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- PDB-2n70: Two-fold symmetric structure of the 18-60 construct of S31N M2 fr... -

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Basic information

Entry
Database: PDB / ID: 2n70
TitleTwo-fold symmetric structure of the 18-60 construct of S31N M2 from Influenza A in lipid bilayers
ComponentsMatrix protein 2
KeywordsVIRAL PROTEIN / M2 / S31N / Influenza
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 / DGSA-distance geometry simulated annealing
AuthorsAndreas, L.B. / Reese, M. / Eddy, M.T. / Gelev, V. / Ni, Q. / Miller, E.A. / Emsley, L. / Pintacuda, G. / Chou, J.J. / Griffin, R.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Structure and Mechanism of the Influenza A M218-60 Dimer of Dimers.
Authors: Andreas, L.B. / Reese, M. / Eddy, M.T. / Gelev, V. / Ni, Q.Z. / Miller, E.A. / Emsley, L. / Pintacuda, G. / Chou, J.J. / Griffin, R.G.
History
DepositionSep 1, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Other
Revision 1.3Aug 9, 2017Group: Experimental preparation / Category: exptl / Item: _exptl.method
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-38 kcal/mol
Surface area15570 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 33structures 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: C19S, S31N, C50S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Udorn/307/1972 H3N2 / Gene: M / Plasmid: PET / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D ZF-TEDOR
1213D ZF-TEDOR-RFDR
1312D HN
1413D (H) CaNH
1512D PAR
1612D PDSD
1712D ZF-TEDOR
1812D RFDR
1913D 1H-1H RFDR
11014D HCHHCH
11112D C-H

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Sample preparation

Details
Solution-IDContentsSolvent system
140 mM sodium phosphate, 30 mM glutamic acid, 3 mM sodium azide, 50 % 1,2-diphytanoyl-sn-glycero-3-phosphocholine, 50 % U-13C,15N matrix protein 2, H2OH2O
240 mM sodium phosphate, 30 mM glutamic acid, 3 mM sodium azide, 50 % 1,2-diphytanoyl-sn-glycero-3-phosphocholine, 50 % U-13C,15N-[12C,14N-ILFY] matrix protein 2, H2OH2O
340 mM sodium phosphate, 30 mM glutamic acid, 3 mM sodium azide, 50 % 1,2-diphytanoyl-sn-glycero-3-phosphocholine, 50 % [1-13C]-Glucose matrix protein 2, H2OH2O
440 mM sodium phosphate, 30 mM glutamic acid, 3 mM sodium azide, 50 % 1,2-diphytanoyl-sn-glycero-3-phosphocholine, 50 % [1,6-13C2]-Glucose matrix protein 2, H2OH2O
540 mM sodium phosphate, 30 mM glutamic acid, 3 mM sodium azide, 50 % aliphatic chain [U-2H] 1,2-diphytanoyl-sn-glycero-3-phosphocholine, 50 % U-13C,15N,2H-[12C,13C2H21H 1-Ile, 12C,13Ca,13C',13C2H21H 2-Leu, 12C,13C2H21H 2-Val] matrix protein 2, H2OH2O
640 mM sodium phosphate, 30 mM glutamic acid, 3 mM sodium azide, 50 % aliphatic chain [U-2H] 1,2-diphytanoyl-sn-glycero-3-phosphocholine, 50 % U-13C,15N,2H-[13CH3 1-Ile] matrix protein 2, H2OH2O
740 mM sodium phosphate, 30 mM glutamic acid, 3 mM sodium azide, 50 % aliphatic chain [U-2H] 1,2-diphytanoyl-sn-glycero-3-phosphocholine, 50 % U-13C,15N,2H-[13C2H21H 2-Leu, 13C2H21H 2-Val] matrix protein 2, H2OH2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
40 mMsodium phosphate-11
30 mMglutamic acid-21
3 mMsodium azide-31
50 %1,2-diphytanoyl-sn-glycero-3-phosphocholine-41
50 %matrix protein 2-5U-13C,15N1
40 mMsodium phosphate-62
30 mMglutamic acid-72
3 mMsodium azide-82
50 %1,2-diphytanoyl-sn-glycero-3-phosphocholine-92
50 %matrix protein 2-10U-13C,15N-[12C,14N-ILFY]2
40 mMsodium phosphate-113
30 mMglutamic acid-123
3 mMsodium azide-133
50 %1,2-diphytanoyl-sn-glycero-3-phosphocholine-143
50 %matrix protein 2-15[1-13C]-Glucose3
40 mMsodium phosphate-164
30 mMglutamic acid-174
3 mMsodium azide-184
50 %1,2-diphytanoyl-sn-glycero-3-phosphocholine-194
50 %matrix protein 2-20[1,6-13C2]-Glucose4
40 mMsodium phosphate-215
30 mMglutamic acid-225
3 mMsodium azide-235
50 %1,2-diphytanoyl-sn-glycero-3-phosphocholine-24aliphatic chain [U-2H]5
50 %matrix protein 2-25U-13C,15N,2H-[12C,13C2H21H 1-Ile, 12C,13Ca,13C',13C2H21H 2-Leu, 12C,13C2H21H 2-Val]5
40 mMsodium phosphate-266
30 mMglutamic acid-276
3 mMsodium azide-286
50 %1,2-diphytanoyl-sn-glycero-3-phosphocholine-29aliphatic chain [U-2H]6
50 %matrix protein 2-30U-13C,15N,2H-[13CH3 1-Ile]6
40 mMsodium phosphate-317
30 mMglutamic acid-327
3 mMsodium azide-337
50 %1,2-diphytanoyl-sn-glycero-3-phosphocholine-34aliphatic chain [U-2H]7
50 %matrix protein 2-35U-13C,15N,2H-[13C2H21H 2-Leu, 13C2H21H 2-Val]7
Sample conditionspH: 7.8 / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE10003
FBML Cambridge InstrumentsFBMLCambridge Instruments7504

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Processing

NMR software
NameDeveloperClassification
TALOS+Cornilescu, Delaglio and Baxstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 33 / Conformers submitted total number: 20

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