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- PDB-2kad: Magic-Angle-Spinning Solid-State NMR Structure of Influenza A M2 ... -

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Basic information

Entry
Database: PDB / ID: 2kad
TitleMagic-Angle-Spinning Solid-State NMR Structure of Influenza A M2 Transmembrane Domain
ComponentsTransmembrane peptide of Matrix protein 2
KeywordsMEMBRANE PROTEIN / transmembrane helix / proton channel / lipid bilayers / influenza A / Alternative splicing / Hydrogen ion transport / Ion transport / Ionic channel / Lipoprotein / Palmitate / Phosphoprotein / Signal-anchor / Transport / Virion
Function / homology
Function and homology information


suppression by virus of host autophagy / proton transmembrane transporter activity / : / protein complex oligomerization / monoatomic ion channel activity / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / Matrix protein 2
Similarity search - Component
MethodSOLID-STATE NMR / torsion angle dynamics
Model details13C and 15N chemical shifts of DLPC-bound M2(22-46) measured by solid-state NMR.
AuthorsHong, M. / Cady, S.D. / Mishanina, T.V.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Structure of amantadine-bound M2 transmembrane peptide of influenza A in lipid bilayers from magic-angle-spinning solid-state NMR: the role of Ser31 in amantadine binding.
Authors: Cady, S.D. / Mishanina, T.V. / Hong, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Amantadine-induced conformational and dynamical changes of the influenza M2 transmembrane proton channel.
Authors: Cady, S.D. / Hong, M.
#2: Journal: J.Phys.Chem.B / Year: 2007
Title: Side-chain conformation of the M2 transmembrane peptide proton channel of influenza a virus from 19F solid-state NMR.
Authors: Luo, W. / Mani, R. / Hong, M.
#3: Journal: J.Am.Chem.Soc. / Year: 2006
Title: Determination of the oligomeric number and intermolecular distances of membrane protein assemblies by anisotropic 1H-driven spin diffusion NMR spectroscopy.
Authors: Luo, W. / Hong, M.
History
DepositionNov 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane peptide of Matrix protein 2
B: Transmembrane peptide of Matrix protein 2
C: Transmembrane peptide of Matrix protein 2
D: Transmembrane peptide of Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9045
Polymers10,7534
Non-polymers1511
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide
Transmembrane peptide of Matrix protein 2 / Proton channel protein M2


Mass: 2688.215 Da / Num. of mol.: 4
Fragment: Transmembrane peptide of influenza A M2 protein: UNP residues 22-46
Source method: obtained synthetically / Details: Solid phase peptide synthesis / References: UniProt: O70632
#2: Chemical ChemComp-308 / (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / Amantadine / Amantadine


Mass: 151.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N / Comment: medication, antagonist*YM

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
Details: 13C and 15N chemical shifts of DLPC-bound M2(22-46) measured by solid-state NMR.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 13C-13C DQF COSY
1212D 15N-13C HETCOR
1312D DARR
1412D INADEQUATE

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Sample preparation

DetailsContents: 4-6 mg/mL Selective U-13C, 15N labeled M2 Transmembrane Peptide, 15-25 mg/mL DLPC, 10 mM sodium phosphate, 0.1 mM sodium azide, 1 mM EDTA, 20-25 mL H2O, Solid-State NMR: Hydrated DLPC gel, ...Contents: 4-6 mg/mL Selective U-13C, 15N labeled M2 Transmembrane Peptide, 15-25 mg/mL DLPC, 10 mM sodium phosphate, 0.1 mM sodium azide, 1 mM EDTA, 20-25 mL H2O, Solid-State NMR: Hydrated DLPC gel, approx. 50% H2O by weight. DLPC:M2TMP:Amantadine 15:1:8
Solvent system: Solid-State NMR: Hydrated DLPC gel, approx. 50% H2O by weight. DLPC:M2TMP:Amantadine 15:1:8
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mg/mLM2 Transmembrane PeptideSelective U-13C, 15N labeled4-61
mg/mLDLPC15-251
10 mMsodium phosphate1
0.1 mMsodium azide1
1 mMEDTA1
mg/mLH2O20-251
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 243 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker DRXBrukerDRX4002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
Insight II2005Accelrys Software Inc.structure solution
Insight II2005Accelrys Software Inc.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: TALOS
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1 / Conformers submitted total number: 1

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