[日本語] English
万見
- PDB-7a3p: Crystal structure of dengue 3 virus envelope glycoprotein in comp... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7a3p
タイトルCrystal structure of dengue 3 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10
要素
  • (Single Chain Variable Fragment) x 2
  • Envelope protein E
キーワードVIRAL PROTEIN / FLAVIVIRUS / CLASS 2 FUSION PROTEIN / DENGUE / Antibody
機能・相同性
機能・相同性情報


clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane
類似検索 - 分子機能
Flavivirus envelope glycoprotein E, stem/anchor domain / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain ...Flavivirus envelope glycoprotein E, stem/anchor domain / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set
類似検索 - ドメイン・相同性
Genome polyprotein
類似検索 - 構成要素
生物種Dengue virus 3 (デング熱ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.19 Å
データ登録者Sharma, A. / Vaney, M.C. / Guardado-Calvo, P. / Duquerroy, S. / Rouvinski, A. / Rey, F.A.
資金援助 フランス, 1件
組織認可番号国
Wellcome Trust フランス
引用
ジャーナル: Cell / 年: 2021
タイトル: The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses.
著者: Arvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado- ...著者: Arvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado-Calvo / Ahmed Haouz / Patrick England / Ren Sun / Z Hong Zhou / Juthathip Mongkolsapaya / Gavin R Screaton / Felix A Rey /
要旨: The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative ...The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative structure-function analysis of C10 bound to the envelope (E) protein dimers of the five viruses it neutralizes. We demonstrate that the C10 Fab has high affinity for ZIKV and DENV1 but not for DENV2, DENV3, and DENV4. We further show that the C10 interaction with the latter viruses requires an E protein conformational landscape that limits binding to only one of the three independent epitopes per virion. This limited affinity is nevertheless counterbalanced by the particle's icosahedral organization, which allows two different dimers to be reached by both Fab arms of a C10 immunoglobulin. The epitopes' geometric distribution thus confers C10 its exceptional neutralization breadth. Our results highlight the importance not only of paratope/epitope complementarity but also the topological distribution for epitope-focused vaccine design.
#1: ジャーナル: Nature / 年: 2016
タイトル: Structural basis of potent Zika-dengue virus antibody cross-neutralization.
著者: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. ...著者: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. / Mongkolsapaya, J. / Heinz, F.X. / Screaton, G.R. / Rey, F.A.
#2: ジャーナル: Nature / 年: 2015
タイトル: Recognition determinants of broadly neutralizing human antibodies against dengue viruses.
著者: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / ...著者: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / Petres, S. / Shepard, W.E. / Despres, P. / Arenzana-Seisdedos, F. / Dussart, P. / Mongkolsapaya, J. / Screaton, G.R. / Rey, F.A.
履歴
登録2020年8月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年12月8日Provider: repository / タイプ: Initial release
改定 1.12021年12月15日Group: Database references / カテゴリ: citation
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_PubMed / _citation.title
改定 1.22021年12月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年5月1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

-
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

-
集合体

登録構造単位
A: Envelope protein E
B: Envelope protein E
H: Single Chain Variable Fragment
L: Single Chain Variable Fragment
I: Single Chain Variable Fragment
M: Single Chain Variable Fragment
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)156,4867
ポリマ－156,2646
非ポリマー2211
水30617
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration, envelope protein (Chain A and chain B) are present as dimers on virion surface and form a dimers in the asymmetric unit. Chain H (antibody heavy chain fragment) forms a ...根拠: gel filtration, envelope protein (Chain A and chain B) are present as dimers on virion surface and form a dimers in the asymmetric unit. Chain H (antibody heavy chain fragment) forms a heterodimer with chain L (antibody light chain fragment) .
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-19 kcal/mol
Surface area53710 Å2
手法PISA
単位格子
Length a, b, c (Å)53.744, 101.412, 249.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 1 through 16 or resid 19...
21(chain B and (resid 1 through 221 or resid 224...
12chain H
22(chain I and resid 2 through 111)
13chain L
23(chain M and resid 2 through 106A)

