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- PDB-4qkc: Influenza A M2 wild type TM domain at low pH in the lipidic cubic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qkc | ||||||
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Title | Influenza A M2 wild type TM domain at low pH in the lipidic cubic phase under cryo diffraction conditions | ||||||
![]() | influenza M2 monomer | ||||||
![]() | VIRAL PROTEIN / transmembrane alpha helix / pH-activated proton channel | ||||||
Function / homology | ![]() suppression by virus of host autophagy / proton transmembrane transporter activity / protein complex oligomerization / monoatomic ion channel activity / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomaston, J.L. / DeGrado, W.F. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.9 KB | Display | ![]() |
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PDB format | ![]() | 32.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 710.7 KB | Display | ![]() |
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Full document | ![]() | 712.7 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qk7C ![]() 4qklC ![]() 4qkmC ![]() 3c9jS ![]() 4qk6 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | 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.) ![]() ![]() |
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-Non-polymers , 5 types, 48 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.13 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2013 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953724 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: chain A of 3C9J Resolution: 1.1→13.064 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 12.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→13.064 Å
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Refine LS restraints |
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LS refinement shell |
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