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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-10738 | |||||||||
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タイトル | Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-8,13) | |||||||||
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機能・相同性 | ![]() host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / Membrane binding and targetting of GAG proteins / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / neuron differentiation / platelet activation / platelet aggregation / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / SARS-CoV-1 activates/modulates innate immune responses / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / unfolded protein binding / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / viral nucleocapsid / secretory granule lumen / DNA recombination / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / DNA-directed DNA polymerase / 加水分解酵素; エステル加水分解酵素 / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / positive regulation of protein phosphorylation / focal adhesion / lipid binding / host cell nucleus / Neutrophil degranulation / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / protein-containing complex / proteolysis / DNA binding / RNA binding / extracellular space / extracellular exosome / zinc ion binding / extracellular region 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.9 Å | |||||||||
![]() | Ni T / Gerard S / Zhao G / Ning J / Zhang P | |||||||||
資金援助 | ![]() ![]()
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![]() | ![]() タイトル: Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. 著者: Tao Ni / Samuel Gerard / Gongpu Zhao / Kyle Dent / Jiying Ning / Jing Zhou / Jiong Shi / Jordan Anderson-Daniels / Wen Li / Sooin Jang / Alan N Engelman / Christopher Aiken / Peijun Zhang / ![]() ![]() 要旨: The mature retrovirus capsid consists of a variably curved lattice of capsid protein (CA) hexamers and pentamers. High-resolution structures of the curved assembly, or in complex with host factors, ...The mature retrovirus capsid consists of a variably curved lattice of capsid protein (CA) hexamers and pentamers. High-resolution structures of the curved assembly, or in complex with host factors, have not been available. By devising cryo-EM methodologies for exceedingly flexible and pleomorphic assemblies, we have determined cryo-EM structures of apo-CA hexamers and in complex with cyclophilin A (CypA) at near-atomic resolutions. The CA hexamers are intrinsically curved, flexible and asymmetric, revealing the capsomere and not the previously touted dimer or trimer interfaces as the key contributor to capsid curvature. CypA recognizes specific geometries of the curved lattice, simultaneously interacting with three CA protomers from adjacent hexamers via two noncanonical interfaces, thus stabilizing the capsid. By determining multiple structures from various helical symmetries, we further revealed the essential plasticity of the CA molecule, which allows formation of continuously curved conical capsids and the mechanism of capsid pattern sensing by CypA. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 4.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 19.3 KB 19.3 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 5.2 KB | 表示 | ![]() |
画像 | ![]() | 79.7 KB | ||
マスクデータ | ![]() | 11.4 MB | ![]() | |
その他 | ![]() ![]() | 10.2 MB 10.2 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 6y9vMC ![]() 6skkC ![]() 6skmC ![]() 6sknC ![]() 6slqC ![]() 6sluC ![]() 6smuC ![]() 6y9wC ![]() 6y9xC ![]() 6y9yC ![]() 6y9zC ![]() 6yj5C ![]() 6zdjC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-マスク #1
ファイル | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_10738_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_10738_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : In vitro assembled HIV-1 capsid in tubular assembly
全体 | 名称: In vitro assembled HIV-1 capsid in tubular assembly |
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要素 |
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-超分子 #1: In vitro assembled HIV-1 capsid in tubular assembly
超分子 | 名称: In vitro assembled HIV-1 capsid in tubular assembly / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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-超分子 #2: HIV-1 capsid
超分子 | 名称: HIV-1 capsid / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
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由来(天然) | 生物種: ![]() ![]() |
組換発現 | 生物種: ![]() ![]() |
-超分子 #3: Cyclophilin A
超分子 | 名称: Cyclophilin A / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: ![]() |
組換発現 | 生物種: ![]() ![]() |
-分子 #1: Gag-Pol polyprotein
分子 | 名称: Gag-Pol polyprotein / タイプ: protein_or_peptide / ID: 1 / コピー数: 12 / 光学異性体: LEVO / EC番号: HIV-1 retropepsin |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 24.531094 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: PIVQNIQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRVHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT NNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...文字列: PIVQNIQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRVHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT NNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPA ATLEEMMTAC QG |
-分子 #2: Peptidyl-prolyl cis-trans isomerase A
分子 | 名称: Peptidyl-prolyl cis-trans isomerase A / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO / EC番号: peptidylprolyl isomerase |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 17.905307 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: VNPTVFFDIA VDGEPLGRVS FELFADKVPK TAENFRALST GEKGFGYKGS CFHRIIPGFM CQGGDFTRHN GTGGKSIYGE KFEDENFIL KHTGPGILSM ANAGPNTNGS QFFICTAKTE WLDGKHVVFG KVKEGMNIVE AMERFGSRNG KTSKKITIAD C GQLE |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | helical array |
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試料調製
濃度 | 2 mg/mL |
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緩衝液 | pH: 8 |
グリッド | モデル: Quantifoil R2/1 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY |
凍結 | 凍結剤: ETHANE |
詳細 | Purified capsid protein were assembled in the presence of Cyclophilin A. |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 実像数: 6500 / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |