+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 6myy | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map | ||||||||||||
![]() |
| ||||||||||||
![]() | VIRAL PROTEIN/IMMUNE SYSTEM / HIV envelope / germline VRC01 antibody / viral fusion protein / glycan shield / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
機能・相同性 | ![]() immunoglobulin complex / immunoglobulin mediated immune response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / antigen binding / clathrin-dependent endocytosis of virus by host cell / blood microparticle / viral protein processing ...immunoglobulin complex / immunoglobulin mediated immune response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / antigen binding / clathrin-dependent endocytosis of virus by host cell / blood microparticle / viral protein processing / immune response / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / plasma membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() ![]() | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | ||||||||||||
![]() | Borst, A.J. / Weidle, C.E. / Gray, M.D. / Frenz, B. / Snijder, J. / Joyce, M.G. / Georgiev, I.S. / Stewart-Jones, G.B.E. / Kwong, P.D. / McGuire, A.T. ...Borst, A.J. / Weidle, C.E. / Gray, M.D. / Frenz, B. / Snijder, J. / Joyce, M.G. / Georgiev, I.S. / Stewart-Jones, G.B.E. / Kwong, P.D. / McGuire, A.T. / DiMaio, F. / Stamatatos, L. / Pancera, M. / Veesler, D. | ||||||||||||
資金援助 | ![]()
| ||||||||||||
![]() | ![]() タイトル: Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. 著者: Andrew J Borst / Connor E Weidle / Matthew D Gray / Brandon Frenz / Joost Snijder / M Gordon Joyce / Ivelin S Georgiev / Guillaume Be Stewart-Jones / Peter D Kwong / Andrew T McGuire / Frank ...著者: Andrew J Borst / Connor E Weidle / Matthew D Gray / Brandon Frenz / Joost Snijder / M Gordon Joyce / Ivelin S Georgiev / Guillaume Be Stewart-Jones / Peter D Kwong / Andrew T McGuire / Frank DiMaio / Leonidas Stamatatos / Marie Pancera / David Veesler / ![]() 要旨: VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding ...VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1-3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design. | ||||||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | 分子: ![]() ![]() |
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 516.1 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 424.5 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
---|
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
|
---|---|
1 |
|
-
要素
-タンパク質 , 1種, 3分子 ABE
#1: タンパク質 | 分子量: 70243.812 Da / 分子数: 3 / 断片: 426c gp120, BG505 gp41 chimera / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 発現宿主: ![]() |
---|
-抗体 , 2種, 6分子 LCFHDG
#2: 抗体 | 分子量: 25008.906 Da / 分子数: 3 / 断片: germline VK3-11 with the mature CDR L3 of VRC01 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #3: 抗体 | 分子量: 25334.305 Da / 分子数: 3 断片: germline VH gene reverted sequences of VH1-2*02, which include CDRH1 and CDRH2 along with the mature CDRH3 of VRC01 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
---|
-糖 , 8種, 54分子 ![](data/chem/img/NAG.gif)
#4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #5: 多糖 | #6: 多糖 | #7: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #8: 多糖 | #9: 多糖 | #10: 多糖 | #11: 糖 | ChemComp-NAG / |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-
試料調製
構成要素 | 名称: 426c DS-SOSIP D3 / タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT |
---|---|
分子量 | 値: 0.45 MDa / 実験値: NO |
由来(天然) | 生物種: ![]() ![]() |
由来(組換発現) | 生物種: ![]() |
緩衝液 | pH: 7 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドのタイプ: C-flat-1.2/1.3 4C |
急速凍結 | 凍結剤: ETHANE |
-
電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 1 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 20 eV |
-
解析
EMソフトウェア |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
対称性 | 点対称性: C3 (3回回転対称) | |||||||||||||||||||||
3次元再構成 | 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 134443 / 詳細: Frequency-limited refinement / 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER |