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

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Basic information

Entry
Database: PDB / ID: 6oug
TitleStructure of drug-resistant V27A mutant of the influenza M2 proton channel bound to spiroadamantyl amine inhibitor, TM + cytosolic helix construct
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / viral protein / proton channel
Function / homology
Function and homology information


suppression by virus of host autophagy / protein complex oligomerization / proton transmembrane transporter activity / monoatomic ion channel activity / symbiont genome entry into host cell via pore formation in plasma membrane / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
Chem-E01 / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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)R35-GM122603 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
DepositionMay 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

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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)38,67610
Polymers38,2378
Non-polymers4392
Water1267
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)19,3385
Polymers19,1194
Non-polymers2191
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-38 kcal/mol
Surface area8140 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)19,3385
Polymers19,1194
Non-polymers2191
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-39 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.420, 49.380, 122.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 4779.651 Da / Num. of mol.: 8 / Mutation: V27A, C50S / Source method: obtained synthetically
Source: (synth.) Influenza A virus (strain A/Memphis/1/1971 H3N2)
References: UniProt: Q3YPZ4
#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 0.04M Sodium chloride, 0.04M Tris pH 8.0, 27% v/v PEG 350 MME, spiroadamantyl amine inhibitor

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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: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3→122.4 Å / Num. obs: 6417 / % possible obs: 99.8 % / Redundancy: 12.5 % / CC1/2: 0.997 / Net I/σ(I): 5.79
Reflection shellResolution: 3→3.118 Å / Mean I/σ(I) obs: 1.24 / Num. unique obs: 992 / CC1/2: 0.465 / % possible all: 99.5

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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: 6BMZ

6bmz


Resolution: 3.01→122.38 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 3.55 / Phase error: 36.51
RfactorNum. reflection% reflection
Rfree0.3006 268 5.08 %
Rwork0.273 --
obs0.2846 5431 85.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.01→122.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 32 7 2037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062075
X-RAY DIFFRACTIONf_angle_d0.8312842
X-RAY DIFFRACTIONf_dihedral_angle_d13.255661
X-RAY DIFFRACTIONf_chiral_restr0.807372
X-RAY DIFFRACTIONf_plane_restr0.004328
LS refinement shellResolution: 3.01→3.118 Å
RfactorNum. reflection% reflection
Rfree0.4859 123 -
Rwork0.2744 2115 -
obs--69 %

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