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

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基本情報

登録情報
データベース: PDB / ID: 7qez
タイトルCrystal structure of the SARS-CoV-2 RBD in complex with the ultrapotent antibody CV2.1169 and CR3022
要素
  • CR3022 heavy chain
  • CR3022 light chain
  • CV2.1169 IgA heavy chain
  • CV2.1169 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 / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
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: 2.89 Å
データ登録者Fernandez, I. / 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

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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
E: CR3022 heavy chain
F: CR3022 light chain
H: CV2.1169 IgA heavy chain
L: CV2.1169 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,7967
ポリマ－119,4795
非ポリマー3172
水181
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
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-62 kcal/mol
Surface area37670 Å2
手法PISA
単位格子
Length a, b, c (Å)97.751, 97.751, 164.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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要素

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タンパク質 , 2種, 2分子 AE

#1: タンパク質 Spike protein S1


分子量: 23068.695 Da / 分子数: 1 / 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: タンパク質 CR3022 heavy chain


分子量: 24321.242 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)

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抗体 , 3種, 3分子 FHL

#3: 抗体 CR3022 light chain


分子量: 24376.963 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
#4: 抗体 CV2.1169 IgA heavy chain


分子量: 24165.072 Da / 分子数: 1 / 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)
#5: 抗体 CV2.1169 light chain


分子量: 23547.096 Da / 分子数: 1 / 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)

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糖 , 1種, 1分子

#6: 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

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非ポリマー , 2種, 2分子

#7: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 1 / 由来タイプ: 合成 / 式: SO4
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.29 Å3/Da / 溶媒含有率: 62.6 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 / 詳細: 15% PEG 8000, 0.5 M lithium sulfate

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データ収集

回折平均測定温度: 77 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: 0.98011 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2021年6月1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: 0.98011 Å / 相対比: 1
反射解像度: 2.88→48.88 Å / Num. obs: 34600 / % possible obs: 99.4 % / 冗長度: 14 % / CC1/2: 0.995 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.072 / Rrim(I) all: 0.271 / Net I/σ(I): 10.2 / Num. measured all: 485839
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
2.88-3.0213.93.5096105544020.2140.9713.6430.996
9.56-48.8813.10.062129349860.9960.0180.06436.899.2

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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
Aimless0.7.4データスケーリング
PDB_EXTRACT3.27データ抽出
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6M0J, 7K3Q, 6YLA

