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- PDB-6ufe: The structure of a potassium selective ion channel at atomic reso... -

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Basic information

Entry
Database: PDB / ID: 6ufe
TitleThe structure of a potassium selective ion channel at atomic resolution
ComponentsTransporter
KeywordsMEMBRANE PROTEIN / ion channel / potassium ion channel
Function / homology
Function and homology information


stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / potassium channel activity / identical protein binding / membrane / metal ion binding
Similarity search - Function
Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
: / Transporter / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLangan, P.S. / Vandavasi, V.G. / Sullivan, B. / Afonine, P.V. / Weiss, K.L.
CitationJournal: Iucrj / Year: 2020
Title: The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation.
Authors: Langan, P.S. / Vandavasi, V.G. / Kopec, W. / Sullivan, B. / Afonne, P.V. / Weiss, K.L. / de Groot, B.L. / Coates, L.
History
DepositionSep 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: 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

Downloads & links

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Assembly

Deposited unit
A: Transporter
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,88620
Polymers20,3922
Non-polymers1,49518
Water1,49583
1
A: Transporter
hetero molecules

A: Transporter
hetero molecules

A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,30036
Polymers40,7844
Non-polymers2,51632
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 area10670 Å2
ΔGint-197 kcal/mol
Surface area16160 Å2
MethodPISA
2
B: Transporter
hetero molecules

B: Transporter
hetero molecules

B: Transporter
hetero molecules

B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,24644
Polymers40,7844
Non-polymers3,46240
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 area14370 Å2
ΔGint-309 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 67.860, 89.620
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-705-

K

21A-706-

K

31A-707-

K

41A-708-

K

51B-203-

K

61B-204-

K

71B-205-

K

81B-206-

K

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Components

#1: Protein Transporter / Voltage-gated potassium channel


Mass: 10195.952 Da / Num. of mol.: 2 / Mutation: D66Y, N68D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: A9485_19160, BACERE00184_02078, CJ306_03585, CN950_06075, CN980_22870, COI98_17615, CON37_12595
Production host: Escherichia coli (E. coli) / References: UniProt: A0A164U772, UniProt: Q81HW2*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
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: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 61537 / % possible obs: 97.4 % / Redundancy: 5.34 % / CC1/2: 0.998 / Net I/σ(I): 12.23
Reflection shellResolution: 1.2→1.23 Å / Num. unique obs: 3673 / CC1/2: 0.489

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OUF

3ouf


Resolution: 1.2→21.459 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1477 2013 3.27 %
Rwork0.1326 --
obs0.1331 61528 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→21.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 88 83 1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.031673
X-RAY DIFFRACTIONf_angle_d4.092324
X-RAY DIFFRACTIONf_dihedral_angle_d157.09592
X-RAY DIFFRACTIONf_chiral_restr0.36290
X-RAY DIFFRACTIONf_plane_restr0.03269
LS refinement shellResolution: 1.2→1.23 Å
RfactorNum. reflection% reflection
Rfree0.2925 124 -
Rwork0.2876 3393 -
obs--78 %

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