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
111METMETSERSER(chain A and (resid 1 through 16 or resid 19...AA1 - 161 - 16
121THRTHRTHRTHR(chain A and (resid 1 through 16 or resid 19...AA19 - 14519 - 145
131VALVALGLUGLU(chain A and (resid 1 through 16 or resid 19...AA158 - 85158 - 85
141METMETTYRTYR(chain A and (resid 1 through 16 or resid 19...AA1 - 3901 - 390
151GLYGLYTYRTYR(chain A and (resid 1 through 16 or resid 19...AA273 - 324273 - 324
161ASPASPTRPTRP(chain A and (resid 1 through 16 or resid 19...AA328 - 389328 - 389
211METMETGLYGLY(chain B and (resid 1 through 221 or resid 224...BB1 - 2211 - 221
221THRTHRPHEPHE(chain B and (resid 1 through 221 or resid 224...BB224 - 238224 - 238
231GLUGLUILEILE(chain B and (resid 1 through 221 or resid 224...BB247 - 276247 - 276
241GLYGLYTHRTHR(chain B and (resid 1 through 221 or resid 224...BB279 - 337279 - 337
251ARGARGTRPTRP(chain B and (resid 1 through 221 or resid 224...BB348 - 389348 - 389
112VALVALVALVALchain HHC2 - 1114 - 128
212VALVALVALVAL(chain I and resid 2 through 111)IE2 - 1114 - 128
113SERSERVALVALchain LLD2 - 1068 - 115
213SERSERVALVAL(chain M and resid 2 through 106A)MF2 - 1068 - 115

NCSアンサンブル:
ID
1
2
3

-
要素

#1: タンパク質 Envelope protein E / Matrix protein / Peptide pr / Protein prM / Small envelope protein M


分子量: 46820.219 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: DENGUE VIRUS SEROTYPE 3 ENVELOPE PROTEIN ECTODOMAIN
由来: (組換発現) Dengue virus 3 (デング熱ウイルス)
細胞株 (発現宿主): SCHNEIDER 2
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: Q07019
#2: 抗体 Single Chain Variable Fragment


分子量: 15679.234 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: variable domain from the heavy chain of antibody EDE1 C10
由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): SCHNEIDER 2
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
#3: 抗体 Single Chain Variable Fragment


分子量: 15632.767 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: variable domain from the light chain of antibody EDE1 C10
由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): SCHNEIDER 2
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
#4: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 17 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.17 Å3/Da / 溶媒含有率: 43.36 %
結晶化温度: 291 K / 手法: 蒸気拡散法 / pH: 7.5 / 詳細: 100 mM HEPES pH 7.5, 15% PEG 8,000

-
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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2013年10月3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: 3.19→49.59 Å / Num. obs: 23920 / % possible obs: 87.3 % / 冗長度: 5.4 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 6.3
反射 シェル解像度: 3.19→3.37 Å / Rmerge(I) obs: 0.476 / Num. unique obs: 2139 / % possible all: 56.9

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PDB_EXTRACT3.25データ抽出
Aimlessデータスケーリング
PHENIX位相決定
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: DENV1 sE from related PDB

