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- PDB-7qf1: Crystal structure of the SARS-CoV-2 RBD in complex with the human... -

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基本情報

登録情報
データベース: PDB / ID: 7qf1
タイトルCrystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.6264
要素
  • CV2.6264 heavy chain
  • CV2.6264 light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / neutralization / antibody / coronavirus
機能・相同性
機能・相同性情報


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (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: 2.8 Å
データ登録者Fernandez, I. / Pederzoli, R. / Rey, F.A.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: J Exp Med / 年: 2022
タイトル: Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2.
著者: Cyril Planchais / Ignacio Fernández / Timothée Bruel / Guilherme Dias de Melo / Matthieu Prot / Maxime Beretta / Pablo Guardado-Calvo / Jérémy Dufloo / Luis M Molinos-Albert / Marija ...著者: Cyril Planchais / Ignacio Fernández / Timothée Bruel / Guilherme Dias de Melo / Matthieu Prot / Maxime Beretta / Pablo Guardado-Calvo / Jérémy Dufloo / Luis M Molinos-Albert / Marija Backovic / Jeanne Chiaravalli / Emilie Giraud / Benjamin Vesin / Laurine Conquet / Ludivine Grzelak / Delphine Planas / Isabelle Staropoli / Florence Guivel-Benhassine / Thierry Hieu / Mikaël Boullé / Minerva Cervantes-Gonzalez / Marie-Noëlle Ungeheuer / Pierre Charneau / Sylvie van der Werf / Fabrice Agou / / / Jordan D Dimitrov / Etienne Simon-Lorière / Hervé Bourhy / Xavier Montagutelli / Félix A Rey / Olivier Schwartz / Hugo Mouquet /
要旨: Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. ...Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. Here, wide SARS-CoV-2 immunoprofiling in Wuhan COVID-19 convalescents combining serological, cellular, and monoclonal antibody explorations revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor-binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern, including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.
履歴
登録2021年12月3日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年5月18日Provider: repository / タイプ: Initial release
改定 1.12023年6月28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_ASTM / _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 1.22024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.32024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Spike protein S1
F: Spike protein S1
B: CV2.6264 light chain
C: CV2.6264 heavy chain
D: CV2.6264 light chain
E: CV2.6264 heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)144,1388
ポリマ－143,5346
非ポリマー6052
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)67.163, 191.319, 220.928
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 334 through 380 or resid 385 through 528))
21chain F
12(chain B and (resid 1 through 3 or resid 5 through 75 or resid 77 through 213))
22(chain D and (resid 1 through 3 or resid 5 through 75 or resid 77 through 213))
13(chain C and (resid 3 through 76 or resid 78...
23(chain E and (resid 3 through 76 or resid 78...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 334 through 380 or resid 385 through 528))A334 - 380
121(chain A and (resid 334 through 380 or resid 385 through 528))A385 - 528
211chain FF334 - 528
112(chain B and (resid 1 through 3 or resid 5 through 75 or resid 77 through 213))B1 - 3
122(chain B and (resid 1 through 3 or resid 5 through 75 or resid 77 through 213))B5 - 75
132(chain B and (resid 1 through 3 or resid 5 through 75 or resid 77 through 213))B77 - 213
212(chain D and (resid 1 through 3 or resid 5 through 75 or resid 77 through 213))D1 - 3
222(chain D and (resid 1 through 3 or resid 5 through 75 or resid 77 through 213))D5 - 75
232(chain D and (resid 1 through 3 or resid 5 through 75 or resid 77 through 213))D77 - 213
113(chain C and (resid 3 through 76 or resid 78...C3 - 76
123(chain C and (resid 3 through 76 or resid 78...C78 - 83
133(chain C and (resid 3 through 76 or resid 78...C85 - 13
143(chain C and (resid 3 through 76 or resid 78...C145 - 187
153(chain C and (resid 3 through 76 or resid 78...C189 - 225
213(chain E and (resid 3 through 76 or resid 78...E3 - 76
223(chain E and (resid 3 through 76 or resid 78...E78 - 83
233(chain E and (resid 3 through 76 or resid 78...E85 - 138
243(chain E and (resid 3 through 76 or resid 78...E145 - 187
253(chain E and (resid 3 through 76 or resid 78...E189 - 225

