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- PDB-5t78: Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 ... -

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基本情報

登録情報
データベース: PDB / ID: 5t78
タイトルCrystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide
要素
  • Fab Fragment - AR20.5 - Heavy chain
  • Fab fragment AR20.5 - Light Chain
  • MUC1 Glycopeptide
キーワードIMMUNE SYSTEM / antibody / Fab
機能・相同性
機能・相同性情報


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator / localization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / transcription coregulator activity / Golgi lumen / p53 binding / Interleukin-4 and Interleukin-13 signaling / vesicle / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleus / plasma membrane
類似検索 - 分子機能
Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
2-acetamido-2-deoxy-beta-D-galactopyranose / Mucin-1
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者Brooks, C.L. / Movahedin, M.
引用ジャーナル: Glycobiology / 年: 2017
タイトル: Glycosylation of MUC1 influences the binding of a therapeutic antibody by altering the conformational equilibrium of the antigen.
著者: Movahedin, M. / Brooks, T.M. / Supekar, N.T. / Gokanapudi, N. / Boons, G.J. / Brooks, C.L.
履歴
登録2016年9月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年1月11日Provider: repository / タイプ: Initial release
改定 1.12017年6月14日Group: Database references / カテゴリ: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.22020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.32023年10月4日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Fab fragment AR20.5 - Light Chain
B: Fab Fragment - AR20.5 - Heavy chain
F: MUC1 Glycopeptide
C: Fab fragment AR20.5 - Light Chain
D: Fab Fragment - AR20.5 - Heavy chain
E: MUC1 Glycopeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,2448
ポリマ－95,8016
非ポリマー4422
水88349
1
A: Fab fragment AR20.5 - Light Chain
B: Fab Fragment - AR20.5 - Heavy chain
F: MUC1 Glycopeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,1224
ポリマ－47,9013
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-20 kcal/mol
Surface area19010 Å2
手法PISA
2
C: Fab fragment AR20.5 - Light Chain
D: Fab Fragment - AR20.5 - Heavy chain
E: MUC1 Glycopeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,1224
ポリマ－47,9013
非ポリマー2211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-22 kcal/mol
Surface area18900 Å2
手法PISA
単位格子
Length a, b, c (Å)97.250, 100.460, 235.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain E and (resseq 2 or (resid 3 and (name...
21(chain F and (resseq 2 or (resid 3 and (name...
12(chain A and (resseq 1:125 or (resid 126 and (name...
22(chain C and (resseq 1:125 or (resid 126 and (name...
13(chain B and (resseq 1:2 or resseq 4:42 or resseq...
23(chain D and (resseq 1:2 or resseq 4:42 or resseq...

