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- PDB-6x5n: Crystal structure of a stabilized PAN ENE bimolecular triplex wit... -

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基本情報

登録情報
データベース: PDB / ID: 6x5n
タイトルCrystal structure of a stabilized PAN ENE bimolecular triplex with a GC-clamped polyA tail, in complex with Fab-BL-3,6
要素
  • Heavy chain Fab Bl-3 6
  • Light chain Fab BL-3 6
  • ggPAN RNA (39-MER)
  • ggcA9 RNA (12-MER)
キーワードImmune System/RNA / Viral encoded RNA / RNA therapeutics / structure-function studies / Small molecules binding / PAN Triplex / ggENE / ggcA9 / RNA / Immune System-RNA complex
機能・相同性RNA / RNA (> 10)
機能・相同性情報
生物種Mus musculus (ハツカネズミ)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.3 Å
データ登録者Swain, M. / Li, M. / Woldawer, A. / LeGrice, S.F.J.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI) 米国
引用ジャーナル: Nucleic Acids Res. / 年: 2021
タイトル: Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands.
著者: Swain, M. / Ageeli, A.A. / Kasprzak, W.K. / Li, M. / Miller, J.T. / Sztuba-Solinska, J. / Schneekloth, J.S. / Koirala, D. / Piccirili, J. / Fraboni, A.J. / Murelli, R.P. / Wlodawer, A. / ...著者: Swain, M. / Ageeli, A.A. / Kasprzak, W.K. / Li, M. / Miller, J.T. / Sztuba-Solinska, J. / Schneekloth, J.S. / Koirala, D. / Piccirili, J. / Fraboni, A.J. / Murelli, R.P. / Wlodawer, A. / Shapiro, B.A. / Baird, N. / Le Grice, S.F.J.
履歴
登録2020年5月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月1日Provider: repository / タイプ: Initial release
改定 2.02021年2月3日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _citation.title / _ndb_struct_na_base_pair.buckle ..._citation.title / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.i_auth_asym_id / _ndb_struct_na_base_pair.i_auth_seq_id / _ndb_struct_na_base_pair.i_label_asym_id / _ndb_struct_na_base_pair.i_label_comp_id / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_auth_asym_id / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.j_label_asym_id / _ndb_struct_na_base_pair.j_label_comp_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.i_auth_asym_id_1 / _ndb_struct_na_base_pair_step.i_auth_asym_id_2 / _ndb_struct_na_base_pair_step.i_auth_seq_id_1 / _ndb_struct_na_base_pair_step.i_auth_seq_id_2 / _ndb_struct_na_base_pair_step.i_label_asym_id_1 / _ndb_struct_na_base_pair_step.i_label_asym_id_2 / _ndb_struct_na_base_pair_step.i_label_comp_id_1 / _ndb_struct_na_base_pair_step.i_label_comp_id_2 / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_auth_asym_id_1 / _ndb_struct_na_base_pair_step.j_auth_asym_id_2 / _ndb_struct_na_base_pair_step.j_auth_seq_id_1 / _ndb_struct_na_base_pair_step.j_auth_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_asym_id_1 / _ndb_struct_na_base_pair_step.j_label_asym_id_2 / _ndb_struct_na_base_pair_step.j_label_comp_id_1 / _ndb_struct_na_base_pair_step.j_label_comp_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.step_name / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_entry_details.has_ligand_of_interest / _pdbx_nonpoly_scheme.auth_seq_num / _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 / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct.title / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom_lim.selection_details / _struct_sheet.number_strands
解説: Ligand geometry / Provider: author / タイプ: Coordinate replacement
改定 2.12021年12月22日Group: Advisory / Database references
カテゴリ: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22021年12月29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_author.identifier_ORCID
改定 2.32023年10月18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_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
l: Light chain Fab BL-3 6
h: Heavy chain Fab Bl-3 6
H: Heavy chain Fab Bl-3 6
L: Light chain Fab BL-3 6
R: ggPAN RNA (39-MER)
A: ggcA9 RNA (12-MER)
r: ggPAN RNA (39-MER)
a: ggcA9 RNA (12-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)152,04110
ポリマ－151,8498
非ポリマー1922
水1,13563
1
l: Light chain Fab BL-3 6
h: Heavy chain Fab Bl-3 6
r: ggPAN RNA (39-MER)
a: ggcA9 RNA (12-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,0215
ポリマ－75,9254
非ポリマー961
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
H: Heavy chain Fab Bl-3 6
L: Light chain Fab BL-3 6
R: ggPAN RNA (39-MER)
A: ggcA9 RNA (12-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,0215
ポリマ－75,9254
非ポリマー961
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)43.299, 76.182, 110.523
Angle α, β, γ (deg.)72.223, 88.584, 86.569
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GGAAchain 'A'AF1 - 121 - 12
211GGAAchain 'a'aH1 - 121 - 12
122GLUGLUSERSERchain 'H'HC4 - 2271 - 224
222GLUGLUSERSERchain 'h'hB4 - 2271 - 224
133SERSERGLUGLUchain 'L'LD1 - 2141 - 214
233SERSERGLUGLUchain 'l'lA1 - 2141 - 214
144GGUU(chain 'R' and (resid 1 through 30 or resid 33...RE1 - 301 - 30
154CCCC(chain 'R' and (resid 1 through 30 or resid 33...RE33 - 3933 - 39
244GGUU(chain 'r' and (resid 1 through 30 or resid 33...rG1 - 301 - 30
254CCCC(chain 'r' and (resid 1 through 30 or resid 33...rG33 - 3933 - 39