解像度: 3.19→19.95 Å / SU ML: 0.4 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 31.72 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2839 1220 5.35 %
Rwork0.2405 21602 -
obs0.243 22822 97.39 %
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: 141.35 Å2 / Biso mean: 67.1441 Å2 / Biso min: 28.25 Å2
精密化ステップサイクル: final / 解像度: 3.19→19.95 Å
タンパク質核酸リガンド溶媒全体
原子数9142 0 14 17 9173
Biso mean--96.39 46.48 -
残基数----1183
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1998X-RAY DIFFRACTION5.796TORSIONAL
12B1998X-RAY DIFFRACTION5.796TORSIONAL
21H756X-RAY DIFFRACTION5.796TORSIONAL
22I756X-RAY DIFFRACTION5.796TORSIONAL
31L648X-RAY DIFFRACTION5.796TORSIONAL
32M648X-RAY DIFFRACTION5.796TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.19-3.320.34341460.307823652511100
3.32-3.470.37411510.27823882539100
3.47-3.650.27651310.2752409254099
3.65-3.880.34491060.25472446255299
3.88-4.170.33071010.24592432253398
4.17-4.590.2171970.20612436253398
4.59-5.240.24221500.20642396254697
5.24-6.560.28451860.24082350253696
6.56-19.950.25241520.22982380253291
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)
11.59690.25370.85753.87540.14753.83790.0752-0.0098-0.20840.77620.22430.1208-0.8789-0.7408-0.22170.61110.05560.09290.48980.05180.4464-77.4038122.440476.1144
21.1637-0.1588-1.61720.31370.11213.2658-0.00020.40770.1011-0.0294-0.05720.0008-0.0218-0.6585-0.02640.37450.02820.00130.49070.04940.4952-70.756111.679538.6144
33.25481.6858-4.08130.2211-1.39876.0087-0.04380.06110.4071-0.0340.68120.5434-0.306-0.5276-0.61830.49930.065-0.03630.7812-0.04470.6702-78.7377119.224953.8806
43.30230.308-1.20973.26720.52715.11170.22640.70.36420.1585-0.0130.0498-0.0565-0.5013-0.33010.26650.02250.02330.49360.05860.5074-64.9865115.851334.6627
50.8199-0.58691.23730.6922-0.53631.6134-0.0379-0.54280.10760.35340.38770.1327-0.1785-0.4471-0.07940.58870.11670.04210.95650.03460.6261-80.2284113.651881.2825
64.1270.0125-1.10790.8793-0.70454.8609-0.0363-1.1184-0.2240.8314-0.1499-0.0665-0.43570.07040.20280.55790.1167-0.05140.92510.01980.5147-70.1564113.897993.175
70.9549-0.2467-0.9493-0.0296-0.13354.11190.0645-0.01870.1022-0.0841-0.2729-0.0971-0.56191.0170.20840.4877-0.11230.01820.49150.06050.5101-37.978113.563732.0767
80.9825-1.5681-0.83541.02540.52093.83060.11140.7370.3554-0.05140.021-0.5850.07830.6163-0.14870.5551-0.06330.0421.3829-0.00580.8119-26.4706116.059314.1812
95.78160.1157-0.47082.3726-1.00976.9321-0.0111-0.02580.6879-0.11430.21830.11430.4254-0.3784-0.15510.33960.0190.00820.40380.05290.3333-44.9709114.822945.6846
100.9962-0.3675-0.072-0.39860.25830.4692-0.01940.9123-0.1535-0.4799-0.1498-0.00040.0924-0.3709-0.00030.8138-0.00390.1310.7184-0.01420.6077-32.4446117.303711.9697
113.2266-0.51-0.70361.17550.03973.6773-0.7087-0.0171-0.20680.0550.08730.01240.79750.81220.65140.6546-0.0330.11670.85240.06110.7277-34.8427109.9978-20.1283
122.21980.5440.2380.81451.05283.5737-0.33390.013-0.1207-0.17050.2347-0.02820.5007-0.75820.0920.8556-0.04590.18530.99350.22520.5053-37.3683109.6788-20.455
131.40930.13892.02615.74191.10392.8771-0.11970.0942-0.58690.6721-0.0085-0.8880.3116-0.0017-0.01950.62850.0449-0.07370.8326-0.0280.5221-41.542881.461614.384
141.45530.61431.23155.10311.65694.42580.2607-0.609-0.06170.5265-0.52490.4107-0.2045-0.70220.36570.5374-0.0409-0.00020.86480.12790.3988-49.692290.708510.6934
155.14062.0293-0.52914.27561.79522.314-0.5807-1.30220.62290.1816-0.37610.21480.0959-0.18681.06360.7725-0.0836-0.20810.7990.12880.5048-47.564785.574517.9147
161.99080.98680.0011.90480.07181.0219-0.0156-0.2223-0.11840.01340.1147-0.3056-0.0307-0.2075-0.11310.46230.0810.00130.75970.04590.3624-43.356592.2865.7794
