+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3jab | ||||||
---|---|---|---|---|---|---|---|
タイトル | Domain organization and conformational plasticity of the G protein effector, PDE6 | ||||||
要素 |
| ||||||
キーワード | HYDROLASE/IMMUNE SYSTEM / phosphodiesterase / photoreceptor / HYDROLASE-IMMUNE SYSTEM complex | ||||||
機能・相同性 | 機能・相同性情報 cGMP effects / Smooth Muscle Contraction / RHOBTB1 GTPase cycle / cyclic-nucleotide phosphodiesterase activity / GMP catabolic process / cellular response to macrophage colony-stimulating factor stimulus / 3',5'-cyclic-GMP phosphodiesterase / cellular response to cGMP / Inactivation, recovery and regulation of the phototransduction cascade / negative regulation of cAMP-mediated signaling ...cGMP effects / Smooth Muscle Contraction / RHOBTB1 GTPase cycle / cyclic-nucleotide phosphodiesterase activity / GMP catabolic process / cellular response to macrophage colony-stimulating factor stimulus / 3',5'-cyclic-GMP phosphodiesterase / cellular response to cGMP / Inactivation, recovery and regulation of the phototransduction cascade / negative regulation of cAMP-mediated signaling / positive regulation of G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / positive regulation of vascular permeability / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier / regulation of mitochondrion organization / Ca2+ pathway / positive regulation of epidermal growth factor receptor signaling pathway / photoreceptor outer segment membrane / 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP-mediated signaling / cGMP catabolic process / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of cAMP-mediated signaling / visual perception / cAMP-mediated signaling / synaptic membrane / cellular response to mechanical stimulus / photoreceptor disc membrane / positive regulation of inflammatory response / presynaptic membrane / mitochondrial outer membrane / molecular adaptor activity / mitochondrial inner membrane / mitochondrial matrix / positive regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Bos taurus (ウシ) Mus musculus (ハツカネズミ) | ||||||
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: 11 Å | ||||||
データ登録者 | Zhang, Z. / He, F. / Constantine, R. / Baker, M.L. / Baehr, W. / Schmid, M.F. / Wensel, T.G. / Agosto, M.A. | ||||||
引用 | ジャーナル: J Biol Chem / 年: 2015 タイトル: Domain organization and conformational plasticity of the G protein effector, PDE6. 著者: Zhixian Zhang / Feng He / Ryan Constantine / Matthew L Baker / Wolfgang Baehr / Michael F Schmid / Theodore G Wensel / Melina A Agosto / 要旨: The cGMP phosphodiesterase of rod photoreceptor cells, PDE6, is the key effector enzyme in phototransduction. Two large catalytic subunits, PDE6α and -β, each contain one catalytic domain and two ...The cGMP phosphodiesterase of rod photoreceptor cells, PDE6, is the key effector enzyme in phototransduction. Two large catalytic subunits, PDE6α and -β, each contain one catalytic domain and two non-catalytic GAF domains, whereas two small inhibitory PDE6γ subunits allow tight regulation by the G protein transducin. The structure of holo-PDE6 in complex with the ROS-1 antibody Fab fragment was determined by cryo-electron microscopy. The ∼11 Å map revealed previously unseen features of PDE6, and each domain was readily fit with high resolution structures. A structure of PDE6 in complex with prenyl-binding protein (PrBP/δ) indicated the location of the PDE6 C-terminal prenylations. Reconstructions of complexes with Fab fragments bound to N or C termini of PDE6γ revealed that PDE6γ stretches from the catalytic domain at one end of the holoenzyme to the GAF-A domain at the other. Removal of PDE6γ caused dramatic structural rearrangements, which were reversed upon its restoration. | ||||||
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 | 3jab.cif.gz | 434.6 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb3jab.ent.gz | 362 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3jab.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 | 3jab_validation.pdf.gz | 742.5 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 3jab_full_validation.pdf.gz | 856.1 KB | 表示 | |
