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- PDB-5wna: Structure of antibody 3D3 bound to the central conserved region o... -

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基本情報

登録情報
データベース: PDB / ID: 5wna
タイトルStructure of antibody 3D3 bound to the central conserved region of RSV G
要素
  • Major surface glycoprotein G
  • mAb 3D3 Fab heavy chain
  • mAb 3D3 Fab light chain
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / RSV / glycoprotein / G glycoprotein / viral protein / viral attachment protein / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


Translation of respiratory syncytial virus mRNAs / adhesion receptor-mediated virion attachment to host cell / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / plasma membrane
類似検索 - 分子機能
Major surface glycoprotein G / Pneumovirus attachment glycoprotein G / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Major surface glycoprotein G
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Human respiratory syncytial virus A (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Fedechkin, S.O. / George, N.L. / Wolff, J.T. / Kauvar, L.M. / DuBois, R.M.
引用ジャーナル: Sci Immunol / 年: 2018
タイトル: Structures of respiratory syncytial virus G antigen bound to broadly neutralizing antibodies.
著者: Fedechkin, S.O. / George, N.L. / Wolff, J.T. / Kauvar, L.M. / DuBois, R.M.
履歴
登録2017年7月31日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年3月14日Provider: repository / タイプ: Initial release
改定 1.12018年3月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023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
改定 1.32024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
H: mAb 3D3 Fab heavy chain
L: mAb 3D3 Fab light chain
B: Major surface glycoprotein G
C: mAb 3D3 Fab heavy chain
D: mAb 3D3 Fab light chain
A: Major surface glycoprotein G


分子量 (理論値)分子数
合計 (水以外)107,1486
ポリマ－107,1486
非ポリマー00
水2,432135
1
H: mAb 3D3 Fab heavy chain
L: mAb 3D3 Fab light chain
B: Major surface glycoprotein G


分子量 (理論値)分子数
合計 (水以外)53,5743
ポリマ－53,5743
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-38 kcal/mol
Surface area20430 Å2
手法PISA
2
C: mAb 3D3 Fab heavy chain
D: mAb 3D3 Fab light chain
A: Major surface glycoprotein G


分子量 (理論値)分子数
合計 (水以外)53,5743
ポリマ－53,5743
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-39 kcal/mol
Surface area20560 Å2
手法PISA
単位格子
Length a, b, c (Å)64.620, 135.010, 73.780
Angle α, β, γ (deg.)90.000, 107.450, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain D and (resseq 1:13 or resseq 15:23 or (resid...
21(chain L and (resseq 1:13 or resseq 15:68 or resseq...
12(chain C and (resseq 1:2 or (resid 3 and (name...
22(chain H and (resseq 1:2 or (resid 3 and (name...
13(chain A and (resseq 162:187 or (resid 189 and (name...
23(chain B and (resseq 161:186 or resseq 188:189))

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
111GLNGLNLEULEU(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 131 - 13
121PROPROCYSCYS(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE15 - 2315 - 23
131ARGARGARGARG(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE2424
141GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
151GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
161GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
171GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
181GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
211GLNGLNLEULEU(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 131 - 13
221PROPROGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB15 - 6815 - 68
231PHEPHELEULEU(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB71 - 12471 - 124
241SERSERASNASN(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB126 - 209126 - 209
251ARGARGARGARG(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB210210
261GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
271GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
281GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
291GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2101GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2111GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2121GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2131GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2141GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
112GLUGLUGLUGLU(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 21 - 2
122GLNGLNGLNGLN(chain C and (resseq 1:2 or (resid 3 and (name...CD33
132GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
142GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
152GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
162GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
172GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
182GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
192GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
212GLUGLUGLUGLU(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 21 - 2
222GLNGLNGLNGLN(chain H and (resseq 1:2 or (resid 3 and (name...HA33
232GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
242GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
252GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
262GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
272GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
282GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
292GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
113ASPASPLYSLYS(chain A and (resseq 162:187 or (resid 189 and (name...AF162 - 1874 - 29
123ILEILEILEILE(chain A and (resseq 162:187 or (resid 189 and (name...AF18931
133ASNASNPROPRO(chain A and (resseq 162:187 or (resid 189 and (name...AF161 - 1903 - 32
143ASNASNPROPRO(chain A and (resseq 162:187 or (resid 189 and (name...AF161 - 1903 - 32
153ASNASNPROPRO(chain A and (resseq 162:187 or (resid 189 and (name...AF161 - 1903 - 32
163ASNASNPROPRO(chain A and (resseq 162:187 or (resid 189 and (name...AF161 - 1903 - 32
213ASNASNCYSCYS(chain B and (resseq 161:186 or resseq 188:189))BC161 - 1863 - 28
223ARGARGILEILE(chain B and (resseq 161:186 or resseq 188:189))BC188 - 18930 - 31