173.45590.31410.97594.34721.70880.9076-0.47710.1305-0.8240.7942-0.00030.87770.9817-0.96770.07691.2144-0.5262-0.16841.54590.06080.4441-59.527586.6515-6.7886
180.7768-0.1508-0.62580.02680.12120.51-0.44250.6538-0.8889-1.17140.9046-0.3496-0.13650.4696-0.10681.12270.0232-0.05341.1831-0.95091.1176-50.589577.6914-21.0425
195.1881-0.19030.63361.3953-0.61043.6318-0.3432-0.40280.826-0.67620.26230.16490.9476-0.75170.2350.5229-0.0959-0.11990.78330.01910.3962-53.258592.985-7.7544
203.87291.16710.51781.40250.71131.50760.760.3218-1.1137-0.7526-0.1019-0.60490.0892-0.048-0.38720.6002-0.08440.1030.5579-0.01430.4916-43.066182.1807-4.7294
216.5214-2.1084-2.27935.16254.18334.32350.86410.63090.4377-1.271-0.4603-0.95191.4143-0.0818-0.48550.90820.00270.04920.63830.06650.4872-40.505292.4957-12.3809
225.89452.0138-3.32572.515-0.96843.7177-0.45290.015-0.4102-0.0467-0.27610.0625-0.1483-0.68230.68460.48650.0054-0.06630.8035-0.03480.399-51.689692.5867-15.008
230.55660.8477-0.01461.1047-0.43282.4066-0.10190.2683-0.1081-0.51290.4875-0.76190.47080.2419-0.40050.8309-0.01770.0970.63150.04470.4844-47.393682.712-10.5895
241.8960.37730.68525.98441.11342.7778-0.12250.23340.27230.31060.62990.50940.573-0.3772-0.26410.56960.0179-0.01280.40150.18240.4579-55.332294.29361.8303
252.59961.1863-0.22621.3924-1.33731.8181-0.01160.345-0.7273-0.2310.2176-0.4710.9061-0.2186-0.3040.729-0.23870.10890.7998-0.23520.6939-51.424875.3825-14.3813
264.6892.7262.20866.8283-1.93873.03110.0237-0.7134-0.27241.2518-0.7883-0.07770.1204-0.57910.26760.7125-0.016-0.00651.1838-0.18160.1493-73.599684.134370.2581
27-0.01020.14190.03030.07380.0274-0.0026-0.54530.7927-0.4163-0.00720.04930.44270.11360.20580.06180.56530.1459-0.22980.2215-0.2360.6333-57.582374.715956.7246
283.3746-3.7073-2.37334.08862.61882.0382-0.4376-0.5418-0.31040.52930.38540.78451.5092-1.01340.37950.4643-0.053-0.06170.3317-0.10550.5706-70.62886.403863.0055
293.4019-2.67621.20114.2171-1.00592.01220.2472-0.887-0.14270.06450.25580.25770.1608-0.8769-0.06530.63270.0422-0.0088-1.0678-0.02420.4878-64.190590.167966.5744
300.2984-0.1093-0.44764.9355-1.01092.56240.59840.01320.2287-0.4441-0.6496-0.3590.38121.0009-0.01670.5166-0.14740.04590.584-0.13840.3885-55.884988.741968.2622
310.3333-0.6389-0.31212.83630.05081.35640.50120.36630.7278-0.08990.0606-0.56-1.42970.5035-0.18960.77030.29530.07090.14270.17250.5976-57.427595.609360.5898
322.7547-2.46960.43653.4302-0.98785.3191-0.60170.08250.6036-0.3665-0.4784-0.3349-0.25131.06650.8610.7569-0.0381-0.05950.51380.10730.5101-58.983790.386656.4088
333.1362-0.24451.28310.9883-0.1261.2905-0.53510.01560.5645-1.0062-0.8117-0.4836-0.5820.59590.18090.8295-0.3382-0.2557-1.4235-0.46950.5301-67.355987.308757.5658
340.03930.10680.85392.40070.48071.72470.04530.15510.0406-0.79240.2953-0.28290.16830.2257-0.23970.4468-0.15250.07090.46690.02840.37-57.350583.788565.0996
353.09031.18690.77221.8568-0.47846.2990.67330.58870.0951-0.27140.45550.3695-1.1181-0.8559-1.11540.56650.0641-0.06710.56990.05460.5401-66.2233105.489166.8348
360.3115-0.2455-0.62812.58981.07290.53030.64490.43460.72110.0984-0.8033-0.420.2775-0.7673-0.11570.3806-0.1039-0.01790.32750.02370.4662-63.81987.265971.6711
372.3333-0.75121.24440.8984-0.13230.75240.58680.9275-0.4611-1.9010.0239-1.88920.4280.609-0.2251.07770.1758-0.19110.3258-0.13170.5979-46.804588.031679.8419
381.3262-0.2783-0.12934.973-2.19674.8832-0.4714-0.1674-0.03220.2475-0.1523-0.97590.094-0.32130.61630.30930.0149-0.02360.436-0.04470.4958-52.787292.797287.5452
390.9344-0.66480.40041.2509-0.08142.0988-0.05780.35880.51071.5748-0.65380.70080.48070.470.48460.6051-0.0077-0.00590.0644-0.07460.429-61.93585.773681.4672