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
111PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF22
121ASPASPASPASP(chain E and (resseq 2 or (resid 3 and (name...EF33
131PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF2 - 82 - 8
141PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF2 - 82 - 8
151PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF2 - 82 - 8
161PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF2 - 82 - 8
171PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF2 - 82 - 8
181PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF2 - 82 - 8
191PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF2 - 82 - 8
1101PROPROPROPRO(chain E and (resseq 2 or (resid 3 and (name...EF2 - 82 - 8
211PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC22
221ASPASPASPASP(chain F and (resseq 2 or (resid 3 and (name...FC33
231PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC2 - 82 - 8
241PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC2 - 82 - 8
251PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC2 - 82 - 8
261PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC2 - 82 - 8
271PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC2 - 82 - 8
281PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC2 - 82 - 8
291PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC2 - 82 - 8
2101PROPROPROPRO(chain F and (resseq 2 or (resid 3 and (name...FC2 - 82 - 8
112ASPASPPROPRO(chain A and (resseq 1:125 or (resid 126 and (name...AA1 - 1251 - 125
122SERSERSERSER(chain A and (resseq 1:125 or (resid 126 and (name...AA126126
132ASPASPARGARG(chain A and (resseq 1:125 or (resid 126 and (name...AA1 - 2161 - 216
142ASPASPARGARG(chain A and (resseq 1:125 or (resid 126 and (name...AA1 - 2161 - 216
152ASPASPARGARG(chain A and (resseq 1:125 or (resid 126 and (name...AA1 - 2161 - 216
162ASPASPARGARG(chain A and (resseq 1:125 or (resid 126 and (name...AA1 - 2161 - 216
172ASPASPARGARG(chain A and (resseq 1:125 or (resid 126 and (name...AA1 - 2161 - 216
182ASPASPARGARG(chain A and (resseq 1:125 or (resid 126 and (name...AA1 - 2161 - 216
192ASPASPARGARG(chain A and (resseq 1:125 or (resid 126 and (name...AA1 - 2161 - 216
212ASPASPPROPRO(chain C and (resseq 1:125 or (resid 126 and (name...CD1 - 1251 - 125
222SERSERSERSER(chain C and (resseq 1:125 or (resid 126 and (name...CD126126
232ASPASPARGARG(chain C and (resseq 1:125 or (resid 126 and (name...CD1 - 2161 - 216
242ASPASPARGARG(chain C and (resseq 1:125 or (resid 126 and (name...CD1 - 2161 - 216
252ASPASPARGARG(chain C and (resseq 1:125 or (resid 126 and (name...CD1 - 2161 - 216
262ASPASPARGARG(chain C and (resseq 1:125 or (resid 126 and (name...CD1 - 2161 - 216
272ASPASPARGARG(chain C and (resseq 1:125 or (resid 126 and (name...CD1 - 2161 - 216
282ASPASPARGARG(chain C and (resseq 1:125 or (resid 126 and (name...CD1 - 2161 - 216
292ASPASPARGARG(chain C and (resseq 1:125 or (resid 126 and (name...CD1 - 2161 - 216
113GLUGLUVALVAL(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 21 - 2
123LEULEUGLUGLU(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB4 - 424 - 42
133LEULEUVALVAL(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB45 - 6445 - 64
143GLYGLYVALVAL(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB66 - 11466 - 114
153SERSERSERSER(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB115115
163GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
173GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
183GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
193GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
1103GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
1113GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
1123GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
1133GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
1143GLUGLUPROPRO(chain B and (resseq 1:2 or resseq 4:42 or resseq...BB1 - 2151 - 215
213GLUGLUVALVAL(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 21 - 2
223LEULEUGLUGLU(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE4 - 424 - 42
233LEULEUVALVAL(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE45 - 6445 - 64
243GLYGLYVALVAL(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE66 - 11466 - 114
253SERSERSERSER(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE115115
263GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215
273GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215
283GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215
293GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215
2103GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215
2113GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215
2123GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215
2133GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215
2143GLUGLUPROPRO(chain D and (resseq 1:2 or resseq 4:42 or resseq...DE1 - 2151 - 215

NCSアンサンブル:
ID
1
2
3

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要素

#1: 抗体 Fab fragment AR20.5 - Light Chain


分子量: 23943.729 Da / 分子数: 2 / 断片: antibody Fab fragment / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 細胞株 (発現宿主): Hybridoma / 発現宿主: Mus musculus (ハツカネズミ)
#2: 抗体 Fab Fragment - AR20.5 - Heavy chain


分子量: 23131.971 Da / 分子数: 2 / 断片: MUC1 peptide APDTRPAP / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 細胞株 (発現宿主): hybridoma / 発現宿主: Mus musculus (ハツカネズミ)
#3: タンパク質・ペプチド MUC1 Glycopeptide


分子量: 824.901 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P15941*PLUS
#4: 糖 ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / 2-(アセチルアミノ)-2-デオキシ-β-D-ガラクトピラノ-ス


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 2 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 49 / 由来タイプ: 天然 / 式: H2O

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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 Å3/Da / 溶媒含有率: 58.98 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 / 詳細: PEG 20000

