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- PDB-2rlf: Proton Channel M2 from Influenza A in complex with inhibitor rima... -

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Basic information

Entry
Database: PDB / ID: 2rlf
TitleProton Channel M2 from Influenza A in complex with inhibitor rimantadine
ComponentsMatrix protein 2
KeywordsPROTON TRANSPORT / m2 / proton channel / rimantadine
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
RIMANTADINE / Matrix protein 2 / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodSOLUTION NMR / simulated annealing
AuthorsChou, J.J. / Schnell, J.R.
CitationJournal: Nature / Year: 2008
Title: Structure and mechanism of the M2 proton channel of influenza A virus.
Authors: Schnell, J.R. / Chou, J.J.
History
DepositionJul 11, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7538
Polymers20,0364
Non-polymers7174
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 150overall energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 5008.885 Da / Num. of mol.: 4 / Fragment: residues 18-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Udorn/307/1972(H3N2))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: A/Udorn/307/1972 H3N2 / Gene: M / Production host: Escherichia coli (E. coli) / References: UniProt: P63231, UniProt: P0DOF8*PLUS
#2: Chemical
ChemComp-RIM / RIMANTADINE / 1-(1-ADAMANTYL)ETHANAMINE / Rimantadine


Mass: 179.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21N / Comment: antivirus*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1253D HNCA
1353D HN(CA)CB
1433D 1H-15N NOESY
1543D 1H-13C NOESY
1663D 1H-15N NOESY
1743D 1H-13C NOESY
182J(NCgamma-aliphatic)
192J(NCgamma-aromatic)
1104J(methyl-NH)
1114J(methyl-CO)
1124J(methyl-CA)
1131interleaved TROSY + HSQC
1141interleaved TROSY + HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75mM [U-100% 15N] protein, 40mM phosphate, 30mM glutamate, 40mM rimantadine, 250mM dihexanoylphosphocholine, 93% H2O/7% D2O93% H2O/7% D2O
20.75mM [U-100% 13C; U-100% 15N] protein, 40mM phosphate, 30mM glutamate, 40mM rimantadine, 250mM dihexanoylphosphocholine, 93% H2O/7% D2O93% H2O/7% D2O
30.75mM [U-100% 15N] protein, 40mM phosphate, 30mM glutamate, 40mM rimantadine, 250mM [U-100% 2H] dihexanoylphosphocholine, 93% H2O/7% D2O93% H2O/7% D2O
40.75mM [U-100% 13C; U-100% 15N] protein, 40mM phosphate, 30mM glutamate, 40mM rimantadine, 250mM [U-100% 2H] dihexanoylphosphocholine, 93% H2O/7% D2O93% H2O/7% D2O
50.75 mM [U-100% 13C; U-100% 15N; 80% 2H] entity, 40 mM phosphate, 30 mM glutamate, 40 mM rimantadine, 250 mM dihexanoylphosphocholine, 93% H2O/7% D2O93% H2O/7% D2O
60.75mM [U-15N; U-2H] protein, 40mM phosphate, 30mM glutamate, 40mM rimantadine, 250mM [U-100% 2H] dihexanoylphosphocholine, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMprotein[U-100% 15N]1
40 mMphosphate1
30 mMglutamate1
40 mMrimantadine1
250 mMdihexanoylphosphocholine1
0.75 mMentity[U-100% 13C; U-100% 15N]2
40 mMphosphate2
30 mMglutamate2
40 mMrimantadine2
250 mMdihexanoylphosphocholine2
0.75 mMentity[U-100% 15N]3
40 mMphosphate3
30 mMglutamate3
40 mMrimantadine3
250 mMdihexanoylphosphocholine[U-100% 2H]3
0.75 mMentity[U-100% 13C; U-100% 15N]4
40 mMphosphate4
30 mMglutamate4
40 mMrimantadine4
250 mMdihexanoylphosphocholine[U-100% 2H]4
0.75 mMentity[U-100% 13C; U-100% 15N; 80% 2H]5
40 mMphosphate5
30 mMglutamate5
40 mMrimantadine5
250 mMdihexanoylphosphocholine5
0.75 mMentity[U-15N; U-2H]6
40 mMphosphate6
30 mMglutamate6
40 mMrimantadine6
250 mMdihexanoylphosphocholine[U-100% 2H]6
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 303.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CARA1.8Keller and Wuthrichdata analysis
CARA1.8Keller and Wuthrichchemical shift assignment
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra, Clorerefinement
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra, Clorestructure solution
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: overall energy / Conformers calculated total number: 150 / Conformers submitted total number: 15

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