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質 Spike protein S1


分子量: 23068.695 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: P0DTC2
#2: 抗体 CV2.6264 light chain


分子量: 23282.717 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: Homo sapiens (ヒト)
#3: 抗体 CV2.6264 heavy chain


分子量: 25415.420 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: Homo sapiens (ヒト)
#4: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 383.349 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#5: 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
研究の焦点であるリガンドがあるかN
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: 4.94 Å3/Da / 溶媒含有率: 75.12 %
結晶化温度: 296 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1 M NaAc, 7% PEG 6000, 30% ethanol

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データ収集

回折平均測定温度: 80 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 2 / 波長: 0.9801 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2020年7月24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: 0.9801 Å / 相対比: 1
反射解像度: 2.8→49.21 Å / Num. obs: 71215 / % possible obs: 100 % / 冗長度: 27.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.445 / Rpim(I) all: 0.086 / Rrim(I) all: 0.453 / Net I/σ(I): 10.4 / Num. measured all: 1950768
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.86286.7712588544990.4241.2986.8940.7100
13.43-49.2121.30.0471578874210.010.04849.998.2

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
Aimless0.2.7データスケーリング
PDB_EXTRACT3.27データ抽出
XDS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: 6M0J, 5VAG

6m0j

5vag


解像度: 2.8→48.21 Å / SU ML: 0.41 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 32.44 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.254 3591 5.06 %
Rwork0.2286 67444 -
obs0.2299 71035 99.85 %
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: 246.51 Å2 / Biso mean: 91.6965 Å2 / Biso min: 30 Å2
精密化ステップサイクル: final / 解像度: 2.8→48.21 Å
タンパク質核酸リガンド溶媒全体
原子数9632 0 39 0 9671
Biso mean--119.93 --
残基数----1248
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1802X-RAY DIFFRACTION9.345TORSIONAL
12F1802X-RAY DIFFRACTION9.345TORSIONAL
21B1918X-RAY DIFFRACTION9.345TORSIONAL
22D1918X-RAY DIFFRACTION9.345TORSIONAL
31C1860X-RAY DIFFRACTION9.345TORSIONAL
32E1860X-RAY DIFFRACTION9.345TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.840.42661410.448225222663
2.84-2.880.45281210.415425592680
2.88-2.920.41081300.397725792709
2.92-2.960.40011170.392225742691
2.96-3.010.41191330.36825392672
3.01-3.060.34641400.361625972737
3.06-3.110.35511260.357825442670
3.11-3.170.31871230.337325872710
3.17-3.230.37041410.3125652706
3.23-3.290.33961590.299325092668
3.29-3.360.35971520.288326022754
3.36-3.440.30731350.277325412676
3.44-3.530.27791590.262725672726
3.53-3.620.30931430.257525632706
3.62-3.730.28161350.250826012736
3.73-3.850.26141480.240525512699
3.85-3.990.24461380.208226072745
3.99-4.150.25191400.202925632703
4.15-4.340.20021400.190926102750
4.34-4.560.19031300.169225992729
4.56-4.850.17471400.162226242764
4.85-5.220.18221330.158826302763
5.22-5.750.18541350.167926352770
5.75-6.580.21791350.190526632798
6.58-8.280.23651480.195826922840
8.28-48.210.20931490.193728212970
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)