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: CLSI / ビームライン: 08ID-1 / 波長: 0.97949 Å
検出器タイプ: RAYONIX MX300HE / 検出器: CCD / 日付: 2013年6月7日
放射モノクロメーター: Si(111) / 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: 0.97949 Å / 相対比: 1
反射解像度: 2.2→49.14 Å / Num. obs: 58751 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / 冗長度: 7.6 % / Biso Wilson estimate: 50.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.49
反射 シェル
解像度 (Å)最高解像度 (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.2-2.261.2791.480.691199.7
2.26-2.321.0991.740.733199.9
2.32-2.390.8782.20.82199.9
2.39-2.460.7032.810.873199.9
2.46-2.540.5663.490.913199.8
2.54-2.630.4424.50.941199.8
2.63-2.730.3275.940.967199.9
2.73-2.840.2358.080.979199.8
2.84-2.970.1710.710.9891100
2.97-3.110.12414.170.993199.9
3.11-3.280.09817.720.9951100
3.28-3.480.0821.180.9961100
3.48-3.720.06923.990.996199.9
3.72-4.020.06625.820.9961100
4.02-4.40.05928.270.9971100
4.4-4.920.05529.590.9971100
4.92-5.680.052300.9981100
5.68-6.960.05229.610.9971100
6.96-9.840.0530.70.997199.8
9.840.0530.070.997197.6

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
XSCALEデータスケーリング
PDB_EXTRACT3.2データ抽出
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5T6P

