- PDB-2l0j: Solid State NMR structure of the M2 proton channel from Influenza... -
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基本情報
登録情報
データベース: PDB / ID: 2l0j
タイトル
Solid State NMR structure of the M2 proton channel from Influenza A Virus in hydrated lipid bilayer
要素
Matrix protein 2
キーワード
TRANSPORT PROTEIN / M2 Proton Channel / Lipid Bilayer / Solid State NMR / Influenza / Conductance Domain / Membrane domain / viral protein
機能・相同性
機能・相同性情報
: / suppression by virus of host autophagy / : / proton transmembrane transporter activity / protein complex oligomerization / monoatomic ion channel activity / membrane => GO:0016020 / host cell plasma membrane / virion membrane / identical protein binding / membrane 類似検索 - 分子機能
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1640 / Influenza virus matrix protein 2 / Influenza Matrix protein (M2) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special 類似検索 - ドメイン・相同性
手法: 個体NMR 詳細: Backbone structure of peptide fragment corresponding to residues (22-62) of M2 proton channel from Influenza A virus in DOPC:DOPE lipid bilayer.
NMR実験
Conditions-ID
Experiment-ID
Solution-ID
タイプ
1
1
1
PISEMA
1
2
1
PISEMA
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試料調製
詳細
内容: 5-15 mM [U-15N] entity-1, 5-15 mM [U-15N]-Leu entity-2, 5-15 mM [U-15N]-Ile entity-3, 5-15 mM [U-15N]-Val entity-4, 5-15 mM [U-15N]-Phe entity-5, 100% H2O 溶媒系: 100% H2O
試料
単位
構成要素
Isotopic labeling
Conc. range (mg/ml)
Solution-ID
mM
entity-1
[U-15N]
5-15
1
mM
entity-2
[U-15N]-Leu
5-15
1
mM
entity-3
[U-15N]-Ile
5-15
1
mM
entity-4
[U-15N]-Val
5-15
1
mM
entity-5
[U-15N]-Phe
5-15
1
試料状態
イオン強度: 10 / pH: 7.5 / 圧: ambient / 温度: 303 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
600
1
Bruker Avance
Bruker
AVANCE
900
2
Bruker DRX
Bruker
DRX
400
3
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解析
NMR software
名称
バージョン
開発者
分類
X-PLOR NIH
2.23
Schwieters, Kuszewski, TjandraandClore
精密化
X-PLOR NIH
2.23
Schwieters, Kuszewski, TjandraandClore
構造決定
XwinNMR
3.6
BrukerBiospin
collection
NAMD
2.7b
Phillips,Braun,Wang,Gumbart ,Tajkhorshid , Villa ,Chipot ,Skeel, Kale , Schulten
手法: simulated annealing, molecular dynamics, molecular dynamics ソフトェア番号: 1 詳細: Monomer structure was calculated using solid state NMR constraints by simulated annealing. A preliminary model for tetramer was assembled placing four copies of monomer consistent with NMR ...詳細: Monomer structure was calculated using solid state NMR constraints by simulated annealing. A preliminary model for tetramer was assembled placing four copies of monomer consistent with NMR derived tilt angles and rotation. The model was annealed again by incorporating distance and orientational restraints.The tetramer model was placed in explicit hydrated lipid bilayer and tetramer model was refined with solid state NMR orientational restraints using NAMD. Finally, The His37-Trp41 geometry was optimized using QM/MM calculations keeping backbone fixed. Note the His-His geometry is consistent with the experimental NMR observation.
代表構造
選択基準: fewest violations
NMRアンサンブル
コンフォーマー選択の基準: structures with the least restraint violations 計算したコンフォーマーの数: 8 / 登録したコンフォーマーの数: 8