PDB-1mp6: Structure of the transmembrane region of the M2 protein H+ channe...

Basic information

• Entry: Database: PDB / ID: 1mp6
• Title: Structure of the transmembrane region of the M2 protein H+ channel by solid state NMR spectroscopy
• Components: Matrix protein M2
• Keywords: MEMBRANE PROTEIN / INFLUENZA A VIRUS / MEMBRANE PROTEIN STRUCTURE / M2 PROTON CHANNEL / SOLID STATE NMR

Function / homology

Function:

: / 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

Domain/homology:

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

Component:

Matrix protein 2 / Matrix protein 2

• Method: SOLID-STATE NMR / simulated annealing
• Authors: Wang, J. / Kim, S. / Kovacs, F. / Cross, T.A.

Citation

Journal: Protein Sci. / Year: 2001
Title: Structure of the transmembrane region of the M2 protein H(+) channel.
Authors: Wang, J. / Kim, S. / Kovacs, F. / Cross, T.A.

#1: Journal: J.Mol.Biol. / Year: 2000
Title: Helix tilt of the M2 transmembrane peptide from influenza A virus: an intrinsic property.
Authors: Kovacs, F. / Denny, J.K. / Song, Z. / Quine, J.R. / Cross, T.A.

History

Deposition	Sep 11, 2002	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 25, 2002	Provider: repository / Type: Initial release
Revision 1.1	Apr 28, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 23, 2022	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Assembly

Deposited unit

A: Matrix protein M2

Summary:

• 2.73 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	2,730	1
Polymers	2,730	1
Non-polymers	0	0
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	1 / 30	The lowest energy conformer with backbone and C beta atoms is deposited, preferred rotameric states of side chains were used during the backbone structure refinement but the side chain atoms were not included in the pdb file.
Representative	Model #1	lowest energy

Components

#1: Protein/peptide

A Matrix protein M2 / M2 protein

Details:

Mass: 2730.295 Da / Num. of mol.: 1 / Fragment: transmembrane peptide (residues 22-46) / Source method: obtained synthetically
Details: This sequence occurs naturally in the Influenza A virus (Udorn/72 strain). The M2 transmembrane peptide was synthesized using solid phase peptide synthesis.
References: UniProt: P03490, UniProt: P0DOF5*PLUS

Experimental details

Experiment

• Experiment: Method: SOLID-STATE NMR
• NMR experiment: Type: SOLID STATE NMR PISEMA
• NMR details: Text: 15N CHEMICAL SHIFT, 1H-15N DIPOLAR COUPLING FREQUENCIES WERE MEASURED FROM SOLID STATE NMR PISEMA EXPERIMENT

Sample preparation

• Details: Contents: Oriented samples of the peptide in hydrated lipid bilayers were prepared by first co-dissolving M2-TMP and dimyristoylphosphatidylcholine (DMPC) in trifluoroethanol (TFE). The solution was then spread onto approximately 60 glass plates. After vacuum drying to remove TFE, 2 microliters of sterile-filtered water was added to each plate, and the plates were then stacked into a glass tube and placed in a chamber containing a saturated solution of K2SO4 for hydration.; Solvent system: Oriented bilayers formed after equilibrating the sample in this chamber at 42C overnight. This sample container was then sealed with a microscope cover glass and epoxy to maintain sample hydration during the experiments.
• Sample conditions: Ionic strength: none / pH: 7.0 / Pressure: ambient / Temperature: 303.00 K
• Crystal grow: Method: other / Details: NMR

NMR measurement

• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
• Radiation wavelength: Relative weight: 1
• NMR spectrometer: Type: Home-built Chemagnetics / Manufacturer: Home-built / Model: Chemagnetics / Field strength: 400 MHz

Processing

• NMR software: Name: TORC / Version: v5.4 / Developer: KETCHEM,ROUX,CROSS / Classification: refinement
• Refinement: Method: simulated annealing / Software ordinal: 1 ; Details: The refined M2-TMP monomer structure was obtained by a geometrical search using a search algorithm 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 observed chemical shifts are compared to calculated values from the molecular coordinates and the known tensor element magnitudes and assumed tensor orientations. 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.
• NMR representative: Selection criteria: lowest energy
• NMR ensemble: Conformer selection criteria: The lowest energy conformer with backbone and C beta atoms is deposited, preferred rotameric states of side chains were used during the backbone structure refinement but the side chain atoms were not included in the pdb file.; Conformers calculated total number: 30 / Conformers submitted total number: 1