NCSアンサンブル:
ID
1
2
3
4

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要素

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RNA鎖 , 2種, 4分子 RrAa

#3: RNA鎖 ggPAN RNA (39-MER)


分子量: 24763.496 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#4: RNA鎖 ggcA9 RNA (12-MER)


分子量: 3913.488 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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抗体 , 2種, 4分子 lLhH

#1: 抗体 Light chain Fab BL-3 6


分子量: 23394.891 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Mus musculus (ハツカネズミ)
#2: 抗体 Heavy chain Fab Bl-3 6


分子量: 23852.641 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Mus musculus (ハツカネズミ)

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非ポリマー , 2種, 65分子

#5: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4 / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 63 / 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Y

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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: 2.28 Å3/Da / 溶媒含有率: 46.1 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 / 詳細: 0.1 M Tris HCL, 0.2 M Li2SO4, 22% PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年2月20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: 1 Å / 相対比: 1
反射解像度: 3.3→72.43 Å / Num. obs: 18323 / % possible obs: 90.8 % / 冗長度: 2.3 % / Biso Wilson estimate: 82.53 Å2 / Rsym value: 0.045 / Net I/σ(I): 12.1
反射 シェル解像度: 3.3→3.56 Å / Rmerge(I) obs: 0.108 / Num. unique obs: 3255

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
XDSデータ削減
SCALEPACK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: 6b14

