+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8jtd | ||||||||||||
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タイトル | BJOX2000.664 trimer in complex with Fab fragment of broadly neutralizing HIV antibody PGT145 | ||||||||||||
要素 |
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キーワード | VIRAL PROTEIN / HIV / Envelope trimer / broadly neutralizing antibody / PGT145 / Cryo-EM | ||||||||||||
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: 4.9 Å | ||||||||||||
データ登録者 | Chatterjee, A. / Chen, C. / Lee, K. / Mangala Prasad, V. | ||||||||||||
資金援助 | 米国, インド, 3件
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引用 | ジャーナル: Npj Viruses / 年: 2023 タイトル: An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting. 著者: Edgar A Hodge / Ananya Chatterjee / Chengbo Chen / Gajendra S Naika / Mint Laohajaratsang / Vidya Mangala Prasad / Kelly K Lee / 要旨: The existence of broadly cross-reactive antibodies that can neutralize diverse HIV-1 isolates (bnAbs) has been appreciated for more than a decade. Many high-resolution structures of bnAbs, typically ...The existence of broadly cross-reactive antibodies that can neutralize diverse HIV-1 isolates (bnAbs) has been appreciated for more than a decade. Many high-resolution structures of bnAbs, typically with one or two well-characterized HIV-1 Env glycoprotein trimers, have been reported. However, an understanding of how such antibodies grapple with variability in their antigenic targets across diverse viral isolates has remained elusive. To achieve such an understanding requires first characterizing the extent of structural and antigenic variation embodied in Env, and then identifying how a bnAb overcomes that variation at a structural level. Here, using hydrogen/deuterium-exchange mass spectrometry (HDX-MS) and quantitative measurements of antibody binding kinetics, we show that variation in structural ordering in the V1/V2 apex of Env across a globally representative panel of HIV-1 isolates has a marked effect on antibody association rates and affinities. We also report cryo-EM reconstructions of the apex-targeting PGT145 bnAb bound to two divergent Env that exhibit different degrees of structural dynamics throughout the trimer structures. Parallel HDX-MS experiments demonstrate that PGT145 bnAb has an exquisitely focused footprint at the trimer apex where binding did not yield allosteric changes throughout the rest of the structure. These results demonstrate that structural dynamics are a cryptic determinant of antigenicity, and mature antibodies that have achieved breadth and potency in some cases are able to achieve their broad cross-reactivity by "threading the needle" and binding in a highly focused fashion, thus evading and overcoming the variable properties found in Env from divergent isolates. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8jtd.cif.gz | 429.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8jtd.ent.gz | 354.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8jtd.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 | 8jtd_validation.pdf.gz | 3.5 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8jtd_full_validation.pdf.gz | 3.5 MB | 表示 | |
XML形式データ | 8jtd_validation.xml.gz | 65.1 KB | 表示 | |
CIF形式データ | 8jtd_validation.cif.gz | 98 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jt/8jtd ftp://data.pdbj.org/pub/pdb/validation_reports/jt/8jtd | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
-タンパク質 , 2種, 6分子 ACDBEF
#1: タンパク質 | 分子量: 54064.277 Da / 分子数: 3 / 由来タイプ: 組換発現 詳細: The HIV trimer map of this study is of BJOX2000.664 but we have given a sequence of BG505.664 as the model of BG505.664 was used to rigid body fit in our map. Because of the low resolution of ...詳細: The HIV trimer map of this study is of BJOX2000.664 but we have given a sequence of BG505.664 as the model of BG505.664 was used to rigid body fit in our map. Because of the low resolution of the map, we have not built the model. 由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) 細胞株 (発現宿主): Expi293F / 発現宿主: Homo sapiens (ヒト) #2: タンパク質 | 分子量: 17146.482 Da / 分子数: 3 / 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) 発現宿主: Homo sapiens (ヒト) |
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-抗体 , 2種, 2分子 JN
#3: 抗体 | 分子量: 28793.164 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) |
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#4: 抗体 | 分子量: 23953.750 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) |
-糖 , 7種, 57分子
#5: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #6: 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 #7: 多糖 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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 | #9: 多糖 | #10: 多糖 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 | #11: 糖 | ChemComp-NAG / |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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: BJOX2000.664 trimer in complex with broadly neutralizing HIV antibody PGT145 タイプ: COMPLEX / Entity ID: #1-#4 / 由来: RECOMBINANT |
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分子量 | 実験値: NO |
由来(天然) | 生物種: Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: EMS Lacey Carbon |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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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 / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 750 nm |
撮影 | 電子線照射量: 162.24 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k 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 |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 667012 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL 詳細: Rigid body fitting followed by real space refinement to improve map occupancy | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 5V8L Accession code: 5V8L / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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