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.
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 PHOSPHODIESTERASE 2A STRUCTURE WAS DETERMINED WITH FULL-LENGTH PROTEIN, BUT ONLY RESIDUES 387-571 WERE USED IN THE FITTED MODEL (CHAINS B, N).
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実験情報
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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
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試料調製
構成要素
ID
名称
タイプ
詳細
Parent-ID
1
Bovine rod PDE6 holoenzyme in complex with the Fab fragment from the ROS-1 monoclonal antibody
COMPLEX
TwoFabmoleculesbindtoPDE6
0
2
Rod cGMP-specific 3',5'-cyclic phosphodiesterase
1
3
monoclonal antibody Fab fragment of ROS-1
1
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.
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
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解析
EMソフトウェア
ID
名称
カテゴリ
1
UCSF Chimera
モデルフィッティング
2
EMAN
3次元再構成
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
ID
プロトコル
空間
詳細
1
RIGIDBODYFIT
REAL
REFINEMENT PROTOCOL--rigid body DETAILS--Domains were separately fitted by manual docking and Fit in Map in Chimera. The fitting of GFA(A,B) was confirmed using Folderhunter.