5t6p


解像度: 2.2→49.123 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.58 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2205 2945 5.02 %
Rwork0.1938 55745 -
obs0.1952 58690 99.87 %
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: 167.53 Å2 / Biso mean: 71.1309 Å2 / Biso min: 38.29 Å2
精密化ステップサイクル: final / 解像度: 2.2→49.123 Å
タンパク質核酸リガンド溶媒全体
原子数6650 0 56 49 6755
Biso mean--67.36 59.81 -
残基数----864
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0096862
X-RAY DIFFRACTIONf_angle_d1.039350
X-RAY DIFFRACTIONf_chiral_restr0.0561046
X-RAY DIFFRACTIONf_plane_restr0.0061180
X-RAY DIFFRACTIONf_dihedral_angle_d11.1494086
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11E76X-RAY DIFFRACTION4.213TORSIONAL
12F76X-RAY DIFFRACTION4.213TORSIONAL
21A2613X-RAY DIFFRACTION4.213TORSIONAL
22C2613X-RAY DIFFRACTION4.213TORSIONAL
31B2333X-RAY DIFFRACTION4.213TORSIONAL
32D2333X-RAY DIFFRACTION4.213TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.23610.4161410.361226052746100
2.2361-2.27470.33391350.326326032738100
2.2747-2.3160.39411540.324426322786100
2.316-2.36060.31151310.302226172748100
2.3606-2.40870.31881130.281926862799100
2.4087-2.46110.29611240.270126032727100
2.4611-2.51840.30421350.269426492784100
2.5184-2.58130.29091300.262426522782100
2.5813-2.65110.3221430.253526032746100
2.6511-2.72910.26531520.249126402792100
2.7291-2.81720.28111570.241526182775100
2.8172-2.91790.29831550.248126582813100
2.9179-3.03470.28281370.252826452782100
3.0347-3.17280.25631260.22626472773100
3.1728-3.340.27421270.226826792806100
3.34-3.54920.23221480.207526392787100
3.5492-3.82320.19481540.181626532807100
3.8232-4.20770.20231260.166227112837100
4.2077-4.81620.15781510.125926802831100
4.8162-6.06610.1661470.137327162863100
6.0661-49.13560.16321590.15712809296899
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)
13.84394.2162.157.95663.17593.7101-0.0161-0.6371-0.03620.6343-0.09240.18550.1027-0.09090.05110.55860.1898-0.06120.6888-0.01910.69325.90830.38536.869
22.83890.2188-0.37544.947-0.03142.20550.0282-0.2766-0.09390.0808-0.1016-0.43440.20360.40610.09170.43980.1733-0.05430.6102-0.00530.493214.0523.58131.667
31.6792-1.69750.27063.2917-0.27742.1588-0.0732-0.13830.01720.1220.1827-0.6343-0.02220.3855-0.05660.40170.1296-0.08290.5692-0.08540.46649.02933.31231.689
43.8853-1.88073.30072.3178-1.94033.5664-0.0369-0.13660.40870.08460.0766-0.2896-0.4031-0.14360.02010.58990.17860.06710.6001-0.04090.6806-4.48159.48522.914
53.5029-2.43013.32964.7162-2.58755.60660.081-0.40830.40120.0660.2817-0.0972-0.3103-0.6496-0.30710.48290.16380.08190.6433-0.04290.7046-6.92459.98425.703
61.63060.87432.09723.41561.22453.26770.10070.3649-0.2237-0.686-0.12290.00290.22480.40650.22470.84460.1058-0.07030.77450.12440.4226.78631.7636.724
74.21640.64322.1273.9536-0.03933.39310.12150.807-0.317-0.7153-0.2353-0.80960.4721.38990.29570.6780.24190.12310.91410.08920.517117.59725.3067.321
84.4907-4.4854-0.01324.75461.12864.46380.53480.3911-0.4847-0.9169-0.60120.6759-0.0541-0.05330.20330.56420.1281-0.06320.4775-0.03020.57523.56327.99417.335
94.38590.92450.74664.38060.44164.8250.05280.4383-0.2565-0.6919-0.04310.09290.79110.7027-0.08580.75290.256-0.04810.653-0.09040.4968.66619.0178.588
105.02310.99792.0214.00740.38193.84520.00690.47010.0606-0.49970.0099-0.02440.35480.3921-0.02770.53620.1363-0.03430.45740.01460.40817.27727.43613.919
115.08591.6495-1.18965.3057-1.28893.1410.1025-0.0440.3598-0.73920.15330.2323-0.23630.1878-0.34780.42590.11120.02130.60620.09480.5639-2.54652.9569.826
122.45013.69531.87436.06052.47834.19540.34310.02920.1245-0.07950.0953-0.5416-0.09980.1191-0.4340.46150.08270.01460.5827-0.05450.71353.44252.12613.041
132.35043.48832.00567.81480.9344.04820.2543-0.3110.5140.28280.0207-0.0518-0.0629-0.1097-0.20540.47340.11940.01940.5767-0.09360.64931.85751.41317.579
141.44342.87142.02749.04623.06896.7836-0.14630.2220.1483-0.31470.6367-0.7477-0.69590.697-0.50290.47340.01650.06670.574-0.05180.78877.58658.0268.624
153.45910.95030.00636.7221-0.15683.96481.23420.0633-0.35790.8229-0.02790.25330.05420.6566-1.07250.6120.16220.06650.7469-0.23560.778218.19814.1721.77
165.96891.53350.80661.6148-0.43991.04280.20190.86010.3289-0.6195-0.1245-0.02210.24150.3385-0.07450.65130.2125-0.03010.5519-0.06150.610321.195-5.32221.792
175.90450.1518-0.12043.278-0.48882.69660.10330.1848-0.4154-0.3257-0.0957-0.07980.37130.11950.00470.60010.2217-0.05050.4922-0.08780.457226.086-14.30128.05
183.1661-1.736-1.24391.92410.51690.9545-0.01540.0236-0.4089-0.0818-0.03870.19560.21490.00150.07590.53270.1283-0.07280.4169-0.0270.43958.601-4.14931.98
193.7723-1.8031-2.79623.3942.54924.68260.32890.5596-0.11-0.6371-0.26340.6079-0.5711-0.5431-0.21150.65840.1623-0.12690.6010.00470.5771-8.3658.34731.119
206.1733-2.0161-2.68555.61754.33266.42290.1722-0.0783-0.3934-0.3260.15860.14920.06970.1418-0.33270.6590.1011-0.15390.5134-0.04740.43870.0181.27431.02
214.2169-1.8616-2.74143.65982.90685.14810.32380.2770.0574-0.4104-0.14330.4244-0.5367-0.5097-0.07420.68290.2364-0.10210.5730.03170.6523-13.98711.10234.527
223.0685-1.0797-0.01965.6268-1.48180.4378-0.332-0.68150.20811.14820.46840.45410.51480.078-0.2220.6320.10520.00790.7653-0.14220.363118.139-5.72852.282
234.60260.5094-0.61415.84921.80743.7991-0.0208-0.5859-0.02830.37290.0892-0.27930.55450.4085-0.02480.56320.1914-0.01750.6109-0.07350.439826.969-9.85346.663
244.45951.8058-0.17336.4491-0.2435.6866-0.0111-0.84530.20490.87890.0114-0.4090.46140.4412-0.18030.75850.2574-0.11230.8313-0.12250.497628.956-7.65453.598
255.1267-0.0151-0.54947.25042.31454.688-0.1203-0.49120.11480.53280.11430.03060.50920.37660.00240.39120.137-0.02820.4583-0.05320.29822.455-6.50445.01
267.6977-1.6935-1.26464.2227-0.55222.79250.2405-1.45210.0784-0.054-0.1360.44550.1002-0.7418-0.14310.52010.09540.02110.32640.06390.4725-3.293.82548.651
276.3832.84452.02633.8212.30543.87410.22260.1556-0.1412-0.0990.06230.46780.0658-0.1206-0.22950.50760.1023-0.06020.4413-0.01640.5471-1.612-1.01143.486
287.1552.69715.3243.87873.11668.37580.5387-0.5579-1.01490.4003-0.17390.28550.7285-0.7798-0.32770.5730.01150.02280.5060.02910.6364-7.981-5.83450.386
294.57290.4381-0.442.16710.20452.58640.89360.5236-0.33980.30370.1722-0.42422.12330.9963-0.74730.82250.2909-0.21960.6266-0.01150.675835.279-17.97637.254
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:18 )A1 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:80 )A19 - 80
3X-RAY DIFFRACTION3( CHAIN A AND RESID 81:118 )A81 - 118
4X-RAY DIFFRACTION4( CHAIN A AND RESID 119:155 )A119 - 155
5X-RAY DIFFRACTION5( CHAIN A AND RESID 156:216 )A156 - 216
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:17 )B1 - 17
7X-RAY DIFFRACTION7( CHAIN B AND RESID 18:33 )B18 - 33
8X-RAY DIFFRACTION8( CHAIN B AND RESID 34:44 )B34 - 44
9X-RAY DIFFRACTION9( CHAIN B AND RESID 45:83 )B45 - 83
10X-RAY DIFFRACTION10( CHAIN B AND RESID 84:114 )B84 - 114
11X-RAY DIFFRACTION11( CHAIN B AND RESID 115:137 )B115 - 137
12X-RAY DIFFRACTION12( CHAIN B AND RESID 138:160 )B138 - 160
13X-RAY DIFFRACTION13( CHAIN B AND RESID 161:187 )B161 - 187
14X-RAY DIFFRACTION14( CHAIN B AND RESID 188:215 )B188 - 215
15X-RAY DIFFRACTION15( CHAIN F AND RESID 2:8 )F2 - 8
16X-RAY DIFFRACTION16( CHAIN C AND RESID 1:25 )C1 - 25
17X-RAY DIFFRACTION17( CHAIN C AND RESID 26:80 )C26 - 80
18X-RAY DIFFRACTION18( CHAIN C AND RESID 81:133 )C81 - 133
19X-RAY DIFFRACTION19( CHAIN C AND RESID 134:160 )C134 - 160
20X-RAY DIFFRACTION20( CHAIN C AND RESID 161:179 )C161 - 179
21X-RAY DIFFRACTION21( CHAIN C AND RESID 180:216 )C180 - 216
22X-RAY DIFFRACTION22( CHAIN D AND RESID 1:17 )D1 - 17
23X-RAY DIFFRACTION23( CHAIN D AND RESID 18:61 )D18 - 61
24X-RAY DIFFRACTION24( CHAIN D AND RESID 62:83 )D62 - 83
25X-RAY DIFFRACTION25( CHAIN D AND RESID 84:114 )D84 - 114
26X-RAY DIFFRACTION26( CHAIN D AND RESID 115:137 )D115 - 137
27X-RAY DIFFRACTION27( CHAIN D AND RESID 138:187 )D138 - 187
28X-RAY DIFFRACTION28( CHAIN D AND RESID 188:215 )D188 - 215
29X-RAY DIFFRACTION29( CHAIN E AND RESID 2:8 )E2 - 8

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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