13.8967-4.1575-0.31218.43440.07424.6459-0.2015-0.08390.8871-0.31550.4026-0.9512-0.244-0.0727-0.09350.5531-0.1041-0.15870.47680.09181.1131-44.969554.4062-66.3027
23.0509-3.1241-1.05453.49852.43397.01920.12091.26411.5753-0.7765-1.2286-1.3785-0.51980.27061.21361.20290.1545-0.03061.2370.23631.0817-52.520660.4083-76.678
33.0159-4.7952-1.2697.78132.25911.60150.12241.00450.514-1.3341-0.18020.5428-0.2698-0.12480.2521.0454-0.12-0.31990.98680.08031.0581-58.267553.8055-76.7156
41.0780.2333-0.23692.9634-3.01243.2972-0.14790.3569-1.6725-0.1960.07030.82750.8689-0.21230.00440.6834-0.1139-0.14530.60240.10031.5258-51.024740.6808-67.5224
51.9349-1.67540.90555.2564-2.36956.38850.1961-0.2975-0.7388-0.1603-0.04980.37290.0316-0.0416-0.12390.5599-0.04750.00150.50.07991.1613-46.449941.228-64.7203
61.7990.16790.23219.8055-6.19043.85170.4194-0.2195-0.54030.8051-0.4016-0.1172-0.27080.39270.05010.69530.0340.02530.6830.28521.4801-40.360127.8018-50.1675
77.6437-2.7884-2.89966.27533.45644.977-0.44330.0557-0.24770.2953-0.00710.27730.4396-0.2010.45570.4838-0.0725-0.040.57150.0760.9094-48.810748.3988-70.7912
85.4153-1.6266-1.76134.59290.80654.66520.8385-0.0840.29221.6765-0.9604-0.1047-0.1785-0.15770.14561.1649-0.27010.08930.81270.18881.3147-36.483338.5628-40.5251
97.12090.7533-5.65569.84540.50514.6541-0.5747-1.0128-0.74872.0910.7966-0.97751.2230.5634-0.34812.0201-0.0642-0.352.09020.46641.672-33.399734.8161-27.1072
104.41520.9745-5.54211.3557-1.09096.8897-1.44780.47390.82960.57741.1848-0.04471.6329-0.76080.40631.7254-0.1559-0.26351.68480.42161.3837-29.849142.2749-26.0016
112.6691-1.83452.72564.7995-1.28132.8824-0.0552-0.1338-0.19881.8601-0.1421-1.2046-1.06241.11580.2061.2709-0.2075-0.02030.98640.41291.6655-28.382247.0852-40.3793
122.7365-3.11362.77339.3229-6.53916.49120.0481-0.09870.97861.45960.0844-0.7886-2.11181.4268-0.03631.1996-0.3081-0.20280.8887-0.1251.214-26.20856.7461-41.8989
135.1881-3.00251.37215.5804-2.6556.15950.2814-0.8596-0.54421.6765-0.1058-1.2057-0.53880.2818-0.20351.3181-0.2649-0.25650.88580.27291.2397-27.844646.0894-38.2214
143.1801-1.62871.95622.3273-3.37166.77440.1408-0.2435-0.66421.1725-0.4909-0.0199-0.13070.25380.18550.7749-0.15130.01420.68290.12051.2419-30.58450.8766-51.0093
151.33251.25930.55449.3124-6.46417.64510.3409-0.2884-0.6538-0.18160.19731.19210.3857-0.4324-0.52890.4912-0.06320.00490.5937-0.0791.0596-31.414659.9938-63.1828
166.7712-0.9981-0.91294.83690.84824.40260.1469-0.807-1.01610.8209-0.3048-0.8957-0.81331.48480.30121.0878-0.1434-0.23020.83040.32441.643-23.192542.825-43.9964
171.65830.59231.05780.20270.42393.92191.6276-1.22111.62-1.3385-1.0143-0.89450.659-1.0506-0.74822.3863-0.02220.611.6743-0.02841.3121-45.566543.0789-23.0585
183.4111-2.8475-1.21115.81510.02692.34970.0005-0.2063-0.93720.194-0.0984-0.0039-0.01180.07360.11790.4566-0.0216-0.00180.64190.31151.2581-34.50272.2179-41.9977
195.4477-3.24410.82861.1254-0.2107-0.28590.0612-0.0577-0.4977-0.00250.14820.45640.0458-0.1414-0.21760.5902-0.00120.07770.61980.25041.3034-10.5772-3.4878-42.6891
208.101-0.1314-0.0963.4418-1.4572.00810.0183-0.30910.3349-0.1997-0.00970.57270.0957-0.1215-0.00070.55620.08820.02870.49010.19861.26532.629-8.416-41.0761
218.23681.97667.32866.09064.39018.07360.14431.0904-0.1975-0.53860.1956-0.8342-0.51220.2838-0.28950.54150.07480.14550.7650.34421.0086-19.84414.2594-63.9069
