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- PDB-5t6p: 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: 5t6p
タイトルCrystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide
要素
  • Fab Fragment - Heavy Chain
  • Fab fragment AR20.5 - Light Chain
  • MUC1 Peptide Fragment
キーワードIMMUNE SYSTEM (免疫系) / antibody (抗体) / 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 / クロマチン / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / 細胞核 / 細胞膜
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 / 抗体 / Immunoglobulin-like / サンドイッチ / Mainly Beta
類似検索 - ドメイン・相同性
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: 1.97 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1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1月18日Group: Derived calculations
改定 1.22017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 1.32017年10月11日Group: Data collection / カテゴリ: reflns_shell / Item: _reflns_shell.percent_possible_all
改定 1.42023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 - Heavy Chain
C: Fab fragment AR20.5 - Light Chain
D: Fab Fragment - Heavy Chain
E: MUC1 Peptide Fragment
F: MUC1 Peptide Fragment


分子量 (理論値)分子数
合計 (水以外)95,8016
ポリマ－95,8016
非ポリマー00
水7,891438
1
A: Fab fragment AR20.5 - Light Chain
B: Fab Fragment - Heavy Chain
F: MUC1 Peptide Fragment


分子量 (理論値)分子数
合計 (水以外)47,9013
ポリマ－47,9013
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-27 kcal/mol
Surface area18510 Å2
手法PISA
2
C: Fab fragment AR20.5 - Light Chain
D: Fab Fragment - Heavy Chain
E: MUC1 Peptide Fragment


分子量 (理論値)分子数
合計 (水以外)47,9013
ポリマ－47,9013
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-28 kcal/mol
Surface area18650 Å2
手法PISA
単位格子
Length a, b, c (Å)69.700, 69.700, 363.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain F
21chain E
12(chain A and (resseq 1:202 or (resid 203 and (name...
22(chain C and (resseq 1:57 or (resid 58 and (name...
13(chain B and (resseq 2 or resseq 4:129 or resseq 138:215))
23(chain D and (resseq 2 or resseq 4:129 or resseq 138:215))

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
111ASPASPPROPROchain FFF3 - 83 - 8
211ASPASPPROPROchain EEE3 - 83 - 8
112ASPASPTHRTHR(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2021 - 202
122HISHISHISHIS(chain A and (resseq 1:202 or (resid 203 and (name...AA203203
132ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
142ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
152ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
162ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
172ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
182ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
192ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
1102ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
1112ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
1122ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
1132ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
1142ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
1152ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
1162ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
1172ASPASPARGARG(chain A and (resseq 1:202 or (resid 203 and (name...AA1 - 2161 - 216
212ASPASPSERSER(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 571 - 57
222LYSLYSLYSLYS(chain C and (resseq 1:57 or (resid 58 and (name...CC5858
232ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
242ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
252ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
262ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
272ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
282ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
292ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2102ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2112ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2122ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2132ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2142ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2152ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2162ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2172ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2182ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2192ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2202ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
2212ASPASPARGARG(chain C and (resseq 1:57 or (resid 58 and (name...CC1 - 2161 - 216
113VALVALVALVAL(chain B and (resseq 2 or resseq 4:129 or resseq 138:215))BB22
123LEULEUPROPRO(chain B and (resseq 2 or resseq 4:129 or resseq 138:215))BB4 - 1294 - 129
133METMETPROPRO(chain B and (resseq 2 or resseq 4:129 or resseq 138:215))BB138 - 215138 - 215
213VALVALVALVAL(chain D and (resseq 2 or resseq 4:129 or resseq 138:215))DD22
223LEULEUPROPRO(chain D and (resseq 2 or resseq 4:129 or resseq 138:215))DD4 - 1294 - 129
233METMETPROPRO(chain D and (resseq 2 or resseq 4:129 or resseq 138:215))DD138 - 215138 - 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, AR20.5 / 発現宿主: Mus musculus (ハツカネズミ)
#2: 抗体 Fab Fragment - 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 AR20.5 / 発現宿主: Mus musculus (ハツカネズミ)
#3: タンパク質・ペプチド MUC1 Peptide Fragment