NCSアンサンブル:
ID
1
2
3

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要素

#1: 抗体 mAb 3D3 Fab heavy chain


分子量: 24778.816 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#2: 抗体 mAb 3D3 Fab light chain


分子量: 23487.041 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#3: タンパク質・ペプチド Major surface glycoprotein G / Attachment glycoprotein G / Membrane-bound glycoprotein / mG


分子量: 5308.158 Da / 分子数: 2
Fragment: Central conserved region of RSV G, UNP residues 161-197
由来タイプ: 組換発現
由来: (組換発現) Human respiratory syncytial virus A (ウイルス)
株: A2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P03423
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 135 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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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: 2.87 Å3/Da / 溶媒含有率: 57.08 %
結晶化温度: 295.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: 23% PEG 3350, 0.05 M zinc acetate

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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: ALS / ビームライン: 8.3.1 / 波長: 1.11503 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年5月19日 / 詳細: Pilatus3 S, 25Hz, S/N 60-0134
放射モノクロメーター: Si(111) Khozu / 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: 1.11503 Å / 相対比: 1
反射解像度: 2.4→48.72 Å / Num. obs: 46906 / % possible obs: 99.5 % / 冗長度: 6.3 % / Biso Wilson estimate: 35.45 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.05 / Rrim(I) all: 0.126 / Net I/σ(I): 12.3
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.485.60.84446170.670.3860.93199
9.3-48.727.10.0358260.9990.0140.03899.3

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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
Aimless0.5.31データスケーリング
PDB_EXTRACT3.22データ抽出
iMOSFLMデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5I30

