- PDB-2l0j: Solid State NMR structure of the M2 proton channel from Influenza... -
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Basic information
Entry
Database: PDB / ID: 2l0j
Title
Solid State NMR structure of the M2 proton channel from Influenza A Virus in hydrated lipid bilayer
Components
Matrix protein 2
Keywords
TRANSPORT PROTEIN / M2 Proton Channel / Lipid Bilayer / Solid State NMR / Influenza / Conductance Domain / Membrane domain / viral protein
Function / homology
Function and homology information
: / 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 Similarity search - Function
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 Similarity search - Domain/homology
Mass: 5021.926 Da / Num. of mol.: 4 / Fragment: UNP Residue 22-62 / Mutation: C50S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Udorn/307/1972 / Gene: M / Production host: Escherichia coli (E. coli) / References: UniProt: P63231, UniProt: P0DOF5*PLUS
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Experimental details
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Experiment
Experiment
Method: SOLID-STATE NMR Details: Backbone structure of peptide fragment corresponding to residues (22-62) of M2 proton channel from Influenza A virus in DOPC:DOPE lipid bilayer.
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
PISEMA
1
2
1
PISEMA
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Sample preparation
Details
Contents: 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 Solvent system: 100% H2O
Method: simulated annealing, molecular dynamics, molecular dynamics Software ordinal: 1 Details: 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 ...Details: 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.
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 8 / Conformers submitted total number: 8
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