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- PDB-6cpv: MicroED structure of NaK ion channel reveals a process of Na+ par... -

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Basic information

Entry
Database: PDB / ID: 6cpv
TitleMicroED structure of NaK ion channel reveals a process of Na+ partition into the selectivity filter
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / ion channel / NaK
Function / homologyIon channel / Potassium channel domain / integral component of membrane / Transporter
Function and homology information
Specimen sourceBacillus cereus (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / 2.5002 Å resolution
AuthorsLiu, S. / Gonen, T.
CitationJournal: Commun Biol / Year: 2018
Title: MicroED structure of the NaK ion channel reveals a Na partition process into the selectivity filter.
Authors: Shian Liu / Tamir Gonen
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 14, 2018 / Release: Sep 12, 2018

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Assembly

Deposited unit
A: Potassium channel protein
B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,80715
Polyers21,4132
Non-polymers39413
Water724
1
A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,03540
Polyers42,8264
Non-polymers1,20836
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area (Å2)9320
ΔGint (kcal/M)-182
Surface area (Å2)17310
MethodPISA
2
B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,19420
Polyers42,8264
Non-polymers36816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area (Å2)7910
ΔGint (kcal/M)-119
Surface area (Å2)19700
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)68.072, 68.072, 89.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI 4

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Components

#1: Protein/peptide Potassium channel protein / / Transporter / Voltage-gated potassium channel


Mass: 10706.538 Da / Num. of mol.: 2 / Fragment: UNP residues 19-110 / Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: A9485_19160, B4155_3291, BACERE00184_02078, CN419_22740, CN950_06075, CN980_22870, COI98_17615, COK18_26145, CON37_12595
Production host: Escherichia coli (E. coli) / References: UniProt: A0A164U772
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Formula: Na / Sodium
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Formula: C6H14O2 / 2-Methyl-2,4-pentanediol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / Reconstruction method: electron crystallography

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Sample preparation

ComponentName: NaK / Type: COMPLEX / Entity ID: 1,2 / Source: RECOMBINANT
Source (natural)Organism: Bacillus cereus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 0.1 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
EM diffractionCamera length: 1750 mm
EM diffraction shellFourier space coverage: 0.76 / High resolution: 2.5002 Å / Low resolution: 3.1486 Å / Multiplicity: 4.1 / Number of structure factors: 2685 / Phase residual: 22.68 deg.
EM diffraction statsFourier space coverage: 81.7 / High resolution: 2.5002 Å / Number of intensities measured: 27479 / Number of structure factors: 5643 / Overall phase error: 20.27 deg. / Overall phase residual: 20.27 deg. / Phase error rejection criteria: 0 / R merge: 0.206 / R sym: 0.206

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Aimless0.5.32data scaling
iMOSFLM7.1.0data reduction
PHASERphasing
EM 3D crystal entityAngle alpha: 90 deg. / Angle beta: 90 deg. / Angle gamma: 90 deg. / Length a: 68.0716 Å / Length b: 68.0716 Å / Length c: 89.3 Å / Space group name: I4 / Space group num: 79
CTF correctionType: NONE
3D reconstructionResolution: 2.5002 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingOverall b value: 41
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E89
Overall SU ML: 0.37 / Cross valid method: THROUGHOUT / Sigma F: 1.41 / Overall phase error: 20.26
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.2632 / R factor R work: 0.2183 / R factor obs: 0.2205 / Highest resolution: 2.5 Å / Lowest resolution: 21.992 Å / Number reflection R free: 283 / Number reflection obs: 5793 / Percent reflection R free: 4.89 / Percent reflection obs: 81.68
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0021513
ELECTRON CRYSTALLOGRAPHYf_angle_d0.4122066
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d9.508859
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.036258
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.002249
Refine LS shell

Refine ID: ELECTRON CRYSTALLOGRAPHY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.50020.32510.26563.1486135255076.00
3.14860.23780.201321.9925148296087.00

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