5i30


解像度: 2.4→48.719 Å / SU ML: 0.31 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.43 / 詳細: PHENIX
Rfactor反射数%反射
Rfree0.2455 2000 4.27 %
Rwork0.1915 --
obs0.1938 46868 99.42 %
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: 119.5 Å2 / Biso mean: 41.9572 Å2 / Biso min: 17.96 Å2
精密化ステップサイクル: final / 解像度: 2.4→48.719 Å
タンパク質核酸リガンド溶媒全体
原子数7120 0 0 135 7255
Biso mean---38.59 -
残基数----934
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0067326
X-RAY DIFFRACTIONf_angle_d0.9359981
X-RAY DIFFRACTIONf_chiral_restr0.051118
X-RAY DIFFRACTIONf_plane_restr0.0071281
X-RAY DIFFRACTIONf_dihedral_angle_d15.734385
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11D1910X-RAY DIFFRACTION10.278TORSIONAL
12L1910X-RAY DIFFRACTION10.278TORSIONAL
21C1929X-RAY DIFFRACTION10.278TORSIONAL
22H1929X-RAY DIFFRACTION10.278TORSIONAL
31A250X-RAY DIFFRACTION10.278TORSIONAL
32B250X-RAY DIFFRACTION10.278TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.35461420.28013196333899
2.46-2.52660.32741400.26033130327099
2.5266-2.60090.2931430.252932203363100
2.6009-2.68480.32631430.231432013344100
2.6848-2.78080.28891420.221732043346100
2.7808-2.89210.30531430.21631923335100
2.8921-3.02370.28791440.21332153359100
3.0237-3.18310.27841420.20543192333499
3.1831-3.38250.24151430.201332183361100
3.3825-3.64360.23651430.173832033346100
3.6436-4.01010.26491430.172432203363100
4.0101-4.590.18961440.154432253369100
4.59-5.78140.18521430.16613209335299
5.7814-48.72950.20471450.17933243338899
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)
11.9818-2.2052-0.13292.7740.29493.81210.28590.10890.2171-1.003-0.2749-0.46470.25660.274-0.02030.35790.04750.02850.32490.12810.304244.593612.964370.2317
22.1108-0.1975-0.40562.6240.05934.53080.33070.14050.0682-0.6536-0.08870.20890.0886-0.2286-0.25110.41730.005-0.05880.22570.06020.238334.331412.926771.1538
33.2029-3.402-0.40565.70262.77993.46650.25830.0896-0.0469-0.9864-0.49870.0907-0.6221-0.03690.30770.4097-0.0098-0.02190.26290.07390.350637.502420.848773.663
41.8092-1.31310.0294.80193.15233.9530.26220.1634-0.2514-0.3113-0.2640.27520.7759-0.1801-0.04170.5723-0.0137-0.10480.29010.00540.219537.3946-1.088372.4798
54.25582.90213.69091.9592.64525.23640.10850.00790.2513-0.0856-0.1806-0.3968-0.24530.00380.04250.338-0.0487-0.06080.21550.09240.38646.267324.134484.5567
66.6066-1.3949-1.66496.74324.30753.2381-0.587-0.97930.03281.59050.00790.0081.0480.21220.1520.43-0.172-0.05870.55340.00580.371754.538220.2655113.4483
73.8721-0.64471.79184.3598-1.58084.321-0.0986-0.22130.04140.1952-0.0331-0.16080.01070.14220.16270.1968-0.0572-0.0240.26940.01370.252453.075718.3071101.8087
87.9131-3.97557.26614.8165-6.60849.8512-0.02370.407-0.24110.011-0.2463-0.5161-0.13351.48370.18670.2775-0.0421-0.02010.3793-0.01250.322461.230119.766699.2022
96.8356-1.13830.44053.7994-4.08087.7418-0.0617-0.40830.33890.21730.0010.0511-0.30460.76750.38330.1924-0.124-0.02470.3012-0.00260.38661.72424.7642105.4294
105.3543-2.28734.56122.0058-1.72825.3592-0.0111-0.21440.071-0.09380.05290.26840.2055-0.26080.04780.2721-0.09680.03840.32860.04670.437729.7128-1.937693.1321
112.0642-1.9616-0.03183.6035-1.97223.6640.26410.113-0.1205-0.4368-0.06280.42170.3726-0.2578-0.1480.2662-0.0477-0.11050.27010.0010.343333.4384-4.508382.5616
120.0716-0.4282-0.55634.7434-1.87834.37540.1044-0.0228-0.1759-0.40470.07870.22410.2447-0.3629-0.14670.2591-0.0878-0.11130.26840.02070.391531.2235-3.007985.1164
