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- PDB-4qkl: Influenza A M2 wild type TM domain at high pH in the lipidic cubi... -

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Basic information

Entry
Database: PDB / ID: 4qkl
TitleInfluenza A M2 wild type TM domain at high pH in the lipidic cubic phase under room temperature diffraction conditions
Componentsinfluenza M2 monomer, TM domain (22-46)
KeywordsVIRAL PROTEIN / transmembrane alpha helix / pH-activated proton channel
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 / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
Matrix protein 2 / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.711 Å
AuthorsThomaston, J.L. / DeGrado, W.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.
Authors: Thomaston, J.L. / Alfonso-Prieto, M. / Woldeyes, R.A. / Fraser, J.S. / Klein, M.L. / Fiorin, G. / DeGrado, W.F.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 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: influenza M2 monomer, TM domain (22-46)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,9325
Polymers2,7541
Non-polymers1784
Water46826
1
A: influenza M2 monomer, TM domain (22-46)
hetero molecules

A: influenza M2 monomer, TM domain (22-46)
hetero molecules

A: influenza M2 monomer, TM domain (22-46)
hetero molecules

A: influenza M2 monomer, TM domain (22-46)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,72820
Polymers11,0174
Non-polymers71116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-x+1,-y+3,z1
crystal symmetry operation3_765-y+2,x+1,z1
crystal symmetry operation4_475y-1,-x+2,z1
Buried area6360 Å2
ΔGint-221 kcal/mol
Surface area6070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.600, 29.600, 68.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-101-

CL

21A-102-

CA

31A-219-

HOH

41A-222-

HOH

51A-224-

HOH

61A-225-

HOH

71A-226-

HOH

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Components

#1: Protein/peptide influenza M2 monomer, TM domain (22-46)


Mass: 2754.340 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is found in the influenza A virus (strain A/Udorn/307/1972 H3N2) and was manually synthesized using Fmoc chemistry. N- and C-terminal modifications are present.
Source: (synth.) Influenza A virus / References: UniProt: W8PGZ1, UniProt: P0DOF5*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: lcp sandwich plates / pH: 8
Details: 1.8 M calcium chloride, 0.9 M Tris HCl pH 8.0, 39.6% v/v PEG 400, 3% w/v xylitol additive, LCP sandwich plates, temperature 293K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2013
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.71→27.15 Å / Num. all: 3201 / Num. obs: 3128 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 2.4 % / Biso Wilson estimate: 18.65 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 3.6
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / Num. unique all: 317 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A of 3C9J

3c9j


Resolution: 1.711→20.93 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 323 10.37 %Phenix-generated
Rwork0.1658 ---
obs0.1691 3115 97.13 %-
all-3201 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.711→20.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms196 0 7 26 229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005267
X-RAY DIFFRACTIONf_angle_d0.606363
X-RAY DIFFRACTIONf_dihedral_angle_d10.95394
X-RAY DIFFRACTIONf_chiral_restr0.03352
X-RAY DIFFRACTIONf_plane_restr0.00442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7105-2.15470.20651610.17451424X-RAY DIFFRACTION99
2.1547-20.93190.19471620.16271368X-RAY DIFFRACTION95

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