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- PDB-2kih: S31N mutant of M2 proton channel -

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Basic information

Entry
Database: PDB / ID: 2kih
TitleS31N mutant of M2 proton channel
ComponentsMatrix protein 2
KeywordsTRANSPORT PROTEIN / S31N / M2 / proton channel / influenza / matrix protein 2 / Cell membrane / Disulfide bond / Hydrogen ion transport / Ion transport / Ionic channel / Membrane / Transmembrane / 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 / membrane => GO:0016020 / 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
Matrix protein 2 / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPielak, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Mechanism of drug inhibition and drug resistance of influenza A M2 channel.
Authors: Pielak, R.M. / Schnell, J.R. / Chou, J.J.
History
DepositionMay 5, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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
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
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: Matrix protein 2
B: Matrix protein 2
C: Matrix protein 2
D: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)20,1444
Polymers20,1444
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 5035.910 Da / Num. of mol.: 4 / Mutation: S31N,C19S,C50S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Udorn/307/1972 H3N2 / Gene: M / Plasmid: trpLE / Production host: Escherichia coli (E. coli) / References: UniProt: P63231, UniProt: P0DOF5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D 1H-15N NOESY
1513D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.8 mM [U-100% 15N] potassium phosphate, sodium azide, glutamate, rimantadine, 0.8 mM [U-100% 13C; U-100% 15N] potassium phosphate, sodium azide, glutamate, rimantadine, 0.8 mM [U-100% 13C; ...Contents: 0.8 mM [U-100% 15N] potassium phosphate, sodium azide, glutamate, rimantadine, 0.8 mM [U-100% 13C; U-100% 15N] potassium phosphate, sodium azide, glutamate, rimantadine, 0.8 mM [U-100% 13C; U-100% 15N; U-90% D2O] potassium phosphate, sodium azide, glutamate, rimantadine, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMpotassium phosphate, sodium azide, glutamate, rimantadine-1[U-100% 15N]1
0.8 mMpotassium phosphate, sodium azide, glutamate, rimantadine-2[U-100% 13C; U-100% 15N]1
0.8 mMpotassium phosphate, sodium azide, glutamate, rimantadine-3[U-100% 13C; U-100% 15N; U-90% D2O]1
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 303.1 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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