6b14


解像度: 3.3→37.99 Å / SU ML: 0.4562 / 交差検証法: FREE R-VALUE / σ(F): 2.18 / 位相誤差: 30.8657
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2668 613 3.35 %
Rwork0.184 17687 -
obs0.1868 18300 90.76 %
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: 112.78 Å2
精密化ステップサイクル: LAST / 解像度: 3.3→37.99 Å
タンパク質核酸リガンド溶媒全体
原子数6642 2164 10 63 8879
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00999218
X-RAY DIFFRACTIONf_angle_d1.335912996
X-RAY DIFFRACTIONf_chiral_restr0.06231546
X-RAY DIFFRACTIONf_plane_restr0.00871282
X-RAY DIFFRACTIONf_dihedral_angle_d11.7175266
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.630.29331290.22543936X-RAY DIFFRACTION80.77
3.63-4.160.34891680.2244615X-RAY DIFFRACTION95.49
4.16-5.240.25071900.17534527X-RAY DIFFRACTION93.06
5.24-37.990.23241260.15984609X-RAY DIFFRACTION93.73
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)
18.433787147140.537876303127-1.914531321988.66558672313-4.634396297476.70431325142-0.265668402413-1.032783294341.075628310760.2435521027580.4215058276150.388096559699-0.4742133519780.385400588781-0.2137581407910.784961437609-0.06629623650070.1423559490940.643251746088-0.337845966240.91257819167939.395141185248.514281837198.3744351406
23.85658247619-0.8409884514621.650054581278.81424247828-2.745753918984.69155261532-0.314374631357-0.1296348058940.5378102390380.1396796223950.18826638554-0.386098517795-0.7967719899450.5079235860020.07258702016240.539838895037-0.2592910223630.1411104484680.51587276831-0.1514494775940.6215721657846.359482655542.451115380596.8645465849
36.796394391452.819739357364.569586990321.146359073091.871482052863.06972366815-1.040000441931.240301726811.59195953072-1.441472137710.8437587903631.5034297344-0.619254794986-0.3858341146240.2470496184791.16690257869-0.306886666438-0.3050901531980.8744607381170.207565889171.0449493334734.440864748553.056644998374.399401277
46.291700671564.348006617987.269660506775.700959083676.64405847562.05030016121-1.062944381320.9986985821160.601759281343-1.560611193451.053695427941.03999501498-1.28589967062-0.27705257496-0.1151788609391.66276189358-0.454917687475-0.1274255113941.356824384440.4937145970821.0393786864923.311230486445.37202833665.7083161323
52.71702062995-1.22681002661-2.044940098460.6309859339460.9885141257541.58300801315-0.2881928001761.941214768631.33729178474-0.923710427359-0.2747924548460.237477339487-0.81830778881-0.3041362751520.6073594534291.537914540550.222923259525-0.1303709265720.9134469078420.3787852652841.2354425548515.715073818347.477468020869.1808113406
60.50114840556-1.234894129530.155260312353.17803496902-0.8793250575623.1718318256-0.03364210342760.783047573347-0.0742586905552-1.020075989580.3691083454380.9515892717960.173448257978-0.406980171033-0.2900728320121.31427503234-0.233057626556-0.3236446253331.0785376290.4067676082730.99012942941524.039834981645.022069768666.9578179829
74.60386520461.02675450991.661294257220.972801172873-0.1371899016310.93723736681-0.2451716166670.64393599710.274101141333-1.574463185260.6952425185830.785705961332-0.133714228619-0.179293576665-0.2668564803812.07937597814-0.477850694824-0.5999747435231.335849223930.7538903458391.2200200200321.761024047454.246836229861.5260293314
87.87061817536-3.421311729331.119495340164.692441471881.325328028346.526451944170.02191617125381.16516409826-0.249349734415-0.692528316624-0.183561018112-0.09377271065430.4277336047130.08802148698890.05361943378570.540430837359-0.09627423604120.08867663961650.4011912754830.01769256730420.37390321570238.437582808621.104282170685.392303252
93.2928189683-0.2862691309882.846468451712.013634705190.09432507738663.411675810730.309446091883-0.0870187114616-0.1900330168510.199251988875-0.01838605737610.3676128000580.2544573699640.352314511089-0.252983696260.313034643857-0.1197601908670.07454392307070.5720431325780.07465035852660.4147677427844.249710768723.3889788895.602261337
102.03080195584-5.38747724799-5.143657517232.050854989881.89460019926.52069485176-0.0425680996641-1.15130018677-1.23152895530.339106634906-0.05719224481270.8067251356160.4377112979050.0002860873569520.04479528092940.548378649715-0.1165637897540.02978675369710.663278513191-0.05175748586320.74977532945540.226666206517.162459511295.6860474118
