PDB-1nyj: The closed state structure of M2 protein H+ channel by solid stat...

基本情報

• 登録情報: データベース: PDB / ID: 1nyj
• タイトル: The closed state structure of M2 protein H+ channel by solid state NMR spectroscopy
• 要素: Matrix protein M2
• キーワード: VIRAL PROTEIN / influenza A virus / membrane protein structure / M2 proton channel / solid state NMR

機能・相同性

分子機能:

symbiont-mediated suppression of host autophagy / proton transmembrane transporter activity / protein complex oligomerization / monoatomic ion channel activity / symbiont genome entry into host cell via pore formation in plasma membrane / host cell plasma membrane / virion membrane / membrane

ドメイン・相同性:

Influenza virus matrix protein 2 / Influenza Matrix protein (M2)

構成要素:

Matrix protein 2

• 手法: 個体NMR / simulated annealing
• データ登録者: Nishimura, K. / Kim, S. / Zhang, L. / Cross, T.A.

引用

ジャーナル: Biochemistry / 年: 2002
タイトル: The closed state of a H+ channel helical bundle combining precise orientational and distance restraints from solid state NMR
著者: Nishimura, K. / Kim, S. / Zhang, L. / Cross, T.A.

#1: ジャーナル: Protein Sci. / 年: 2001
タイトル: Structure of the transmembrane region of the M2 protein H+ channel
著者: Wang, J. / Kim, S. / Kovacs, F. / Cross, T.A.

履歴

登録	2003年2月12日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2003年3月25日	Provider: repository / タイプ: Initial release
改定 1.1	2008年4月29日	Group: Version format compliance
改定 1.2	2011年7月13日	Group: Version format compliance
改定 1.3	2022年2月23日	Group: Database references / Derived calculations カテゴリ: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.4	2024年5月22日	Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

集合体

登録構造単位

A: Matrix protein M2

B: Matrix protein M2

C: Matrix protein M2

D: Matrix protein M2

概要:

• 10.9 kDa, 4 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	10,921	4
ポリマ－	10,921	4
非ポリマー	0	0
水	0	0

1

概要:

• 登録構造と同一
• 登録者が定義した集合体

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555	x,y,z	1

NMR アンサンブル

	データ	基準
コンフォーマー数 (登録 / 計算)	1 / 1	The tetrameric oligomer conformation of M2-TMP was constructed using the monomer structure refined by solid-state NMR orientational data. The monomer structure was the lowest energy conformer from 30 simulated annealing attempts.
代表モデル

要素

#1: タンパク質・ペプチド

A B C D
Matrix protein M2

詳細:

分子量: 2730.295 Da / 分子数: 4 / 断片: Transmembrane peptide (residue 22-46) / 由来タイプ: 合成
詳細: THE PEPTIDE WAS SYNTHESIZED USING SOLID PHASE PEPTIDE SYNTHESIS. THIS SEQUENCE OCCURS NATURALLY IN THE INFLUENZA A VIRUS (UDORN/72).
参照: UniProt: P35938

実験情報

実験

• 実験: 手法: 個体NMR
• NMR実験: タイプ: Solid state NMR PISEMA and REDOR
• NMR実験の詳細: Text: The heteronuclear distance was obtained by means of solid state NMR REDOR experiments. 13C-REDOR was performed on a DMX-300 with an XY8-pulse sequence for irradiation of 15N nuclei to compensate for errors in the flip angle, off resonance effect, and variation in the H1 field. The spinning speed was controlled at 4000 1 Hz and the experiments were performed at 38 C. REDOR and full echo spectra were recorded at various dipolar evolution times, Nctr, (where Nc and tr are the rotor cycle number and rotor period, respectively) from 2 to 16 ms to observe reasonable dipolar dephasing of the signals.

試料調製

• 詳細: 内容: To prepare an unoriented hydrated lipid bilayer sample, M2-TMP and dimyristoylphosphatidylcholine (DMPC) in a 1:16 molar ratio were co-solubilized in trifluoroethanol (TFE). After lyophilization, the white powder was hydrated by adding 50% (by total sample dry weight) pH 7.0, HPLC grade water followed by incubation for 2 days at 42 oC. The sample was then dispersed in 30 ml of 20 mM Citric/Na2HPO4 buffer at pH 7.0 and incubated at 45 oC for 2 hours before centrifuging at 20000 x g for 3 hours. After excess water was removed, the pellet was transferred to an eppendorf tube, tightly sealed to maintain the same hydration level, and then incubated at 45 oC for 2 days. Then, the sample was transferred to a glass insert for a Bruker 7 mm spinner and sealed with epoxy.; 溶媒系: To prepare an oriented bilayer sample, 20 mg of M2-TMP and 38.5 mg of DMPC (1:8 molar ratio) were co-dissolved in 1.5 ml of TFE. The sample was spread on 50 glass slides. After drying the organic solvent from the slides approximately 1.2 l of buffer (0.2 M phosphate and 0.1 M citric acid, pH 7.0) was added to each slide and then they were stacked into a glass tubing with a 6.0 x 6.0 mm internal dimension cross section.
• 試料状態: イオン強度: none / pH: 7 / 圧: ambient / 温度: 303.00 K
• 結晶化: 手法: other / 詳細: NMR

NMR測定

• 放射: プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M
• 放射波長: 相対比: 1

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
Home-built Chemagnetics	Home-built	Chemagnetics	400	1
Bruker DMX 300	Bruker	DMX 300	300	2

解析

• NMR software: 名称: TORC / バージョン: V5.4 / 開発者: Ketchem, Roux, Cross / 分類: 精密化
• 精密化: 手法: simulated annealing / ソフトェア番号: 1 ; 詳細: The symmetric, tetrameric bundle model of M2-TMP was constructed from the monomer structure (1MP6). The M2-TMP monomer coordinates were obtained by a geometrical search using a search algorithim to obtain a minimum of the global penalty function that incorporates all the orientational restraints and the CHARMM empirical function. The orientational restraints imposed on the structure during refinement are 15 15N chemical shifts and 15 15N-1H dipolar couplings from PISEMA experiments. The refinement was carried out in vacuo with the initial coordinates of an ideal a-helix structure (3.6 residues per turn) having a range of tilt and rotational orientations with respect to the bilayer spanning the values obtained from the PISA wheels. The resulting tetrameric bundle model was used to search the side chain orientations in accord with the experimentally measured distance between 15ND1 His37 and 13CG Trp41. Both chi 1 and chi 2 angles of the residues were searched extensively using 10 increments to discern whether the interaction was intramolecular or intermolecular and to find out which residues accounted for the observed spin interaction before characterizing the rotameric states of the sidechains. Note that while the His37 and Trp41 sidechain rotameric states are defined by the distance restraint, the rotameric states of other residues are taken from the backbone dependent sidechain rotamer library.
• NMRアンサンブル: コンフォーマー選択の基準: The tetrameric oligomer conformation of M2-TMP was constructed using the monomer structure refined by solid-state NMR orientational data. The monomer structure was the lowest energy conformer from 30 simulated annealing attempts.; 計算したコンフォーマーの数: 1 / 登録したコンフォーマーの数: 1