6m0j

7k3q

6yla


解像度: 2.89→48.88 Å / SU ML: 0.49 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 31.2 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.281 1785 5.19 %
Rwork0.2386 32579 -
obs0.2409 34364 99.77 %
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: 223.36 Å2 / Biso mean: 91.2269 Å2 / Biso min: 42.24 Å2
精密化ステップサイクル: final / 解像度: 2.89→48.88 Å
タンパク質核酸リガンド溶媒全体
原子数6613 0 19 1 6633
Biso mean--114.93 51.49 -
残基数----848
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-2.970.39391380.37042447258597
2.97-3.060.33461170.334425142631100
3.06-3.160.35261460.314825192665100
3.16-3.270.39951430.308424712614100
3.27-3.40.32241040.287125402644100
3.4-3.560.31491310.255224942625100
3.56-3.740.28131370.239725312668100
3.74-3.980.2681290.235225022631100
3.98-4.280.25411630.207924872650100
4.28-4.720.21861480.188924842632100
4.72-5.40.25211580.196525052663100
5.4-6.80.25751270.234525292656100
6.8-48.880.31431440.249925562700100
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)
16.8368-1.39531.8636.5312-4.10777.66840.9132-0.1398-0.25810.1634-0.5153-0.34021.11510.7349-0.35460.7310.0076-0.26270.6286-0.07040.6984152.962872.077831.0035
28.58263.43921.07512.56392.10582.9888-0.2893-0.76390.23230.97470.0569-1.21280.11871.01580.11820.95990.0257-0.1060.7021-0.09510.8017152.11483.363138.0969
35.32660.86125.2322.52171.79387.19460.19790.1943-0.1166-0.00990.1645-0.07890.181-0.1343-0.31910.5597-0.040.05270.51010.00090.4874138.495377.863418.046
48.46360.9948-3.35638.8965-3.23645.79690.3809-0.1307-0.18720.88730.32990.3383-0.40530.4256-0.7030.5167-0.0385-0.02880.4657-0.20340.5311148.573179.382928.0207
56.7343-3.952-2.13688.7724-1.44484.8901-0.06120.38040.8319-1.40130.7783-1.1314-0.34540.2393-0.49790.6373-0.24260.07620.6438-0.09890.6511151.5831113.120939.6721
66.4652-0.01180.55157.1708-2.66171.06850.192-0.5207-0.1306-0.13940.10340.00090.3794-0.0292-0.27610.5905-0.0851-0.0830.5773-0.10040.3745147.2406102.939340.3388
72.83521.5269-2.29452.54461.20415.33210.71530.6504-0.1413-0.1953-0.75450.1695-0.0238-0.9924-0.04910.8343-0.15770.04190.93520.01050.6436139.9851100.50333.1256
89.0528-5.06521.256.7759-1.14262.22881.03190.5880.3731-1.4225-0.3681-0.2473-0.84690.0673-0.72431.0609-0.03720.05130.5818-0.020.3484147.0337106.654431.7338
96.9318-2.53821.87752.7749-3.00083.32450.3502-0.0506-0.10520.94930.19010.876-0.6513-0.5953-0.49210.7380.01440.13810.6463-0.02260.3657143.1473113.001741.1739
107.41044.75482.73255.84325.23014.9989-0.6544-0.2678-0.3567-0.88760.2084-0.91660.3099-0.15590.33130.8381-0.0179-0.00210.60950.02460.5971148.374596.933144.4972
114.1103-1.6323-1.22733.74375.31027.58510.7256-0.19221.06550.9762-0.628-0.8847-1.0565-0.10340.06430.848-0.24170.00120.62560.04790.8729147.7122126.530544.5977
124.9405-1.71213.20112.24891.20549.0196-0.05080.1563-0.5346-0.41871.0667-1.1363-1.17950.6244-1.07290.7124-0.10420.14150.4466-0.15751.1204150.8526133.58365.0616
132.1045-3.52177.31583.2706-3.19225.33750.0798-0.0689-0.8496-0.4540.7688-0.80.16540.4941-0.70840.76650.00990.07210.8932-0.18070.7837156.5346126.500357.7112
146.45451.1197-1.94823.4741.6696.9386-0.0352-0.21250.9034-0.04680.721-0.10250.14770.2857-0.50270.5187-0.05590.04720.3802-0.1880.7177149.1247125.536561.1875
157.3079-1.42270.47716.02613.17212.3023-0.5831-1.18011.8210.73180.2573-0.41770.54510.29260.15330.60910.02390.02530.9803-0.15820.8415155.973130.30771.6585
