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- PDB-6nv1: Structure of drug-resistant V27A mutant of the influenza M2 proto... -

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Basic information

Entry
Database: PDB / ID: 6nv1
TitleStructure of drug-resistant V27A mutant of the influenza M2 proton channel bound to spiroadamantyl amine inhibitor
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / proton channel
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
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
Chem-E01 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsThomaston, J.L. / Liu, L. / DeGrado, W.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-GM056423 United States
CitationJournal: Biochemistry / Year: 2020
Title: X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance.
Authors: Thomaston, J.L. / Konstantinidi, A. / Liu, L. / Lambrinidis, G. / Tan, J. / Caffrey, M. / Wang, J. / Degrado, W.F. / Kolocouris, A.
History
DepositionFeb 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: Matrix protein 2
F: Matrix protein 2
G: Matrix protein 2
H: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,17220
Polymers21,8108
Non-polymers3,36212
Water54030
1
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)12,2309
Polymers10,9054
Non-polymers1,3245
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-46 kcal/mol
Surface area6340 Å2
MethodPISA
2
E: Matrix protein 2
F: Matrix protein 2
G: Matrix protein 2
H: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,94311
Polymers10,9054
Non-polymers2,0387
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-47 kcal/mol
Surface area6900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.806, 49.950, 75.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 2726.287 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: A4D7H3
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-E01 / (1r,1'S,3'S,5'S,7'S)-spiro[cyclohexane-1,2'-tricyclo[3.3.1.1~3,7~]decan]-4-amine


Mass: 219.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H25N
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 300 K / Method: lipidic cubic phase
Details: 0.045 M HEPES pH 7.5, 19.8% w/v PEG 4000, 0.01 M L-proline, monoolein, MNG-34, spiroadamantyl amine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.5→41.58 Å / Num. obs: 6840 / % possible obs: 99.25 % / Redundancy: 10.3 % / CC1/2: 1 / Rmerge(I) obs: 0.1262 / Net I/σ(I): 13.27
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.7294 / Mean I/σ(I) obs: 3.52 / Num. unique obs: 653 / CC1/2: 0.941 / % possible all: 98.93

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BKK

6bkk


Resolution: 2.5→41.579 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 676 9.95 %
Rwork0.22 --
obs0.2239 6792 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→41.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 234 30 1696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121686
X-RAY DIFFRACTIONf_angle_d1.4932244
X-RAY DIFFRACTIONf_dihedral_angle_d21.831632
X-RAY DIFFRACTIONf_chiral_restr0.919290
X-RAY DIFFRACTIONf_plane_restr0.005240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.69310.29951310.26671170X-RAY DIFFRACTION99
2.6931-2.9640.26971320.23421203X-RAY DIFFRACTION99
2.964-3.39280.25511330.21351213X-RAY DIFFRACTION99
3.3928-4.27390.27531400.18851232X-RAY DIFFRACTION99
4.2739-41.58440.23171400.22831298X-RAY DIFFRACTION99

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