XML形式データ | 3jab_validation.xml.gz | 77.5 KB | 表示 | |
CIF形式データ | 3jab_validation.cif.gz | 109.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ja/3jab ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3jab | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-タンパク質 , 2種, 4分子 AMBN
#1: タンパク質 | 分子量: 20725.941 Da / 分子数: 2 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / Cell: photoreceptor / 細胞内の位置: disk membrane / Organelle: outer segment / 組織: retina / 参照: UniProt: A0A0M3KKT0*PLUS #2: タンパク質 | 分子量: 20671.434 Da / 分子数: 2 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / Cell: photoreceptor / 細胞内の位置: disk membrane / Organelle: outer segment / 組織: retina / 参照: UniProt: P14099*PLUS |
---|
-Phosphodiesterase ... , 2種, 4分子 CODP
#3: タンパク質 | 分子量: 38282.086 Da / 分子数: 2 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / Cell: photoreceptor / 細胞内の位置: disk membrane / Organelle: outer segment / 組織: retina / 参照: UniProt: Q28156*PLUS #4: タンパク質・ペプチド | 分子量: 2185.436 Da / 分子数: 2 / 断片: UNP residues 70-87 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / Cell: photoreceptor / 細胞内の位置: disk membrane / Organelle: outer segment / 組織: retina / 参照: UniProt: P04972 |
---|
-抗体 , 2種, 4分子 LRHQ
#5: 抗体 | 分子量: 23540.990 Da / 分子数: 2 / 断片: Fab / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 組織: Ascites fluid #6: 抗体 | 分子量: 23878.586 Da / 分子数: 2 / 断片: Fab / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 組織: Ascites fluid |
---|
-非ポリマー , 1種, 4分子
#7: 化合物 | ChemComp-IBM / |
---|
-詳細
配列の詳細 | THE IMAGED PDE6 WAS DERIVED FROM BOS TAURUS, BUT SOME MODELED SEQUENCES ARE FROM HOMO SAPIENS ...THE IMAGED PDE6 WAS DERIVED FROM BOS TAURUS, BUT SOME MODELED SEQUENCES ARE FROM HOMO SAPIENS (CHAINS B, C, N, O) OR GALLUS GALLUS (CHAINS A, M). THE PHOSPHODIE |
---|
-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 | 値: 0.32 MDa / 実験値: NO | ||||||||||||||||||||
緩衝液 | 名称: 20 mM sodium phosphate, 150 mM sodium chloride / pH: 7.5 / 詳細: 20 mM sodium phosphate, 150 mM sodium chloride | ||||||||||||||||||||
試料 | 濃度: 0.5 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 glow-discharged Quantifoil grids with 2.0 A holes | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / Temp: 93 K / 湿度: 95 % 詳細: Applied 3 uL sample per grid and blotted for 1 second before plunging into liquid ethane (FEI VITROBOT MARK III). 手法: Applied 3 uL sample per grid and blotted for 1 second before plunging. |
-電子顕微鏡撮影
顕微鏡 | モデル: JEOL 2010F / 日付: 2011年8月8日 / 詳細: Parallel beam illumination |
---|---|
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): 60000 X / Cs: 2 mm 非点収差: Objective lens astigmatism was corrected at 100,000 times magnification. |
試料ホルダ | 試料ホルダーモデル: GATAN LIQUID NITROGEN / 最高温度: 94 K |
撮影 | 電子線照射量: 15 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) |
電子光学装置 | エネルギーフィルター名称: FEI |
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 |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | 詳細: EMAN ctfit | ||||||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||||||
3次元再構成 | 手法: projection match / 解像度: 11 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 12373 / ピクセルサイズ(公称値): 1.81 Å / ピクセルサイズ(実測値): 1.81 Å 詳細: A total of 21,100 particles were picked from ice images and CTF corrected using Ctfit. After an initial 3D model was generated as described for PDE6, three noise-seeded models were generated ...詳細: A total of 21,100 particles were picked from ice images and CTF corrected using Ctfit. After an initial 3D model was generated as described for PDE6, three noise-seeded models were generated and used as initial models in the Multirefine procedure. A model with two Ros-1 Fab bound with a population of ~15,000 particles emerged and was subjected to further refinement using standard iterative projection matching, class averaging, and Fourier reconstruction. The final 3D maps with C2 symmetry were generated from 12,373 particles. クラス平均像の数: 20 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||
原子モデル構築 |
| ||||||||||||||||||||||||||||
原子モデル構築 |
| ||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST
|