169.44773.48318.27175.74910.96828.19040.28440.24131.0588-0.0876-0.1578-0.3209-0.58021.6354-0.57250.6653-0.0580.31790.6173-0.08851.1308158.8038133.998160.1243
176.42056.28945.369.66466.96625.3342-0.5034-0.98750.7233-0.6528-0.50711.4209-1.2282-1.39051.28920.3702-0.02480.0330.8613-0.11360.8827132.7432100.202358.1878
1810.03295.56944.86284.31064.00233.7933-0.6703-0.4559-0.65520.75690.39070.4504-0.6655-0.0820.09260.87550.02830.07050.6519-0.02870.636138.244895.707166.6199
194.86511.148-0.41470.6584-0.09991.99220.56450.0068-0.4147-0.94710.08410.13832.65580.1331-0.28151.4578-0.55870.03641.102-0.14920.741135.08783.880547.1657
207.31314.5132-0.71033.8791.89745.4385-0.7233-0.06250.5712-1.13390.76430.5261-0.01710.4311-0.00930.5303-0.0211-0.01490.5233-0.03320.4841146.529699.71255.1288
213.2136-0.45080.49263.58915.19118.5211-0.5073-0.3425-0.15761.63330.53380.27261.03340.4218-0.08751.0158-0.063-0.10520.60690.14140.6003143.356989.274558.6544
221.16520.0556-0.52644.96611.93011.797-0.0206-0.1850.1919-0.04710.1502-0.28170.11810.0632-0.16040.5043-0.03570.0540.59870.00410.5521142.5146111.917362.3577
233.8621-2.112-0.74035.3628-2.09572.6816-0.0711-0.08960.462-0.38830.2880.19740.5862-0.4246-0.21660.5162-0.0942-0.09640.7049-0.09040.4166136.7606127.985868.8335
244.752-3.4124-1.4193.01171.36552.96060.2163-0.39141.1328-0.49970.205-1.6238-0.09950.0722-0.39730.6186-0.03860.07860.6206-0.18910.5918142.9827127.041967.0569
253.4431-2.8331-1.28215.33131.53441.2461-0.175-0.22590.5790.32960.20030.04220.2235-0.129-0.04460.54390.0072-0.05070.9304-0.33690.6318135.7344133.552275.7975
263.31152.162-1.80581.5506-0.87562.31230.33820.31041.9777-1.02010.2320.8380.2927-0.87460.26241.45050.12090.25490.39420.02551.4243123.9749101.5772-3.6951
279.63130.8484-3.16047.87670.02295.26640.1406-0.13860.90270.1795-0.4120.33280.14070.02470.23280.52160.0751-0.03480.56290.03320.6892122.697592.1364-2.3778
288.0451-1.62870.42859.6361-3.31937.36540.57980.14550.23320.0888-0.35570.2748-0.060.2623-0.13090.48-0.04820.02160.54870.07420.7108130.678588.9253-3.8168
297.69945.2282-3.11469.9607-5.73819.36050.3138-0.0355-1.01340.9605-1.7063-1.1538-0.99441.36321.6210.68550.1364-0.20640.80150.07931.2092121.829390.1216-3.7832
308.91345.004-6.30233.8089-5.52447.87330.8045-0.82881.0204-0.8688-1.62870.3166-0.2781.83470.96190.86690.1155-0.01620.761-0.01491.057119.853996.2738-6.1584
312.9533-4.11991.30225.7648-1.77422.0011-0.25150.26170.86330.34090.5168-0.91851.73172.0277-0.06171.42370.1845-0.59230.96090.14061.5242117.150377.0048-17.4134
321.7323-0.88590.5728.5775-0.8970.17960.4788-0.20033.0391.0484-1.93682.4294-0.94340.46971.04380.6973-0.0461-0.03141.9969-0.31041.723396.051382.6179-16.6751
334.2246-2.72491.55193.88631.80174.3048-0.52140.86810.5036-1.12380.63580.8364-0.4162-0.21560.24820.5197-0.02420.07881.11780.71621.802112.425772.792-14.4907
349.69746.44173.5515.96493.4395.7528-0.1857-1.31251.0448-0.6854-0.02530.2227-0.5025-0.82020.15830.52860.06240.04680.81880.08681.2165110.663683.7794-5.6188
355.5166-1.64885.60097.5252-2.43645.94280.7057-1.43561.10580.2365-1.21832.74610.9905-3.29060.02670.8158-0.09840.00931.5368-0.36461.5251104.55579.2604-0.0198
369.4974-5.6435-1.78663.5932.04196.65212.5782.9926-1.0292-2.9232-3.56861.5088-1.4823-2.62131.2881.12740.5131-0.20191.4639-0.13221.18106.78772.6625-10.213
375.6031.5861-4.74420.8185-1.26534.0107-1.2103-1.87661.2453-0.2289-0.03920.4682-1.4068-0.64160.61841.1250.63390.16661.4926-0.33993.042396.632387.1275-7.7939