115.335789825680.3859755149884.907535803452.82931325316-0.355562283568.07747633084-0.140364688128-0.16888651370.08146437500810.1625560835290.14310371953-0.0225718532658-0.3999059756460.4003407427750.01670383758020.564012702015-0.07080080494230.05801725972020.338497147151-0.05761752045890.31306936718344.124528394828.189970327194.764927052
124.53120397921-0.0639995689944-1.741187270865.4815094606-3.578584582025.44558234409-0.3375255387731.552476518090.16594714136-1.425703248440.728531577621-0.0528033619084-0.471489796316-0.652284932268-0.4401801305491.1606818199-0.3423868364710.07703349370190.8727146666020.003908037923660.59482488997629.499448362433.367395331567.8443623301
134.30030719241-3.5020943454-0.6802878042055.23853021157-0.6850899160419.02057874175-0.6019356052051.65638061763-0.138658214971-1.693951744530.206255320821-0.8049665157240.09960910182270.6475965145770.4480773713441.08798493023-0.349257476750.2020293843771.00769108867-0.06311192849490.70690673309334.756357089637.111527613264.7105402049
145.902153851262.24241065644-2.451865924085.50489663986-5.508461725066.9343052875-0.5324396833441.34715425819-0.108846333894-1.01489344440.533770373424-0.114542724873-1.83756269420.805224958287-0.03042125997491.87208562563-0.488114157755-0.06396261685510.958410981747-0.2369922823980.83046379209131.40411494129.844530856959.3631244789
152.05177675233-1.28432364652-1.635707467322.25330668589-0.7474146538234.165086922550.9224553632190.548899174003-0.57715270979-0.435599168303-0.5616449471070.02631149248110.3861998334611.29259177568-0.3281486830560.7007850326720.335222199989-0.1427314084621.08914877435-0.2142838426790.62445681081518.80374365244.48840300372.56246534633
162.015174440320.8868615781453.936115411329.61199969917-0.1984627828127.302735640910.3336745152971.67145130676-0.801469613088-0.6412402814440.104890208199-0.01635263046970.007070445062450.986976173989-0.4274516908580.4403751700820.1365107424090.0417754876890.982025873632-0.108065080540.56783207256215.899984470849.8345688923-0.0905039295038
178.22743279752-4.88049826229-4.036724621085.727343551211.121012132072.634661924130.4665256490970.39068299314-0.535868869829-0.04155563213070.0799531298794-0.1916485255450.7937867822011.30599964862-0.34975717850.7434660614610.444922229279-0.2249051376021.24494359919-0.4443524795410.70125817211918.803832075439.68518410762.77639590258
184.290170607240.214273172555-0.3914850803164.637841378313.829010715493.55686403615-0.396721945003-1.91623964937-1.389083200111.864002581761.56898814951.460037841881.49521197287-0.657636030973-1.128307119721.299421091220.4260672334530.02597241564241.534157189170.4030690360551.069515201673.7232289346630.588397272432.3449529675
195.59796158743-4.110936826940.9693275715317.23512036119-4.451441564798.873255381550.00457076467407-0.734438512707-0.6169808422730.7922529658580.520281643042-0.1108072499020.6622315219731.29873612833-0.5476813376030.8368553300280.263916056743-0.2736169159171.00726807854-0.2264018988861.006357632668.9755623619232.544485158425.1186486554
209.55621671624-3.941401781170.1789095851612.04394782005-6.632273356746.12282582839-0.608101517637-1.63900216779-0.962279465621.546041684660.9715753412710.4289899473780.1890075808860.396761722988-0.3700971145591.917756456580.483586674501-0.6179738466231.058224102620.05819244001061.8128883550110.733147918525.773525819332.5910185217
212.068562431012.83921042447-0.7188300034595.017068394560.1228461762856.671617530990.481237924201-2.03777815215-0.9781099449171.846382731310.468393720262-0.1011045167630.7554715840.625986889116-0.8395297677081.50777971230.483976634474-0.1527387329611.421678583110.1959567590461.0543795058610.715729862735.363828242336.6082551366
220.2252114041090.1353045845930.07510501314550.1271055601480.09476003223241.767640402250.2026568418970.20299461426-0.2722872127520.167215297522-0.0958956041349-0.232111266722-0.110961891361-0.0769357370884-0.02776158397282.559801650740.938864684175-1.270487900181.32590105608-0.8877213003321.6194777389116.630929559118.8223858474-2.81645249003
230.96874054196-0.203670872587-0.001970555461460.315942515345-0.236383796620.2333262213070.1018982977080.521995098971-0.513796447115-0.219745028158-0.1534484673320.02921031854470.9051481573050.479388242458-0.05314432218581.815233626031.9054545671-0.4614936212131.29629893187-0.6899252346520.96204822186825.550565009724.9040840011-1.96640852223
