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- PDB-6mjh: The S31N mutant of the influenza A M2 proton channel in two disti... -

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Basic information

Entry
Database: PDB / ID: 6mjh
TitleThe S31N mutant of the influenza A M2 proton channel in two distinct conformational states
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / viral protein / proton channel / S31N
Function / homology
Function and homology information


: / 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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsThomaston, J.L. / DeGrado, W.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: X-ray Crystal Structure of the Influenza A M2 Proton Channel S31N Mutant in Two Conformational States: An Open and Shut Case.
Authors: Thomaston, J.L. / Wu, Y. / Polizzi, N. / Liu, L. / Wang, J. / DeGrado, W.F.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: 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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)22,44713
Polymers22,2518
Non-polymers1965
Water1,38777
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)11,2467
Polymers11,1254
Non-polymers1203
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-52 kcal/mol
Surface area6680 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)11,2016
Polymers11,1254
Non-polymers762
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-26 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.290, 36.150, 76.450
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Matrix protein 2


Mass: 2781.365 Da / Num. of mol.: 8 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/pigeon/Jiangsu/K23/2013(H9N2))
References: UniProt: A0A0R5TVW3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5
Details: LCP: monoolein, M2TM S31N monomer, and 50 mM MNG-3-C8 detergent Precipitant solution: 0.2 M NaCl, 0.05 M calcium acetate pH 5.0, 29% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.06→37.15 Å / Num. obs: 11019 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / CC1/2: 0.997 / Rpim(I) all: 0.062 / Net I/σ(I): 8
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 780 / CC1/2: 0.666 / Rpim(I) all: 0.476 / % possible all: 82.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LBW, 5JOO

3lbw

5joo


Resolution: 2.06→35.236 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.99
RfactorNum. reflection% reflection
Rfree0.2485 1099 9.99 %
Rwork0.2168 --
obs0.2199 10997 90.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→35.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 5 80 1669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021600
X-RAY DIFFRACTIONf_angle_d0.5732192
X-RAY DIFFRACTIONf_dihedral_angle_d12.031944
X-RAY DIFFRACTIONf_chiral_restr0.04296
X-RAY DIFFRACTIONf_plane_restr0.004256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0601-2.15390.31931250.25671121X-RAY DIFFRACTION82
2.1539-2.26740.29731290.21891157X-RAY DIFFRACTION86
2.2674-2.40940.22661370.20791231X-RAY DIFFRACTION90
2.4094-2.59540.26581380.20031245X-RAY DIFFRACTION92
2.5954-2.85650.23981390.20781246X-RAY DIFFRACTION92
2.8565-3.26960.24691430.21251300X-RAY DIFFRACTION94
3.2696-4.11830.2281410.19431260X-RAY DIFFRACTION93
4.1183-35.24090.24581470.24141338X-RAY DIFFRACTION93

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