383.7188-2.0942-3.86882.55552.69284.2878-1.10692.54680.7679-0.28140.07840.88671.6475-0.52151.23060.9759-0.0309-0.17191.1655-0.00351.0188112.519782.787-10.9138
397.46062.0171-2.58583.17821.17742.26850.9558-5.2132-1.27550.2673-0.54981.39870.60791.2082-0.59110.43050.13650.03241.19310.08510.7849124.144176.6268-7.5765
405.5198-2.66234.58741.572-1.67674.6549-0.8441-0.0685-0.9896-0.3518-0.15820.4135-2.2124-1.61570.7121.12950.2456-0.30430.37880.05861.4306119.0681.7716-12.3076
415.0488-6.4132-5.82528.06567.34626.67830.7115-4.0708-1.8092.69770.7009-0.9817-1.90142.2027-0.67281.1047-0.1869-0.18111.03060.57231.6852100.992888.4397-17.5455
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 368 )A333 - 368
2X-RAY DIFFRACTION2chain 'A' and (resid 369 through 393 )A369 - 393
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 494 )A394 - 494
4X-RAY DIFFRACTION4chain 'A' and (resid 495 through 528 )A495 - 528
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 17 )E1 - 17
6X-RAY DIFFRACTION6chain 'E' and (resid 18 through 52 )E18 - 52
7X-RAY DIFFRACTION7chain 'E' and (resid 53 through 64 )E53 - 64
8X-RAY DIFFRACTION8chain 'E' and (resid 65 through 83 )E65 - 83
9X-RAY DIFFRACTION9chain 'E' and (resid 84 through 99 )E84 - 99
10X-RAY DIFFRACTION10chain 'E' and (resid 100 through 112 )E100 - 112
11X-RAY DIFFRACTION11chain 'E' and (resid 113 through 125 )E113 - 125
12X-RAY DIFFRACTION12chain 'E' and (resid 126 through 151 )E126 - 151
13X-RAY DIFFRACTION13chain 'E' and (resid 152 through 163 )E152 - 163
14X-RAY DIFFRACTION14chain 'E' and (resid 164 through 181 )E164 - 181
15X-RAY DIFFRACTION15chain 'E' and (resid 182 through 200 )E182 - 200
16X-RAY DIFFRACTION16chain 'E' and (resid 201 through 221 )E201 - 221
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 13 )F1 - 13
18X-RAY DIFFRACTION18chain 'F' and (resid 14 through 25 )F14 - 25
19X-RAY DIFFRACTION19chain 'F' and (resid 26 through 38 )F26 - 38
20X-RAY DIFFRACTION20chain 'F' and (resid 39 through 54 )F39 - 54
21X-RAY DIFFRACTION21chain 'F' and (resid 55 through 81 )F55 - 81
22X-RAY DIFFRACTION22chain 'F' and (resid 82 through 134 )F82 - 134
23X-RAY DIFFRACTION23chain 'F' and (resid 135 through 169 )F135 - 169
24X-RAY DIFFRACTION24chain 'F' and (resid 170 through 193 )F170 - 193
25X-RAY DIFFRACTION25chain 'F' and (resid 194 through 218 )F194 - 218
26X-RAY DIFFRACTION26chain 'H' and (resid 1 through 16 )H1 - 16
27X-RAY DIFFRACTION27chain 'H' and (resid 17 through 44 )H17 - 44
28X-RAY DIFFRACTION28chain 'H' and (resid 45 through 84 )H45 - 84
29X-RAY DIFFRACTION29chain 'H' and (resid 85 through 108 )H85 - 108
30X-RAY DIFFRACTION30chain 'H' and (resid 109 through 123 )H109 - 123
31X-RAY DIFFRACTION31chain 'L' and (resid 1 through 7 )L1 - 7
32X-RAY DIFFRACTION32chain 'L' and (resid 8 through 18 )L8 - 18
33X-RAY DIFFRACTION33chain 'L' and (resid 19 through 30 )L19 - 30
34X-RAY DIFFRACTION34chain 'L' and (resid 31 through 49 )L31 - 49
35X-RAY DIFFRACTION35chain 'L' and (resid 50 through 63 )L50 - 63
36X-RAY DIFFRACTION36chain 'L' and (resid 64 through 76 )L64 - 76
37X-RAY DIFFRACTION37chain 'L' and (resid 77 through 85 )L77 - 85
38X-RAY DIFFRACTION38chain 'L' and (resid 86 through 91 )L86 - 91
39X-RAY DIFFRACTION39chain 'L' and (resid 92 through 96 )L92 - 96
40X-RAY DIFFRACTION40chain 'L' and (resid 97 through 101 )L97 - 101
41X-RAY DIFFRACTION41chain 'L' and (resid 102 through 108 )L102 - 108

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る