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: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 438 / 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: 2.66 Å3/Da / 溶媒含有率: 53.76 %
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
Reflection twinOperator: -h,-k,l / Fraction: 0.1
反射解像度: 1.91→46.44 Å / Num. obs: 81198 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / 冗長度: 10 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.34
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
1.91-1.960.7652.860.911198.8
1.96-2.010.7053.280.8141100
2.01-2.070.5434.250.8671100
2.07-2.140.4345.270.9111100
2.14-2.210.3745.960.9331100
2.21-2.280.4025.420.956197.7
2.28-2.370.287.960.961100
2.37-2.470.2239.890.9721100
2.47-2.580.18811.610.9791100
2.58-2.70.16313.150.9841100
2.7-2.850.13615.480.9871100
2.85-3.020.12117.370.991100
3.02-3.230.11218.870.9911100
3.23-3.490.10420.130.9911100
3.49-3.820.120.440.992199.9
3.82-4.270.09321.340.9941100
4.27-4.930.08622.030.9941100
4.93-6.040.07622.080.9951100
6.04-8.540.06922.010.995199.5
8.540.0721.230.993193.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
PDB_EXTRACT3.2データ抽出
XDSデータ削減
XDSデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4HGW

4hgw


解像度: 1.97→46.437 Å / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.91
Rfactor反射数%反射
Rfree0.2324 3612 4.88 %
Rwork0.2213 --
obs0.2228 74059 99.81 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 181.61 Å2 / Biso mean: 47.8871 Å2 / Biso min: 17.4 Å2
精密化ステップサイクル: final / 解像度: 1.97→46.437 Å
タンパク質核酸リガンド溶媒全体
原子数6596 0 0 438 7034
Biso mean---39.3 -
残基数----856
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0046776
X-RAY DIFFRACTIONf_angle_d0.8319234
X-RAY DIFFRACTIONf_chiral_restr0.0461032
X-RAY DIFFRACTIONf_plane_restr0.0041166
X-RAY DIFFRACTIONf_dihedral_angle_d10.9294036
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11F54X-RAY DIFFRACTION4.084TORSIONAL
12E54X-RAY DIFFRACTION4.084TORSIONAL
21A2619X-RAY DIFFRACTION4.084TORSIONAL
22C2619X-RAY DIFFRACTION4.084TORSIONAL
31B2401X-RAY DIFFRACTION4.084TORSIONAL
32D2401X-RAY DIFFRACTION4.084TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9703-2.00420.30561910.30063469366095
2.0042-2.04070.31791820.29073480366295
2.0407-2.07990.29571870.29953415360295
2.0799-2.12240.28741550.28153542369796
2.1224-2.16850.28151770.28883467364495
2.1685-2.2190.27031710.31083432360395
2.219-2.27450.49171830.46623377356092
2.2745-2.33590.33161850.30513511369695
2.3359-2.40470.27771910.27883487367895
2.4047-2.48230.2681430.2783516365996
2.4823-2.5710.27291680.27823504367295
2.571-2.67390.26382160.26483480369694
2.6739-2.79560.27471470.25273559370696
2.7956-2.94290.22641660.24183488365495
2.9429-3.12720.23932160.22383497371394
3.1272-3.36850.23931600.2163580374096
3.3685-3.70730.21642010.19753540374195
3.7073-4.24320.1741640.16563610377496
4.2432-5.34390.16651970.13973665386295
5.3439-39.36940.19932080.18863817402594
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)
11.48170.07820.25044.1632-0.77792.2554-0.1614-0.04670.14280.2129-0.048-0.2749-0.00310.12470.16420.23670.11570.02080.25380.0140.208770.581174.899456.4106
21.0626-1.09640.03463.4107-1.02651.10420.06520.21350.0917-0.0007-0.2937-0.28080.04080.11230.21480.27270.10260.05120.29830.0280.176561.998889.188947.8825
37.4513-1.26262.28562.2497-0.69282.02970.0447-0.05340.74210.0106-0.1612-0.0348-0.2276-0.140.11670.34210.08650.07550.26890.05290.248253.4086108.22544.4865
40.81230.18960.90023.04940.11511.0331-0.00970.11120.0853-0.2955-0.07860.5073-0.1648-0.48840.28050.38170.0945-0.06770.3902-0.05320.304847.764672.997539.7892