130.94130.53782.35480.43450.95626.85-0.09130.0629-0.0632-0.16040.1112-0.1703-0.0616-0.17640.08960.3612-0.0822-0.00760.33970.10680.304238.80610.1757105.2072
141.8559-1.0021-0.7929.5138-5.52618.5296-0.0452-0.26370.29820.10670.1755-0.4234-0.31840.323-0.06290.2522-0.0276-0.05470.3072-0.09280.28851.421427.2195111.5138
151.7084-0.7536-0.52596.66191.16291.8984-0.1319-0.39740.10570.07310.12570.03670.1363-0.17980.05310.2001-0.0502-0.01910.41420.0120.23139.822918.4191112.0287
161.7638-1.8624-0.49574.16460.67211.2999-0.1009-0.40160.10260.18290.17770.01790.0446-0.0264-0.06260.192-0.069-0.02930.4177-0.00430.294342.280919.7477112.2445
172.42880.5293-2.97816.6813-2.3174.08230.71660.985-0.3147-1.1471-0.6530.71190.0018-0.3774-0.12640.67350.0424-0.31310.41410.03870.511525.70883.365665.2542
180.0599-0.0841-0.3010.06960.33211.03080.53580.5216-0.2481-0.5689-0.45270.36810.58690.1288-0.06170.8180.1517-0.21530.4907-0.08590.322838.638-9.209460.8257
195.05160.8016-3.25330.316-0.93073.01870.6111.09240.5010.4487-0.17040.1948-0.7253-0.41060.99341.24630.289-0.50510.5189-0.11890.225935.5779-9.523557.3049
205.132-4.20831.57478.5248-5.4145.33480.0054-0.152-0.2214-0.85180.05550.3694-0.0574-0.44530.00020.27940.0265-0.03830.2808-0.09320.241149.385-29.626473.9593
215.61760.20770.09260.4493-0.03833.74630.25080.63330.0661-1.121-0.02770.483-0.2954-0.374-0.27020.55590.0483-0.06240.3903-0.00540.249249.8565-19.160264.9936
224.07150.6806-2.58034.3734-1.28586.01230.40150.0233-0.1659-0.6251-0.2481-0.1262-0.2980.4147-0.07480.38990.00860.03640.2032-0.01170.225259.5237-21.654672.7898
230.774-1.14460.39986.5405-1.26672.70790.22340.2244-0.0036-0.5887-0.1822-0.3521-0.22770.2728-0.00560.34590.02170.03030.29440.02030.26158.1543-21.415470.0282
241.11621.5118-1.93483.7032-2.29893.2676-0.0452-0.0619-0.1724-0.3769-0.076-0.06780.3948-0.09480.13680.2755-0.005-0.07980.2493-0.00590.266849.2874-32.356281.9646
254.6368-2.07070.02076.9597-3.35541.8315-0.0972-1.18780.22091.6616-0.11450.4114-0.1814-0.70520.1970.4084-0.06080.0760.5831-0.07220.330840.6418-33.2084112.1792
263.01611.4568-0.23022.93810.22023.6986-0.0833-0.28350.1946-0.1144-0.1310.3491-0.1722-0.33810.1620.1260.0253-0.02350.27270.01280.265842.4651-30.9051100.1404
276.72880.4129-3.70575.87722.55083.3840.03060.03810.30970.0533-0.4880.6081-0.2829-1.2110.53940.21430.0085-0.0660.3787-0.04280.347133.3675-34.2303100.4982
287.1569-3.2711-4.58744.15472.36425.09510.06590.0402-0.2583-0.01750.054-0.6119-0.24670.1707-0.1340.1976-0.0835-0.07780.3131-0.04930.411964.92-9.942592.5524
291.33-0.7283-0.16522.33821.31052.90350.1024-0.0526-0.1123-0.5027-0.1635-0.6197-0.33780.43210.01910.2894-0.08270.10230.32240.01950.366461.2118-7.038482.0471
300.5042-1.1711-0.23782.79031.2584.47370.1091-0.04430.0647-0.22140.0478-0.412-0.38490.3422-0.09140.2452-0.08760.06740.2928-0.02380.439461.899-5.793587.6523
310.85360.56670.78944.3920.56314.28910.41640.0443-0.0491-0.51830.365-0.5798-0.33810.5828-0.47610.3412-0.10970.11930.3213-0.05620.374166.7422-15.748876.1338
323.32870.1535-3.16411.0353-0.72993.5187-0.321-0.08550.02920.66320.6676-0.2218-0.04080.252-0.21490.2917-0.1094-0.02810.2347-0.10780.326956.2866-12.5801104.6235
331.97050.7960.84137.6256-0.31053.8316-0.1219-0.2197-0.12890.11340.16720.05450.1408-0.0495-0.07490.21150.01310.00590.31520.01970.268348.2854-33.0834108.9589
342.2823-3.5592-0.47919.2756-1.69811.37-0.1775-0.2757-0.07850.04210.17650.0144-0.0110.1420.05360.1775-0.0361-0.01590.31850.01010.293555.0288-28.8342107.6457