227.81780.69020.32174.65791.75913.81570.13890.01110.397-0.1962-0.518-0.3187-0.4409-0.20130.27820.53430.05320.08550.65540.36881.2593-30.770516.4259-57.1817
237.7848-0.78260.95485.2941-1.24496.06960.56671.25541.4917-0.1688-0.5128-0.9017-0.27070.09490.06210.58630.09630.11250.71070.39211.2142-26.446222.1557-60.8125
246.5413-4.04950.52072.5007-0.53722.00620.10180.18261.01630.5185-0.108-0.0769-0.52030.1181-0.10060.6375-0.0190.02740.67030.41481.2437-20.195116.0933-54.9897
252.9423-1.16160.00774.062-0.21052.97680.14331.0169-0.1725-0.0694-0.40790.3871-0.0394-0.43140.17050.56790.01230.010.76750.41051.2488-34.935511.4206-55.1132
265.4134-2.41260.36683.69671.36181.57560.10991.04870.4727-0.6050.08950.90510.0418-0.0399-0.12970.4468-0.0128-0.01540.66290.15441.04122.3536-2.9579-55.7799
273.7355-0.6131.07246.3581-0.12992.4150.23071.01990.1448-0.6448-0.30430.61990.20030.2727-0.00970.61250.1228-0.20130.8640.13881.2683-6.4555-7.5646-59.6179
283.77881.3383-1.52120.5122-0.21162.7899-0.3902-0.40320.0519-0.23850.70480.1519-0.40110.7829-0.21850.7515-0.04590.09540.6480.29831.7116-2.63655.0034-50.5818
292.2584-0.11140.13031.9932-2.4626.05310.61750.963-0.191-0.4423-0.0515-0.21060.52120.1585-0.42790.4399-0.0014-0.040.5994-0.05121.3169-0.1592-13.8225-54.6457
305.82811.3019-0.25037.37341.88023.81430.09451.7238-1.0566-1.25950.16572.2727-0.2235-0.5121-0.24830.68440.1195-0.04620.93020.17950.79551.5253-7.8783-63.9308
314.96152.5626-5.95396.2038-5.00259.0895-0.06350.8817-0.07510.13560.2273-0.0912-0.448-0.8359-0.21410.51480.0011-0.04780.5753-0.04570.7876-22.91875.5079-90.8189
326.15871.6775-3.98412.658-1.91376.95590.02870.17180.6628-0.13660.48060.8254-0.3323-0.8445-0.51220.41170.0336-0.04420.43-0.03260.9023-25.674374.3344-81.4732
330.74611.70040.16174.92221.83134.79040.4433-0.21170.807-0.322-0.022-0.0678-0.56450.2444-0.35880.4656-0.03980.03190.4166-0.05260.9171-17.395777.3249-80.3868
341.5841-0.3597-0.90070.49231.58293.48610.07060.23960.0118-0.0990.1415-0.12580.08080.2368-0.27020.51170.02540.0110.5464-0.07850.9342-14.004266.2779-96.737
351.7246-1.4999-1.50663.89164.20944.592-0.11430.35970.00120.20340.46050.3478-0.13110.0126-0.32620.58320.03920.00580.8096-0.13590.9549-13.245160.4334-112.2641
363.4045-0.40422.1282.13610.08354.2169-0.1540.76230.4353-0.2577-0.0188-0.44670.04540.2652-0.49030.5552-0.02850.05681.2253-0.2750.2168-18.427752.4608-113.5296
372.0204-0.04220.63397.38461.63543.21280.11390.3718-0.0915-0.472-0.60440.35640.0037-0.10680.46590.45120.01860.09060.7483-0.14960.5807-11.383757.5221-115.7019
385.5477-0.0395-0.84176.69483.4345.9961-0.273-0.293-0.9460.54170.8573-1.72930.64070.8619-0.4640.50650.0623-0.06310.47840.00850.6225-9.106550.2655-77.4185
392.9657-1.348-3.05552.7870.65024.47720.165-0.34060.41280.21390.18590.05810.4329-0.1868-0.24320.493-0.0356-0.04060.4538-0.13940.6293-17.607158.4822-71.826
409.14074.29154.76282.54961.7217.5924-0.9421-0.39810.04890.32390.24250.4743-0.0966-0.99070.29950.63620.0092-0.01570.5311-0.01790.6998-17.27750.412-70.453
413.233-2.9346-3.93644.73824.45078.01290.1529-0.2071-1.23670.04630.0871-0.260.6002-0.4648-0.18990.5537-0.0148-0.10370.37170.03770.7994-17.224852.4468-80.8289
425.9338-1.0652-3.24047.42373.02675.94390.4164-0.79451.80840.83250.0655-1.1351-0.2990.2908-0.53850.38250.00290.03950.42690.06390.4633-16.803165.3932-72.1023