54.2049-1.46560.0882.93350.53811.2163-0.03430.1177-0.1506-0.3253-0.05480.33340.0161-0.16430.06460.31460.08180.0110.2768-0.0040.214356.616866.090540.5972
61.7778-0.8375-0.74921.51121.50772.3793-0.0581-0.4670.46460.28820.02150.2365-0.0801-0.28180.2670.32520.21170.06520.4117-0.05090.324654.337971.961851.7386
73.7935-0.110.87433.36220.67092.7607-0.0867-0.5628-0.33640.35670.00650.41340.228-0.39390.03430.34380.0420.08280.39250.01140.330550.666560.418648.5035
84.13720.64220.94433.5533-0.30312.1968-0.1177-0.12120.00130.11370.03450.5949-0.012-0.33540.18050.20660.09020.02280.31640.02870.294546.959267.019443.1637
94.13280.00210.99652.320.09151.739-0.25620.00850.0604-0.06350.07780.13450.12420.10060.13250.26580.0820.03720.2242-0.00240.177361.735168.905344.562
106.5469-3.46780.20532.61481.10721.9056-0.00720.10140.90020.0879-0.23620.3903-0.6195-0.3445-0.17010.28390.1359-0.0640.3599-0.04950.45649.430677.239942.1012
111.27542.2957-0.6414.4671-2.07813.2372-0.08620.5552-0.2433-0.21130.24450.67940.119-0.0739-0.31080.24870.230.0240.658-0.15350.656142.208893.556235.606
123.54250.8975-0.66780.9506-0.53270.30680.12530.414-0.13070.077-0.00930.3084-0.0296-0.04330.00450.36040.28820.0060.5801-0.1820.385452.116199.413134.212
134.4353-0.3103-0.73542.4371-0.73060.8862-0.210.6562-1.6265-0.1534-0.12060.08120.3339-0.05670.56240.33270.1504-0.10380.5246-0.350.965351.511188.974633.8562
145.0173-0.213-1.50222.3195-0.89224.58280.02091.1219-0.7499-0.228-0.1127-0.11570.05760.06890.18140.30580.1274-0.00010.5564-0.06750.363455.367697.605533.8674
152.3771-2.0766-1.67941.82061.55352.4019-0.39390.8902-1.2718-0.0967-0.03610.11240.3737-0.59170.63340.41010.0418-0.01610.8639-0.68191.088947.436287.726230.8224
164.38991.2581-2.10385.5460.61043.4745-0.13011.1443-0.776-0.4326-0.280.12810.2087-0.7148-0.13030.42520.1852-0.04781.2635-0.39730.439648.97396.206825.0899
171.5442-0.5459-0.06964.2435-1.11392.98310.00390.0146-0.0821-0.10760.0286-0.2093-0.0310.0725-0.00360.166-0.07250.00220.1815-0.03670.2049104.2044110.55155.1495
182.6424-0.0644-0.40814.7513-0.86991.93070.0145-0.1756-0.03760.4287-0.0449-0.8451-0.21590.5168-0.02450.23-0.0538-0.05410.3123-0.02370.3201111.0324113.46159.0578
191.76181.33630.30115.3644-1.44471.07420.1798-0.0792-0.25650.1342-0.2155-0.22-0.0510.2180.09860.2664-0.0380.05110.2347-0.01230.2044102.6956104.23399.9177
206.27992.3482-0.90063.2568-0.59131.19150.5303-0.9743-0.25380.4365-0.55870.1376-0.09310.141-0.06860.4117-0.1403-0.03230.32830.02840.279384.522583.789722.3671
215.15080.9702-0.87482.5024-0.33031.47950.3499-0.0192-1.45830.3557-0.2915-0.31150.2561-0.06230.01250.4108-0.0762-0.06990.25910.03350.499385.282478.932518.2874
225.78971.3671.48063.42031.22712.4319-0.115-0.51950.34360.2993-0.07140.6165-0.2036-0.40530.14860.30690.00330.09010.3203-0.06610.322685.8809119.850416.4361
235.69051.2423-0.29928.69651.05934.28290.04350.4186-0.762-0.26940.18620.11410.2914-0.53860.0040.1984-0.0537-0.04760.2861-0.0610.20289.6385114.91716.1596
245.19881.28791.5186.36451.79294.4997-0.18770.22110.671-0.12750.0690.0985-0.5615-0.31270.02590.34430.016-0.00280.31560.01940.439489.192129.75687.1299
254.32260.64521.16134.27611.10294.10780.04880.02430.35530.0113-0.12980.4519-0.1256-0.48610.04910.27150.04180.01510.3701-0.02960.428482.7113125.311311.668
268.4731-0.8912.00084.5301-2.60755.5318-0.0951.0667-0.7463-0.75270.18530.87380.1747-0.5375-0.08390.3374-0.0742-0.05830.5702-0.0430.625377.3239113.40243.416
277.93241.50871.16463.79470.25062.7935-0.0675-0.1294-0.35280.21030.05280.2183-0.1803-0.2105-0.01850.23490.00290.0640.1907-0.04040.281191.4733116.844514.594
280.40620.6624-1.15184.2424-2.31045.98050.1391-0.39910.40130.4671-0.11320.5013-0.2421-0.1325-0.07330.2877-0.20830.01370.4929-0.12010.580473.590295.941221.5986