351.49760.82631.31898.98240.01122.6283-0.0017-0.3948-0.25880.73560.1136-0.06410.2418-0.0981-0.08650.18660.01770.05310.41280.08650.314553.1741-36.9899114.9681
363.7902-2.38533.03692.6995-3.56424.69431.10720.33480.1051-1.7958-0.6146-1.34710.09581.0964-0.48970.71810.03860.13830.5780.05730.509271.3573-18.558763.9793
371.98-2.36441.314.6106-1.76566.99840.42720.08190.3894-0.9519-0.3315-0.8702-0.63350.65370.23980.7880.0090.46410.46430.20030.314362.4905-8.844463.7746
382.12610.36120.19511.25930.21320.04720.38780.86710.29-0.499-0.1110.0163-0.26550.4045-0.18310.79510.09960.04820.39910.14110.373652.09872.043459.3072
395.04660.8207-0.14076.7564-0.38370.0146-0.06511.0040.0417-1.69890.0708-0.2739-0.5550.65350.01290.91930.07070.15380.48970.10880.385658.0426-0.25557.1369
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )H1 - 33
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 76 )H34 - 76
3X-RAY DIFFRACTION3chain 'H' and (resid 77 through 91 )H77 - 91
4X-RAY DIFFRACTION4chain 'H' and (resid 92 through 114 )H92 - 114
5X-RAY DIFFRACTION5chain 'H' and (resid 115 through 130 )H115 - 130
6X-RAY DIFFRACTION6chain 'H' and (resid 131 through 145 )H131 - 145
7X-RAY DIFFRACTION7chain 'H' and (resid 146 through 201 )H146 - 201
8X-RAY DIFFRACTION8chain 'H' and (resid 202 through 214 )H202 - 214
9X-RAY DIFFRACTION9chain 'H' and (resid 215 through 227 )H215 - 227
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 18 )L1 - 18
11X-RAY DIFFRACTION11chain 'L' and (resid 19 through 61 )L19 - 61
12X-RAY DIFFRACTION12chain 'L' and (resid 62 through 100 )L62 - 100
13X-RAY DIFFRACTION13chain 'L' and (resid 101 through 112 )L101 - 112
14X-RAY DIFFRACTION14chain 'L' and (resid 113 through 127 )L113 - 127
15X-RAY DIFFRACTION15chain 'L' and (resid 128 through 154 )L128 - 154
16X-RAY DIFFRACTION16chain 'L' and (resid 155 through 211 )L155 - 211
17X-RAY DIFFRACTION17chain 'B' and (resid 161 through 168 )B161 - 168
18X-RAY DIFFRACTION18chain 'B' and (resid 169 through 179 )B169 - 179
19X-RAY DIFFRACTION19chain 'B' and (resid 180 through 190 )B180 - 190
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 17 )C1 - 17
21X-RAY DIFFRACTION21chain 'C' and (resid 18 through 33 )C18 - 33
22X-RAY DIFFRACTION22chain 'C' and (resid 34 through 57 )C34 - 57
23X-RAY DIFFRACTION23chain 'C' and (resid 58 through 112 )C58 - 112
24X-RAY DIFFRACTION24chain 'C' and (resid 113 through 130 )C113 - 130
25X-RAY DIFFRACTION25chain 'C' and (resid 131 through 145 )C131 - 145
26X-RAY DIFFRACTION26chain 'C' and (resid 146 through 199 )C146 - 199
27X-RAY DIFFRACTION27chain 'C' and (resid 200 through 225 )C200 - 225
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 18 )D1 - 18
29X-RAY DIFFRACTION29chain 'D' and (resid 19 through 61 )D19 - 61
30X-RAY DIFFRACTION30chain 'D' and (resid 62 through 90 )D62 - 90
31X-RAY DIFFRACTION31chain 'D' and (resid 91 through 100 )D91 - 100
32X-RAY DIFFRACTION32chain 'D' and (resid 101 through 112 )D101 - 112
33X-RAY DIFFRACTION33chain 'D' and (resid 113 through 143 )D113 - 143
34X-RAY DIFFRACTION34chain 'D' and (resid 144 through 173 )D144 - 173
35X-RAY DIFFRACTION35chain 'D' and (resid 174 through 211 )D174 - 211
36X-RAY DIFFRACTION36chain 'A' and (resid 161 through 165 )A161 - 165
37X-RAY DIFFRACTION37chain 'A' and (resid 166 through 173 )A166 - 173
38X-RAY DIFFRACTION38chain 'A' and (resid 174 through 180 )A174 - 180
39X-RAY DIFFRACTION39chain 'A' and (resid 181 through 190 )A181 - 190

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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