+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j5m | ||||||
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タイトル | Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs | ||||||
要素 |
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キーワード | VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 trimeric spike / gp140 / SOSIP / broadly neutralizing antibody / PGV04 / Env / envelope glycoprotein / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / identical protein 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: 5.8 Å | ||||||
データ登録者 | Lyumkis, D. / Julien, J.-P. / Wilson, I.A. / Ward, A.B. | ||||||
引用 | ジャーナル: Science / 年: 2013 タイトル: Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. 著者: Dmitry Lyumkis / Jean-Philippe Julien / Natalia de Val / Albert Cupo / Clinton S Potter / Per-Johan Klasse / Dennis R Burton / Rogier W Sanders / John P Moore / Bridget Carragher / Ian A Wilson / Andrew B Ward / 要旨: The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly ...The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly neutralizing antibodies (bnAbs), Env is a focus for rational vaccine design. We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution. The structure reveals the spatial arrangement of Env components, including the V1/V2, V3, HR1, and HR2 domains, as well as shielding glycans. The structure also provides insights into trimer assembly, gp120-gp41 interactions, and the CD4bs epitope cluster for bnAbs, which covers a more extensive area and defines a more complex site of vulnerability than previously described. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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 | 3j5m.cif.gz | 450.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j5m.ent.gz | 360 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j5m.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 | 3j5m_validation.pdf.gz | 419.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j5m_full_validation.pdf.gz | 452.4 KB | 表示 | |
XML形式データ | 3j5m_validation.xml.gz | 59.2 KB | 表示 | |
CIF形式データ | 3j5m_validation.cif.gz | 94.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j5/3j5m ftp://data.pdbj.org/pub/pdb/validation_reports/j5/3j5m | 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
#1: タンパク質 | 分子量: 53121.105 Da / 分子数: 3 / 断片: UNP residues 30-504 / 変異: T332N,A501C / 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 / 細胞株 (発現宿主): HEK / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6 #2: タンパク質 | 分子量: 5464.728 Da / 分子数: 3 / 断片: SEE REMARK 999 / 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 / 細胞株 (発現宿主): HEK / 発現宿主: Homo sapiens (ヒト) #3: 抗体 | 分子量: 23073.822 Da / 分子数: 3 / 断片: Fab / 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): HEK / 発現宿主: Homo sapiens (ヒト) #4: 抗体 | 分子量: 24644.771 Da / 分子数: 3 / 断片: Fab / 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): HEK / 発現宿主: Homo sapiens (ヒト) 配列の詳細 | THE SEQUENCE OF CHAINS B, F, AND J IS ...THE SEQUENCE OF CHAINS B, F, AND J IS AVGIGAVFLG | |
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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 |
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分子量 | 値: 0.6 MDa / 実験値: NO | ||||||||||||||||||||
緩衝液 | 名称: TBS / pH: 7.5 / 詳細: TBS | ||||||||||||||||||||
試料 | 濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||
試料支持 | 詳細: 400 mesh C-Flat CF-22-4C, plasma treated for 5 seconds | ||||||||||||||||||||
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE 詳細: 3 uL sample applied to grid, adsorbed for 30 seconds, blotted, and plunge-frozen in liquid ethane 手法: Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 ...手法: Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 seconds, followed by blotting with a small piece of filter paper and plunge-freezing into liquid ethane using a manual cryo-plunger in an ambient environment (4 C). |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 / 日付: 2013年2月21日 / 詳細: electron counting mode |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 29000 X / 倍率(補正後): 29000 X / 最大 デフォーカス(公称値): 5000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2 mm 非点収差: objective lens astigmatism was corrected by observing Thon rings with the Leginon software カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC |
撮影 | 電子線照射量: 32 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
画像スキャン | デジタル画像の数: 6355 |
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 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: Frealign | |||||||||||||||
対称性 | 点対称性: C3 (3回回転対称) | |||||||||||||||
3次元再構成 | 手法: projection matching using a resolution-limited scheme 解像度: 5.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 49572 / ピクセルサイズ(公称値): 1.21 Å / ピクセルサイズ(実測値): 1.21 Å 詳細: Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers (Single particle details: reconstructed using a resolution-limited refinement procedure ...詳細: Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers (Single particle details: reconstructed using a resolution-limited refinement procedure implemented in Xmipp and Frealign) (Single particle--Applied symmetry: C3) 対称性のタイプ: POINT | |||||||||||||||
原子モデル構築 | 空間: REAL | |||||||||||||||
原子モデル構築 |
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精密化ステップ | サイクル: LAST
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