+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5viy | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | BG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195 | ||||||||||||
要素 |
| ||||||||||||
キーワード | VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 Env / broadly neutralizing antibodies / cryo-EM / single particle analysis / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
機能・相同性 | 機能・相同性情報 IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / complement activation, classical pathway / positive regulation of establishment of T cell polarity / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / blood microparticle / Potential therapeutics for SARS / 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 / virion membrane / structural molecule activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) Homo sapiens (ヒト) | ||||||||||||
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: 6.2 Å | ||||||||||||
データ登録者 | Wang, H. / Bjorkman, P.J. | ||||||||||||
資金援助 | 米国, 3件
| ||||||||||||
引用 | ジャーナル: Elife / 年: 2017 タイトル: Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies. 著者: Haoqing Wang / Harry B Gristick / Louise Scharf / Anthony P West / Rachel P Galimidi / Michael S Seaman / Natalia T Freund / Michel C Nussenzweig / Pamela J Bjorkman / 要旨: The HIV-1 envelope (Env) glycoprotein binds to host cell receptors to mediate membrane fusion. The prefusion Env trimer is stabilized by V1V2 loops that interact at the trimer apex. Broadly ...The HIV-1 envelope (Env) glycoprotein binds to host cell receptors to mediate membrane fusion. The prefusion Env trimer is stabilized by V1V2 loops that interact at the trimer apex. Broadly neutralizing antibodies (bNAbs) against V1V2 loops, exemplified by PG9, bind asymmetrically as a single Fab to the apex of the symmetric Env trimer using a protruding CDRH3 to penetrate the Env glycan shield. Here we characterized a distinct mode of V1V2 epitope recognition by the new bNAb BG1 in which two Fabs bind asymmetrically per Env trimer using a compact CDRH3. Comparisons between cryo-EM structures of Env trimer complexed with BG1 (6.2 Å resolution) and PG9 (11.5 Å resolution) revealed a new V1V2-targeting strategy by BG1. Analyses of the EM structures provided information relevant to vaccine design including molecular details for different modes of asymmetric recognition of Env trimer and a binding model for BG1 recognition of V1V2 involving glycan flexibility. | ||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5viy.cif.gz | 1.2 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb5viy.ent.gz | 995.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5viy.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 5viy_validation.pdf.gz | 3.5 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 5viy_full_validation.pdf.gz | 3.6 MB | 表示 | |
XML形式データ | 5viy_validation.xml.gz | 104.7 KB | 表示 | |
CIF形式データ | 5viy_validation.cif.gz | 164.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/vi/5viy ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5viy | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-Envelope glycoprotein ... , 2種, 6分子 ABCDEF
#1: タンパク質 | 分子量: 17146.482 Da / 分子数: 3 / 断片: UNP residues 509-661 / 由来タイプ: 組換発現 由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) 遺伝子: env / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6 #2: タンパク質 | 分子量: 54064.277 Da / 分子数: 3 / 断片: UNP residues 30-505 / 由来タイプ: 組換発現 由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) 遺伝子: env / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6 |
---|
-抗体 , 4種, 10分子 GIHJKMOLNP
#3: 抗体 | 分子量: 23527.102 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IGKC / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01834 #4: 抗体 | 分子量: 24931.861 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) / 参照: UniProt: S6B291 #5: 抗体 | 分子量: 24788.809 Da / 分子数: 3 / 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) / 参照: UniProt: S6B291 #6: 抗体 | 分子量: 23460.047 Da / 分子数: 3 / 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) / 参照: UniProt: Q8TCD0 |
---|
-糖 , 9種, 57分子
#7: 多糖 | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #8: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #9: 多糖 | #10: 多糖 | #11: 多糖 | #12: 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 #13: 多糖 | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | #14: 多糖 | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #15: 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 |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 | 単位: MEGADALTONS / 実験値: NO | ||||||||||||||||||||||||||||||
由来(天然) |
| ||||||||||||||||||||||||||||||
由来(組換発現) |
| ||||||||||||||||||||||||||||||
緩衝液 | pH: 8 | ||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE-PROPANE |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 80 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.11_2567: / 分類: 精密化 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: C1 (非対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 6.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 66000 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | ||||||||||||||||||||||||
精密化 | 最高解像度: 6.2 Å | ||||||||||||||||||||||||
拘束条件 |
|