' and (resid 153 through 191 )H153 - 191
13X-RAY DIFFRACTION13chain 'H' and (resid 192 through 209 )H192 - 209
14X-RAY DIFFRACTION14chain 'H' and (resid 210 through 220 )H210 - 220
15X-RAY DIFFRACTION15chain 'L' and (resid 1 through 18 )L1 - 18
16X-RAY DIFFRACTION16chain 'L' and (resid 19 through 102 )L19 - 102
17X-RAY DIFFRACTION17chain 'L' and (resid 103 through 114 )L103 - 114
18X-RAY DIFFRACTION18chain 'L' and (resid 115 through 145 )L115 - 145
19X-RAY DIFFRACTION19chain 'L' and (resid 146 through 156 )L146 - 156
20X-RAY DIFFRACTION20chain 'L' and (resid 157 through 175 )L157 - 175
21X-RAY DIFFRACTION21chain 'L' and (resid 176 through 198 )L176 - 198
22X-RAY DIFFRACTION22chain 'L' and (resid 199 through 214 )L199 - 214
23X-RAY DIFFRACTION23chain 'B' and (resid 324 through 353 )B324 - 353
24X-RAY DIFFRACTION24chain 'B' and (resid 354 through 380 )B354 - 380
25X-RAY DIFFRACTION25chain 'B' and (resid 381 through 393 )B381 - 393
26X-RAY DIFFRACTION26chain 'B' and (resid 394 through 409 )B394 - 409
27X-RAY DIFFRACTION27chain 'B' and (resid 410 through 442 )B410 - 442
28X-RAY DIFFRACTION28chain 'B' and (resid 443 through 459 )B443 - 459
29X-RAY DIFFRACTION29chain 'B' and (resid 460 through 494 )B460 - 494
30X-RAY DIFFRACTION30chain 'B' and (resid 495 through 527 )B495 - 527
31X-RAY DIFFRACTION31chain 'C' and (resid 1 through 17 )C1 - 17
32X-RAY DIFFRACTION32chain 'C' and (resid 18 through 32 )C18 - 32
33X-RAY DIFFRACTION33chain 'C' and (resid 33 through 44 )C33 - 44
34X-RAY DIFFRACTION34chain 'C' and (resid 45 through 60 )C45 - 60
35X-RAY DIFFRACTION35chain 'C' and (resid 61 through 83 )C61 - 83
36X-RAY DIFFRACTION36chain 'C' and (resid 84 through 98 )C84 - 98
37X-RAY DIFFRACTION37chain 'C' and (resid 99 through 113 )C99 - 113
38X-RAY DIFFRACTION38chain 'C' and (resid 114 through 126 )C114 - 126
39X-RAY DIFFRACTION39chain 'C' and (resid 127 through 152 )C127 - 152
40X-RAY DIFFRACTION40chain 'C' and (resid 153 through 191 )C153 - 191
41X-RAY DIFFRACTION41chain 'C' and (resid 192 through 209 )C192 - 209
42X-RAY DIFFRACTION42chain 'C' and (resid 210 through 220 )C210 - 220
43X-RAY DIFFRACTION43chain 'D' and (resid 1 through 18 )D1 - 18
44X-RAY DIFFRACTION44chain 'D' and (resid 19 through 38 )D19 - 38
45X-RAY DIFFRACTION45chain 'D' and (resid 39 through 61 )D39 - 61
46X-RAY DIFFRACTION46chain 'D' and (resid 62 through 102 )D62 - 102
47X-RAY DIFFRACTION47chain 'D' and (resid 103 through 114 )D103 - 114
48X-RAY DIFFRACTION48chain 'D' and (resid 115 through 145 )D115 - 145
49X-RAY DIFFRACTION49chain 'D' and (resid 146 through 156 )D146 - 156
50X-RAY DIFFRACTION50chain 'D' and (resid 157 through 175 )D157 - 175
51X-RAY DIFFRACTION51chain 'D' and (resid 176 through 198 )D176 - 198
52X-RAY DIFFRACTION52chain 'D' and (resid 199 through 214 )D199 - 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