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- PDB-2ljc: Structure of the influenza AM2-BM2 chimeric channel bound to rima... -

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Basic information

Entry
Database: PDB / ID: 2ljc
TitleStructure of the influenza AM2-BM2 chimeric channel bound to rimantadine
ComponentsM2 protein, BM2 protein chimera
KeywordsTransport protein/Inhibitor / M2 channel / rimantadine binding / drug complex / TRANSPORT PROTEIN / Transport protein-Inhibitor complex
Function / homology
Function and homology information


suppression by virus of host autophagy / proton transmembrane transporter activity / proton transmembrane transport / : / protein complex oligomerization / monoatomic ion channel activity / host cell plasma membrane / virion membrane / membrane / plasma membrane
Similarity search - Function
Influenza B matrix protein 2 / Influenza B matrix protein 2 (BM2) / 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
Influenza B virus
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsPielak, R.M. / Oxenoid, K. / Chou, J.J.
CitationJournal: Structure / Year: 2011
Title: Structural investigation of rimantadine inhibition of the AM2-BM2 chimera channel of influenza viruses.
Authors: Pielak, R.M. / Oxenoid, K. / Chou, J.J.
History
DepositionSep 10, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M2 protein, BM2 protein chimera
B: M2 protein, BM2 protein chimera
C: M2 protein, BM2 protein chimera
D: M2 protein, BM2 protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4015
Polymers15,2214
Non-polymers1791
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 75structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
M2 protein, BM2 protein chimera


Mass: 3805.371 Da / Num. of mol.: 4 / Mutation: C19S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus, Influenza B virus
Strain: H3N2, B/Taiwan/70061/2006Influenza A virus subtype H3N2
Gene: BM2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9YP62, UniProt: B4UQM4
#2: Chemical ChemComp-RIM / RIMANTADINE / 1-(1-ADAMANTYL)ETHANAMINE / Rimantadine


Mass: 179.302 Da / Num. of mol.: 1 / 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
1222D 1H-13C HSQC
1313D HNCA
1423D 1H-15N NOESY
1523D 1H-13C NOESY aliphatic
1623D 1H-13C NOESY aromatic
1733D 1H-15N NOESY
1843D 1H-15N NOESY
1952D 1H-13C HSQC (28m CT)
1101Interleaved HSQC-TROSY
1116Interleaved HSQC-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N; U-80% 2H] AM2-BM2 peptide, 300 mM DHPC, 40 mM sodium phosphate, 50 mM RIMANTADINE, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM [U-100% 13C; U-100% 15N] AM2-BM2 peptide, 300 mM [U-99% 2H] DHPC, 40 mM sodium phosphate, 50 mM RIMANTADINE, 95% H2O/5% D2O95% H2O/5% D2O
31.5 mM [U-100% 15N; U-99% 2H] AM2-BM2 peptide, 300 mM [U-99% 2H] DHPC, 40 mM sodium phosphate, 50 mM RIMANTADINE, 95% H2O/5% D2O95% H2O/5% D2O
40.9 mM [U-100% 15N; U-99% 2H] AM2-BM2 peptide, 0.9 mM [U-10% 13C] AM2-BM2 peptide, 300 mM [U-99% 2H] DHPC, 40 mM sodium phosphate, 50 mM RIMANTADINE, 95% H2O/5% D2O95% H2O/5% D2O
51.4 mM [U-15% 13C] AM2-BM2 peptide, 300 mM [U-99% 2H] DHPC, 40 mM sodium phosphate, 50 mM RIMANTADINE, 95% H2O/5% D2O95% H2O/5% D2O
60.5 mM [U-100% 13C; U-100% 15N; U-80% 2H] AM2-BM2 peptide, 300 mM DHPC, 40 mM sodium phosphate, 50 mM RIMANTADINE, 5.4 mg DNA nanotube, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMAM2-BM2 peptide-1[U-100% 13C; U-100% 15N; U-80% 2H]1
300 mMDHPC-21
40 mMsodium phosphate-31
50 mMRIMANTADINE-41
1.5 mMAM2-BM2 peptide-5[U-100% 13C; U-100% 15N]2
300 mMDHPC-6[U-99% 2H]2
40 mMsodium phosphate-72
50 mMRIMANTADINE-82
1.5 mMAM2-BM2 peptide-9[U-100% 15N; U-99% 2H]3
300 mMDHPC-10[U-99% 2H]3
40 mMsodium phosphate-113
50 mMRIMANTADINE-123
0.9 mMAM2-BM2 peptide-13[U-100% 15N; U-99% 2H]4
0.9 mMAM2-BM2 peptide-14[U-10% 13C]4
300 mMDHPC-15[U-99% 2H]4
40 mMsodium phosphate-164
50 mMRIMANTADINE-174
1.4 mMAM2-BM2 peptide-18[U-15% 13C]5
300 mMDHPC-19[U-99% 2H]5
40 mMsodium phosphate-205
50 mMRIMANTADINE-215
0.5 mMAM2-BM2 peptide-22[U-100% 13C; U-100% 15N; U-80% 2H]6
300 mMDHPC-236
40 mMsodium phosphate-246
50 mMRIMANTADINE-256
5.4 mg/mLDNA nanotube-266
Sample conditionsIonic strength: 100 / pH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 75 / Conformers submitted total number: 15

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