296.6818-1.77962.06527.0672-2.6796.6460.5855-0.99780.19650.8779-0.72690.35890.52270.20080.16520.5247-0.24340.14160.5498-0.1720.341682.659990.360226.3746
303.9748-0.36990.04173.6055-0.30352.90440.0804-0.74471.12990.7532-0.24760.08160.05950.07770.2960.3957-0.16220.04720.4781-0.14470.445183.981196.096222.5962
314.2688-1.38010.8760.8129-0.67920.6075-0.2697-1.5380.02411.38770.0575-0.2287-0.29080.02390.16471.2269-0.1919-0.06291.53730.13570.379988.304288.668141.0943
325.3780.13130.42584.37650.47214.36720.2677-1.02481.33290.7779-0.09690.50250.0399-0.06520.09740.4836-0.19040.10310.5901-0.37490.814877.4805102.611726.308
336.95730.2614-0.16562.62140.82393.79660.0249-1.63550.93761.2308-0.30690.52850.07140.01520.13870.6633-0.29640.20371.0814-0.35330.687377.323195.124533.5846
341.41320.18-0.3170.21160.05520.1199-0.0597-0.31020.5850.00170.2223-0.5432-0.35880.2130.1810.3790.0057-0.06260.2695-0.10340.3926101.511127.09127.1869
351.85410.44471.98270.31390.12382.7225-0.0753-0.1065-0.48550.34860.255-0.35150.74590.11520.16680.43930.09270.04350.2461-0.0330.267166.243159.698252.1431
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 80 )A1 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 133 )A81 - 133
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 216 )A134 - 216
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 17 )B2 - 17
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 40 )B18 - 40
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 51 )B41 - 51
7X-RAY DIFFRACTION7chain 'B' and (resid 52 through 73 )B52 - 73
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 91 )B74 - 91
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 106 )B92 - 106
10X-RAY DIFFRACTION10chain 'B' and (resid 107 through 114 )B107 - 114
11X-RAY DIFFRACTION11chain 'B' and (resid 115 through 129 )B115 - 129
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 148 )B138 - 148
13X-RAY DIFFRACTION13chain 'B' and (resid 149 through 160 )B149 - 160
14X-RAY DIFFRACTION14chain 'B' and (resid 161 through 196 )B161 - 196
15X-RAY DIFFRACTION15chain 'B' and (resid 197 through 206 )B197 - 206
16X-RAY DIFFRACTION16chain 'B' and (resid 207 through 215 )B207 - 215
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 53 )C1 - 53
18X-RAY DIFFRACTION18chain 'C' and (resid 54 through 80 )C54 - 80
19X-RAY DIFFRACTION19chain 'C' and (resid 81 through 118 )C81 - 118
20X-RAY DIFFRACTION20chain 'C' and (resid 119 through 149 )C119 - 149
21X-RAY DIFFRACTION21chain 'C' and (resid 150 through 216 )C150 - 216
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 40 )D2 - 40
23X-RAY DIFFRACTION23chain 'D' and (resid 41 through 51 )D41 - 51
24X-RAY DIFFRACTION24chain 'D' and (resid 52 through 61 )D52 - 61
25X-RAY DIFFRACTION25chain 'D' and (resid 62 through 83 )D62 - 83
26X-RAY DIFFRACTION26chain 'D' and (resid 84 through 91 )D84 - 91
27X-RAY DIFFRACTION27chain 'D' and (resid 92 through 114 )D92 - 114
28X-RAY DIFFRACTION28chain 'D' and (resid 115 through 129 )D115 - 129
29X-RAY DIFFRACTION29chain 'D' and (resid 138 through 148 )D138 - 148
30X-RAY DIFFRACTION30chain 'D' and (resid 149 through 186 )D149 - 186
31X-RAY DIFFRACTION31chain 'D' and (resid 187 through 196 )D187 - 196
32X-RAY DIFFRACTION32chain 'D' and (resid 197 through 206 )D197 - 206
33X-RAY DIFFRACTION33chain 'D' and (resid 207 through 215 )D207 - 215
34X-RAY DIFFRACTION34chain 'E' and (resid 3 through 8 )E3 - 8
35X-RAY DIFFRACTION35chain 'F' and (resid 3 through 8 )F3 - 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://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