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- PDB-6bmz: Influenza A M2 transmembrane domain bound to a spiroadamantane in... -

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Basic information

Entry
Database: PDB / ID: 6bmz
TitleInfluenza A M2 transmembrane domain bound to a spiroadamantane inhibitor
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / influenza M2 / proton channel / spiroadamantane
Function / homology
Function and homology information


symbiont-mediated suppression of host autophagy / proton transmembrane transporter activity / protein complex oligomerization / monoatomic ion channel activity / symbiont genome entry into host cell via pore formation in plasma membrane / channel activity / 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 / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.634 Å
AuthorsThomaston, J.L. / DeGrado, W.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM056423 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters.
Authors: Thomaston, J.L. / Polizzi, N.F. / Konstantinidi, A. / Wang, J. / Kolocouris, A. / DeGrado, W.F.
History
DepositionNov 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
I: Matrix protein 2
J: Matrix protein 2
K: Matrix protein 2
L: Matrix protein 2
M: Matrix protein 2
N: Matrix protein 2
O: Matrix protein 2
P: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,08924
Polymers44,06916
Non-polymers1,0198
Water1,20767
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)11,2726
Polymers11,0174
Non-polymers2552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area5550 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)11,2726
Polymers11,0174
Non-polymers2552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-37 kcal/mol
Surface area5570 Å2
MethodPISA
3
I: Matrix protein 2
J: Matrix protein 2
K: Matrix protein 2
L: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2726
Polymers11,0174
Non-polymers2552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-37 kcal/mol
Surface area5680 Å2
MethodPISA
4
M: Matrix protein 2
N: Matrix protein 2
O: Matrix protein 2
P: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2726
Polymers11,0174
Non-polymers2552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-35 kcal/mol
Surface area5660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.620, 72.590, 99.250
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


Mass: 2754.340 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q20MD5, UniProt: Q9Q0L9*PLUS
#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.: 4 / Source method: obtained synthetically / Formula: C15H25N
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 0.1 M HEPES pH 7, 30% v/v PEG 400, monoolein, spiroadamantane amine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.63→72.59 Å / Num. obs: 11007 / % possible obs: 99.3 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.164 / Net I/σ(I): 8.7
Reflection shellResolution: 2.63→2.76 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 3 / Num. unique obs: 1442 / CC1/2: 0.92 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LBW

3lbw


Resolution: 2.634→58.591 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 1094 9.99 %
Rwork0.2255 --
obs0.2307 10947 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.634→58.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 68 67 3115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023088
X-RAY DIFFRACTIONf_angle_d0.4374248
X-RAY DIFFRACTIONf_dihedral_angle_d10.3981052
X-RAY DIFFRACTIONf_chiral_restr0.04594
X-RAY DIFFRACTIONf_plane_restr0.002462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.634-2.75390.33791330.24851209X-RAY DIFFRACTION98
2.7539-2.8990.26531340.20121196X-RAY DIFFRACTION98
2.899-3.08070.28211340.19871218X-RAY DIFFRACTION99
3.0807-3.31850.29451350.20941220X-RAY DIFFRACTION98
3.3185-3.65240.29281350.20751216X-RAY DIFFRACTION99
3.6524-4.18080.23141360.20821233X-RAY DIFFRACTION99
4.1808-5.26690.2441390.2171242X-RAY DIFFRACTION99
5.2669-58.60580.31931480.28751319X-RAY DIFFRACTION98

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