242.33438567743-1.280598206760.6278697891522.31759916706-0.8000821509532.120618715480.2205387764420.503515237582-0.295464133421-0.397678677472-0.3512881731860.08572437881120.09430316265010.2328229905740.1003919083091.733269961711.05103075777-0.7484622831341.20167523335-0.5438186728721.1162702323319.792264358625.79671793840.212916900007
253.044882772541.730040601661.449607530076.05882182084-5.729693040149.089589952611.218114085620.179718561192-1.24763338996-0.4449443251610.7485454824060.8898808150761.44172621542-0.234176629113-1.998746492792.04287638460.486501090336-0.3795423971571.12531068204-0.1084164968661.4963841024411.087827813613.906441518520.9366465997
261.99987130848-1.31875661728.367659512481.96186637139-4.625307791912.00046745648-0.563319606595-1.29984826559-1.313347813651.247511068811.031958387070.9288349057330.616785180875-0.616212890869-0.4931871935411.559271399510.5135048128870.5005042233431.509239035180.6316592385761.83984794209-4.4745698024131.246084781637.1748384501
277.24903708091-2.417287916731.850794175047.315506138512.506747363081.971634663190.255527620067-0.207035444059-1.688732060250.2910067078850.939301342241.468441824290.719222643887-0.525807967895-1.157909660552.040728407740.14651008051-0.5679098809570.8604798144740.2722039724332.014961237536.6802038186514.652114668622.8029232582
281.184379264910.9452726324062.688433349190.8644486945792.185271013336.11055893725-0.140645263431-1.41163061702-2.596350809880.5133036191290.5573027746171.157488257982.45774636673-2.76415999543-0.4224097739851.62719513398-0.3368944491340.05093113089181.54479316390.7513606294322.21983802972-9.981382249816.060384976928.8298081557
296.23054105368-3.51968923574-0.3515040127014.80056870783-0.3893232416867.310545413840.579004029427-0.17844194501-1.004366961390.7743589322470.868060544955-0.0497773746171.051990229980.217486596632-1.383320368031.553437213370.203633248153-0.801075156490.9339098600260.001396866501482.2667591920910.892089094419.464395002319.9980810088
300.153549648270.245906230224-0.02170170752390.388662262272-0.03157673601530.00348791108167-0.51680722004-0.784882521102-0.7653247510890.6920931357310.310469199894-0.6179216960491.53361547805-0.8954905036920.1784025499461.58662846989-0.1830966592250.07691831526271.339991674150.4414244174531.72309035523-7.5062773311721.337461980134.0491060546
316.500963346062.046233921183.30601692541.67965173627-0.6931251178844.612745617890.991557596688-0.967198394102-1.160554212971.50487696710.166483450121-0.2558047901740.524817564623-1.0274723482-1.160087156391.75877684626-0.1686245234530.1532839371081.041050811570.4080656393511.5516450739-0.59204692228511.800942051234.0859403646
328.73205437623-5.9204491444-2.38169153888.34291934949-1.013794888496.832514798870.9212486155951.67942388515-0.80356192511-2.53670195192-0.4108955776090.7163576691380.8960122495090.512975367153-0.5108334493861.978634277940.240639433106-0.1418281986592.147214752850.01911168038550.85759937673940.7918833340.9045355925-45.2739247588
333.96659560504-6.087829908674.539324911912.00461597575-2.463565114272.008392851080.6374151535810.722035063052-0.113249628266-0.231555752015-0.186680739831.12587793042-0.7965446297010.113003623825-0.4356900021751.21100036071-0.0423506325980.2769623553671.417807091330.01773413373081.1837612248531.622454707143.94806665-30.4960195839
341.481436722421.78996525889-2.045263348225.479589505122.196067523869.15352253173-0.980758010408-1.1688053115-0.888247109935-0.5115505852180.853321947736-0.0192021210979-0.4697786493170.03835971751430.1296365535990.9929606213220.5143011800440.1238187740391.558285374540.03187062985550.8623900727736.353763831743.252966355-16.5610141258
357.47794581946-0.17795243438-1.372795146372.00666591129-2.119958070698.31270668580.7749870834752.55479941687-2.36198831961-3.65960289958-0.04539650272060.9874982758552.90397027854-1.12756523123-0.6776034332772.43132223975-0.331681690723-0.1769442135271.39973967684-0.2387737819121.4307687596132.721897411836.1074351231-39.3502488644
365.21611175869-0.1398883105294.308140846083.39440382856-2.111539836694.733229548340.3660918871310.774604612207-0.64205661893-0.495401020037-0.2207380215711.257834973481.43123194461-0.307575063812-0.08841428770742.229241190410.3300279395780.02680147040291.56830224330.1974443661281.3093113386532.82468107345.9420659171-51.7624424394