433.48950.6354-1.50632.7727-0.97843.69540.11170.1550.00570.0034-0.1264-0.03770.04280.4940.04470.48690.0298-0.00480.755-0.29640.7410.905652.6448-104.7206
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 358 )A334 - 358
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 371 )A359 - 371
3X-RAY DIFFRACTION3chain 'A' and (resid 372 through 393 )A372 - 393
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 421 )A394 - 421
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 469 )A422 - 469
6X-RAY DIFFRACTION6chain 'A' and (resid 470 through 494 )A470 - 494
7X-RAY DIFFRACTION7chain 'A' and (resid 495 through 527 )A495 - 527
8X-RAY DIFFRACTION8chain 'F' and (resid 334 through 358 )F334 - 358
9X-RAY DIFFRACTION9chain 'F' and (resid 359 through 371 )F359 - 371
10X-RAY DIFFRACTION10chain 'F' and (resid 372 through 393 )F372 - 393
11X-RAY DIFFRACTION11chain 'F' and (resid 394 through 409 )F394 - 409
12X-RAY DIFFRACTION12chain 'F' and (resid 410 through 421 )F410 - 421
13X-RAY DIFFRACTION13chain 'F' and (resid 422 through 442 )F422 - 442
14X-RAY DIFFRACTION14chain 'F' and (resid 443 through 469 )F443 - 469
15X-RAY DIFFRACTION15chain 'F' and (resid 470 through 494 )F470 - 494
16X-RAY DIFFRACTION16chain 'F' and (resid 495 through 516 )F495 - 516
17X-RAY DIFFRACTION17chain 'F' and (resid 517 through 527 )F517 - 527
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 75 )B1 - 75
19X-RAY DIFFRACTION19chain 'B' and (resid 76 through 163 )B76 - 163
20X-RAY DIFFRACTION20chain 'B' and (resid 164 through 213 )B164 - 213
21X-RAY DIFFRACTION21chain 'C' and (resid 2 through 24 )C2 - 24
22X-RAY DIFFRACTION22chain 'C' and (resid 25 through 60 )C25 - 60
23X-RAY DIFFRACTION23chain 'C' and (resid 61 through 83 )C61 - 83
24X-RAY DIFFRACTION24chain 'C' and (resid 84 through 99 )C84 - 99
25X-RAY DIFFRACTION25chain 'C' and (resid 100 through 122 )C100 - 122
26X-RAY DIFFRACTION26chain 'C' and (resid 123 through 156 )C123 - 156
27X-RAY DIFFRACTION27chain 'C' and (resid 157 through 176 )C157 - 176
28X-RAY DIFFRACTION28chain 'C' and (resid 177 through 186 )C177 - 186
29X-RAY DIFFRACTION29chain 'C' and (resid 187 through 202 )C187 - 202
30X-RAY DIFFRACTION30chain 'C' and (resid 203 through 225 )C203 - 225
31X-RAY DIFFRACTION31chain 'D' and (resid 1 through 18 )D1 - 18
32X-RAY DIFFRACTION32chain 'D' and (resid 19 through 38 )D19 - 38
33X-RAY DIFFRACTION33chain 'D' and (resid 39 through 75 )D39 - 75
34X-RAY DIFFRACTION34chain 'D' and (resid 76 through 128 )D76 - 128
35X-RAY DIFFRACTION35chain 'D' and (resid 129 through 150 )D129 - 150
36X-RAY DIFFRACTION36chain 'D' and (resid 151 through 163 )D151 - 163
37X-RAY DIFFRACTION37chain 'D' and (resid 164 through 213 )D164 - 213
38X-RAY DIFFRACTION38chain 'E' and (resid 2 through 24 )E2 - 24
39X-RAY DIFFRACTION39chain 'E' and (resid 25 through 60 )E25 - 60
40X-RAY DIFFRACTION40chain 'E' and (resid 61 through 83 )E61 - 83
41X-RAY DIFFRACTION41chain 'E' and (resid 84 through 99 )E84 - 99
42X-RAY DIFFRACTION42chain 'E' and (resid 100 through 122 )E100 - 122
43X-RAY DIFFRACTION43chain 'E' and (resid 123 through 225 )E123 - 225

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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