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- PDB-2l0j: Solid State NMR structure of the M2 proton channel from Influenza... -

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Basic information

Entry
Database: PDB / ID: 2l0j
TitleSolid State NMR structure of the M2 proton channel from Influenza A Virus in hydrated lipid bilayer
ComponentsMatrix protein 2
KeywordsTRANSPORT 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 / membrane / identical protein binding
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
Matrix protein 2 / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodSOLID-STATE NMR / simulated annealing, molecular dynamics, molecular dynamics
AuthorsSharma, M. / Yi, M. / Dong, H. / Qin, H. / Peterson, E. / Busath, D.D. / Zhou, H.X. / Cross, T.A.
CitationJournal: Science / Year: 2010
Title: Insight into the mechanism of the influenza a proton channel from a structure in a lipid bilayer.
Authors: Sharma, M. / Yi, M. / Dong, H. / Qin, H. / Peterson, E. / Busath, D.D. / Zhou, H.X. / Cross, T.A.
History
DepositionJul 8, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)20,0884
Polymers20,0884
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 8structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide
Matrix protein 2


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

ExperimentMethod: 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-IDExperiment-IDSolution-IDType
111PISEMA
121PISEMA

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Sample preparation

DetailsContents: 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
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-15N]5-151
mMentity-2[U-15N]-Leu5-151
mMentity-3[U-15N]-Ile5-151
mMentity-4[U-15N]-Val5-151
mMentity-5[U-15N]-Phe5-151
Sample conditionsIonic strength: 10 / pH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance9002
Bruker DRXBrukerDRX4003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR_NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR_NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
xwinnmr3.6Bruker Biospincollection
NAMD2.7bPhillips,Braun,Wang,Gumbart ,Tajkhorshid , Villa ,Chipot ,Skeel, Kale , Schultenrefinement
PIPATHAsbury, Quine,Achuthan, Hu, Chapman, Bertram, Crosschemical shift assignment
RefinementMethod: 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 representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 8 / Conformers submitted total number: 8

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