401.34950.9836-1.18762.8741-3.26494.54460.20760.09230.2072-0.17080.06060.31640.04770.1421-0.30270.30020.0619-0.05040.65460.01250.5244-66.514394.392788.0187
410.2235-0.5625-0.26321.4660.61010.2661-0.243-1.04790.07260.81490.54280.9012-0.14350.25380.06270.5627-0.1884-0.04890.2825-0.2180.2828-55.322695.351989.727
420.6504-0.7423-0.00080.6091.25833.4126-0.4242-0.3456-0.3838-0.00850.3773-0.24760.918-0.88210.51190.5457-0.10760.10030.3726-0.06920.5391-59.231884.965487.0327
431.3885-0.7531-0.26012.489-1.4081.8598-0.2836-0.60820.2108-0.6726-0.7005-1.5202-0.03940.55050.36870.5111-0.1711-0.11350.2044-0.03470.5824-53.270889.322679.768
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 26 )A1 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 176 )A27 - 176
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 201 )A177 - 201
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 269 )A202 - 269
5X-RAY DIFFRACTION5chain 'A' and (resid 270 through 308 )A270 - 308
6X-RAY DIFFRACTION6chain 'A' and (resid 309 through 390 )A309 - 390
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 167 )B1 - 167
8X-RAY DIFFRACTION8chain 'B' and (resid 168 through 201 )B168 - 201
9X-RAY DIFFRACTION9chain 'B' and (resid 202 through 254 )B202 - 254
10X-RAY DIFFRACTION10chain 'B' and (resid 255 through 296 )B255 - 296
11X-RAY DIFFRACTION11chain 'B' and (resid 297 through 355 )B297 - 355
12X-RAY DIFFRACTION12chain 'B' and (resid 356 through 388 )B356 - 388
13X-RAY DIFFRACTION13chain 'H' and (resid 2 through 28 )H2 - 28
14X-RAY DIFFRACTION14chain 'H' and (resid 29 through 66 )H29 - 66
15X-RAY DIFFRACTION15chain 'H' and (resid 67 through 87 )H67 - 87
16X-RAY DIFFRACTION16chain 'H' and (resid 88 through 111 )H88 - 111
17X-RAY DIFFRACTION17chain 'L' and (resid 2 through 8 )L2 - 8
18X-RAY DIFFRACTION18chain 'L' and (resid 9 through 18 )L9 - 18
19X-RAY DIFFRACTION19chain 'L' and (resid 19 through 38 )L19 - 38
20X-RAY DIFFRACTION20chain 'L' and (resid 39 through 48 )L39 - 48
21X-RAY DIFFRACTION21chain 'L' and (resid 49 through 61 )L49 - 61
22X-RAY DIFFRACTION22chain 'L' and (resid 62 through 75 )L62 - 75
23X-RAY DIFFRACTION23chain 'L' and (resid 76 through 91 )L76 - 91
24X-RAY DIFFRACTION24chain 'L' and (resid 92 through 101 )L92 - 101
25X-RAY DIFFRACTION25chain 'L' and (resid 102 through 106A)L102 - 106
26X-RAY DIFFRACTION26chain 'I' and (resid 1 through 6 )I1 - 6
27X-RAY DIFFRACTION27chain 'I' and (resid 7 through 17 )I7 - 17
28X-RAY DIFFRACTION28chain 'I' and (resid 18 through 28 )I18 - 28
29X-RAY DIFFRACTION29chain 'I' and (resid 29 through 40 )I29 - 40
30X-RAY DIFFRACTION30chain 'I' and (resid 41 through 52 )I41 - 52
31X-RAY DIFFRACTION31chain 'I' and (resid 52A through 63 )I52
32X-RAY DIFFRACTION32chain 'I' and (resid 64 through 72 )I64 - 72
33X-RAY DIFFRACTION33chain 'I' and (resid 73 through 82 )I73 - 82
34X-RAY DIFFRACTION34chain 'I' and (resid 82A through 96 )I82
35X-RAY DIFFRACTION35chain 'I' and (resid 97 through 100F)I97 - 100
36X-RAY DIFFRACTION36chain 'I' and (resid 100G through 111 )I100
37X-RAY DIFFRACTION37chain 'M' and (resid 0 through 8 )M0 - 8
38X-RAY DIFFRACTION38chain 'M' and (resid 9 through 32 )M9 - 32
39X-RAY DIFFRACTION39chain 'M' and (resid 33 through 48 )M33 - 48
40X-RAY DIFFRACTION40chain 'M' and (resid 49 through 61 )M49 - 61
41X-RAY DIFFRACTION41chain 'M' and (resid 62 through 75 )M62 - 75
42X-RAY DIFFRACTION42chain 'M' and (resid 76 through 91 )M76 - 91
43X-RAY DIFFRACTION43chain 'M' and (resid 92 through 106A)M92 - 106

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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