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- PDB-4qkc: Influenza A M2 wild type TM domain at low pH in the lipidic cubic... -

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Basic information

Entry
Database: PDB / ID: 4qkc
TitleInfluenza A M2 wild type TM domain at low pH in the lipidic cubic phase under cryo diffraction conditions
Componentsinfluenza M2 monomer
KeywordsVIRAL PROTEIN / transmembrane alpha helix / pH-activated 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 / identical protein binding / membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Matrix protein 2 / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 5, 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: influenza M2 monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6457
Polymers2,7541
Non-polymers8916
Water75742
1
A: influenza M2 monomer
hetero molecules

A: influenza M2 monomer
hetero molecules

A: influenza M2 monomer
hetero molecules

A: influenza M2 monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,58028
Polymers11,0174
Non-polymers3,56324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area7180 Å2
ΔGint-240 kcal/mol
Surface area6510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.310, 29.310, 67.310
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-46-

LEU

21A-101-

CA

31A-102-

CL

41A-216-

HOH

51A-217-

HOH

61A-218-

HOH

71A-225-

HOH

81A-226-

HOH

91A-233-

HOH

101A-237-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide influenza M2 monomer


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

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Non-polymers , 5 types, 48 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 283 K / Method: lcp sandwich plates / pH: 5.5
Details: 1.8 M calcium chloride, 0.9 M MES pH 5.5, 39.6% v/v PEG 400, 5% v/v Jeffamine M-600 pH 7.0 additive, LCP sandwich plates, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.953724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2013
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 1.1→20.73 Å / Num. all: 11654 / Num. obs: 11596 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.7 % / Biso Wilson estimate: 9.15 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3 / % 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: 1.1→13.064 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 12.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1276 1157 10.1 %
Rwork0.1077 --
obs0.1097 11453 99.37 %
all-11654 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→13.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms196 0 57 42 295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.043421
X-RAY DIFFRACTIONf_angle_d1.054564
X-RAY DIFFRACTIONf_dihedral_angle_d17.463175
X-RAY DIFFRACTIONf_chiral_restr0.05277
X-RAY DIFFRACTIONf_plane_restr0.00858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1001-1.15010.18891440.1561273X-RAY DIFFRACTION99
1.1501-1.21070.12541450.11191279X-RAY DIFFRACTION99
1.2107-1.28650.11141450.09371299X-RAY DIFFRACTION100
1.2865-1.38570.12241440.09271295X-RAY DIFFRACTION100
1.3857-1.5250.12291420.0811283X-RAY DIFFRACTION100
1.525-1.74520.10391480.08651297X-RAY DIFFRACTION100
1.7452-2.19710.10821480.10151303X-RAY DIFFRACTION100
2.1971-13.06460.14431410.12411267X-RAY DIFFRACTION97

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