- PDB-2kod: A high-resolution NMR structure of the dimeric C-terminal domain ... -
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基本情報
登録情報
データベース: PDB / ID: 2kod
タイトル
A high-resolution NMR structure of the dimeric C-terminal domain of HIV-1 CA
要素
HIV-1 CA C-terminal domain
キーワード
VIRAL PROTEIN (ウイルスタンパク質) / HIV-1 capsid / C-terminal domain (C末端)
機能・相同性
機能・相同性情報
integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / ウイルスのライフサイクル / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 逆転写酵素 / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / 加水分解酵素; エステル加水分解酵素 / DNAポリメラーゼ / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / 生体膜 / identical protein binding 類似検索 - 分子機能
ジャーナル: Cell / 年: 2009 タイトル: Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. 著者: In-Ja L Byeon / Xin Meng / Jinwon Jung / Gongpu Zhao / Ruifeng Yang / Jinwoo Ahn / Jiong Shi / Jason Concel / Christopher Aiken / Peijun Zhang / Angela M Gronenborn / 要旨: Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three- ...Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays of the capsid protein (CA) hexamer revealed three interfaces. Here, we present a cryoEM study of a tubular assembly of CA and a high-resolution NMR structure of the CA C-terminal domain (CTD) dimer. In the solution dimer structure, the monomers exhibit different relative orientations compared to previous X-ray structures. The solution structure fits well into the EM density map, suggesting that the dimer interface is retained in the assembled CA. We also identified a CTD-CTD interface at the local three-fold axis in the cryoEM map and confirmed its functional importance by mutagenesis. In the tubular assembly, CA intermolecular interfaces vary slightly, accommodating the asymmetry present in tubes. This provides the necessary plasticity to allow for controlled virus capsid dis/assembly.
1.4 mM [U-100% 13C; U-100% 15N] HIV-1 CA C-terminal domain, 1.4 mM NATURAL ABUNDANCE HIV-1 CA C-terminal domain, 25 mM sodium phosphate, 2 mM DTT, 0.02 % sodium azide, 93% H2O/7% D2O
93% H2O/7% D2O
2
2 mM [U-100% 13C; U-100% 15N] HIV-1 CA C-terminal domain, 25 mM sodium phosphate, 2 mM DTT, 0.02 % sodium azide, 93% H2O/7% D2O
93% H2O/7% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
1.4mM
HIV-1 CA C-terminal domain
[U-100% 13C; U-100% 15N]
1
1.4mM
NATURAL ABUNDANCE HIV-1 CA C-terminal domain
1
25mM
sodiumphosphate
1
2mM
DTT
1
0.02 %
sodiumazide
1
2mM
HIV-1 CA C-terminal domain
[U-100% 13C; U-100% 15N]
2
25mM
sodiumphosphate
2
2mM
DTT
2
0.02 %
sodiumazide
2
試料状態
イオン強度: 25 / pH: 6.5 / 圧: ambient / 温度: 298 K
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NMR測定
NMRスペクトロメーター
タイプ
製造業者
モデル
磁場強度 (MHz)
Spectrometer-ID
Bruker Avance
Bruker
Avance
900
1
Bruker Avance
Bruker
Avance
800
2
Bruker Avance
Bruker
Avance
700
3
Bruker Avance
Bruker
Avance
600
4
-
解析
NMR software
名称
バージョン
開発者
分類
TOPSPIN
2.1
Bruker
collection
NMRPipe
Delaglio, F. etal.
解析
SPARKY
Goddard, T.D. etal.
データ解析
SPARKY
Goddard, T.D. etal.
peakpicking
CYANA
Guntert, P. etal.
noepeakassignments
CANDID
Herrmann, T. etal.
noepeakassignments
X-PLOR_NIH
Schwieters, C.D. etal.
精密化
精密化
手法: simulated annealing / ソフトェア番号: 1 詳細: The residues 223-231 exhibit unfolded/disordered structure and thus no meaning should be given to the coordinates for these residues.
代表構造
選択基準: lowest energy
NMRアンサンブル
コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 500 / 登録したコンフォーマーの数: 30