379.474145403817.47775906241.998863756132.00807372001-5.385196733562.008554663290.6460046841753.924893041791.89965341849-1.223907579862.28925330592-0.67770093022-1.3394929063-0.0930300328716-3.049538132881.9070757088-0.1278104437650.6889310049711.926719436660.07133497310181.6125479672352.918147615746.6340864546-60.3940595411
389.01638174054-1.99223512379-5.485339119683.212090547411.343433514693.350192757771.158951031470.4518626547020.224437538328-1.02912296765-0.111968376267-0.147691378498-0.713665578250.210876663476-1.09584289581.713550359180.1447804575470.02293152179341.963249908290.003631684025941.0269786985843.688731925544.5905885994-46.5326463339
392.40752812411-0.362872462834-1.863038092790.50102899804-1.481853514627.633612903930.364814169024-0.441990561918-0.004847453870761.014168704590.6375827194560.362577076296-1.40027040289-1.0304354599-1.027393464741.62299388148-0.1956496408120.1155503311171.112466225540.06121987122730.65362115458360.138284958925.2128184168125.906645574
402.68530444175-0.2524794837493.25961101811.37208094748-0.4704355553348.90385864445-0.0906105079047-0.682021192457-0.4426800490321.805644534140.5909440443160.0115484207488-2.007492174461.06373297557-0.5059429017081.75824410204-0.1298524145670.01844263668341.172880359910.02553112589160.85129334228960.302787564523.2571449771132.323994367
416.387615689211.572893767181.970435622672.058925677720.05409258275554.233268249850.0442825339638-0.754520509505-0.07026576423820.8301803011790.262322107766-0.5891722539890.604242537942-0.393175910489-0.27284532811.881122054620.213208526162-0.1904727615911.42038377341-0.06169592467020.99366955410866.437311294221.1904530776142.255253401
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'l' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'l' and (resid 27 through 102 )
3X-RAY DIFFRACTION3chain 'l' and (resid 103 through 119 )
4X-RAY DIFFRACTION4chain 'l' and (resid 120 through 151 )
5X-RAY DIFFRACTION5chain 'l' and (resid 152 through 164 )
6X-RAY DIFFRACTION6chain 'l' and (resid 165 through 192 )
7X-RAY DIFFRACTION7chain 'l' and (resid 193 through 215 )
8X-RAY DIFFRACTION8chain 'h' and (resid 4 through 20 )
9X-RAY DIFFRACTION9chain 'h' and (resid 21 through 63 )
10X-RAY DIFFRACTION10chain 'h' and (resid 64 through 86 )
11X-RAY DIFFRACTION11chain 'h' and (resid 87 through 115 )
12X-RAY DIFFRACTION12chain 'h' and (resid 116 through 165 )
13X-RAY DIFFRACTION13chain 'h' and (resid 166 through 212 )
14X-RAY DIFFRACTION14chain 'h' and (resid 213 through 228 )
15X-RAY DIFFRACTION15chain 'H' and (resid 4 through 63 )
16X-RAY DIFFRACTION16chain 'H' and (resid 64 through 86 )
17X-RAY DIFFRACTION17chain 'H' and (resid 87 through 123 )
18X-RAY DIFFRACTION18chain 'H' and (resid 124 through 157 )
19X-RAY DIFFRACTION19chain 'H' and (resid 158 through 187 )
20X-RAY DIFFRACTION20chain 'H' and (resid 188 through 200 )
21X-RAY DIFFRACTION21chain 'H' and (resid 201 through 228 )
22X-RAY DIFFRACTION22chain 'L' and (resid 1 through 26 )
23X-RAY DIFFRACTION23chain 'L' and (resid 27 through 76 )
24X-RAY DIFFRACTION24chain 'L' and (resid 77 through 102 )
25X-RAY DIFFRACTION25chain 'L' and (resid 103 through 119 )
26X-RAY DIFFRACTION26chain 'L' and (resid 120 through 133 )
27X-RAY DIFFRACTION27chain 'L' and (resid 134 through 146 )
28X-RAY DIFFRACTION28chain 'L' and (resid 147 through 159 )
29X-RAY DIFFRACTION29chain 'L' and (resid 160 through 175 )
30X-RAY DIFFRACTION30chain 'L' and (resid 176 through 197 )
31X-RAY DIFFRACTION31chain 'L' and (resid 198 through 215 )
32X-RAY DIFFRACTION32chain 'R' and (resid 1 through 5 )
33X-RAY DIFFRACTION33chain 'R' and (resid 6 through 10 )
34X-RAY DIFFRACTION34chain 'R' and (resid 11 through 25 )
35X-RAY DIFFRACTION35chain 'R' and (resid 26 through 30 )
36X-RAY DIFFRACTION36chain 'R' and (resid 31 through 35 )
37X-RAY DIFFRACTION37chain 'R' and (resid 36 through 39 )
38X-RAY DIFFRACTION38chain 'A' and (resid 1 through 12 )
39X-RAY DIFFRACTION39chain 'r' and (resid 1 through 15 )
40X-RAY DIFFRACTION40chain 'r' and (resid 16 through 39 )
41X-RAY DIFFRACTION41chain 'a' and (resid 1 through 12 )

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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://pdbjlc1.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