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- PDB-6v8y: Structure of a Sodium Potassium ion Channel -

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Basic information

Entry
Database: PDB / ID: 6v8y
TitleStructure of a Sodium Potassium ion Channel
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / ion channel
Function / homologyTwo pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / membrane / : / Transporter
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsRoy, R. / Weiss, K.L. / Coates, L.
CitationJournal: Iucrj / Year: 2021
Title: Structural plasticity of the selectivity filter in a nonselective ion channel.
Authors: Roy, R.N. / Hendriks, K. / Kopec, W. / Abdolvand, S. / Weiss, K.L. / de Groot, B.L. / Lange, A. / Sun, H. / Coates, L.
History
DepositionDec 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,52215
Polymers21,4132
Non-polymers1,10913
Water1,27971
1
A: Potassium channel protein
B: Potassium channel protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,04330
Polymers42,8264
Non-polymers2,21726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13470 Å2
ΔGint-261 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.716, 88.137, 49.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-406-

K

21A-407-

K

31A-408-

NA

41B-204-

K

51B-334-

HOH

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Components

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


Mass: 10706.538 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: See paper for details

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.53→38.34 Å / Num. obs: 49908 / % possible obs: 97.1 % / Redundancy: 7.04 % / CC1/2: 0.999 / Net I/σ(I): 16.2
Reflection shellResolution: 1.53→1.58 Å / Num. unique obs: 2568 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHY

2ahy


Resolution: 1.53→38.322 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.37
RfactorNum. reflection% reflection
Rfree0.1777 2591 5.19 %
Rwork0.1569 --
obs0.1579 49908 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→38.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 69 71 1581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081602
X-RAY DIFFRACTIONf_angle_d0.9632199
X-RAY DIFFRACTIONf_dihedral_angle_d20.624554
X-RAY DIFFRACTIONf_chiral_restr0.054271
X-RAY DIFFRACTIONf_plane_restr0.006262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.55790.30651380.30032127X-RAY DIFFRACTION83
1.5579-1.58780.24951320.28742557X-RAY DIFFRACTION97
1.5878-1.62020.28621620.2662548X-RAY DIFFRACTION99
1.6202-1.65550.35311380.24122592X-RAY DIFFRACTION98
1.6555-1.6940.24891520.21412524X-RAY DIFFRACTION97
1.694-1.73640.20711680.19692555X-RAY DIFFRACTION98
1.7364-1.78330.22941470.19242503X-RAY DIFFRACTION97
1.7833-1.83580.20611140.17712569X-RAY DIFFRACTION97
1.8358-1.8950.15931660.16842506X-RAY DIFFRACTION97
1.895-1.96280.17461400.15062549X-RAY DIFFRACTION97
1.9628-2.04130.14831430.13332531X-RAY DIFFRACTION96
2.0413-2.13420.16391160.12082523X-RAY DIFFRACTION96
2.1342-2.24670.1751210.13332529X-RAY DIFFRACTION96
2.2467-2.38750.13311480.12862479X-RAY DIFFRACTION95
2.3875-2.57180.16491120.12182491X-RAY DIFFRACTION95
2.5718-2.83050.17081480.12232452X-RAY DIFFRACTION93
2.8305-3.23990.14021290.1322459X-RAY DIFFRACTION94
3.2399-4.08120.17871020.14212427X-RAY DIFFRACTION91
4.0812-38.2220.17611150.18972396X-RAY DIFFRACTION91

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