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- PDB-6u9y: Wild-type MthK pore in 11 mM K+ -

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Basic information

Entry
Database: PDB / ID: 6u9y
TitleWild-type MthK pore in 11 mM K+
ComponentsCalcium-gated potassium channel MthK
KeywordsTRANSPORT PROTEIN / Potassium ion channel MthK
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
: / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / Potassium channel domain / Ion channel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / : / Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPosson, D.J. / Nimigean, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088352 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM087865 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Selectivity filter ion binding affinity determines inactivation in a potassium channel.
Authors: Boiteux, C. / Posson, D.J. / Allen, T.W. / Nimigean, C.M.
History
DepositionSep 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2937
Polymers8,9801
Non-polymers3146
Water54030
1
A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,17328
Polymers35,9184
Non-polymers1,25524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area6480 Å2
ΔGint-62 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.811, 63.811, 44.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-102-

K

31A-103-

K

41A-104-

K

51A-105-

K

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Components

#1: Protein Calcium-gated potassium channel MthK


Mass: 8979.500 Da / Num. of mol.: 1 / Fragment: UNP residues 18-99 / Mutation: UNP residues 18-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1:1 protein (in 100 mM sodium chloride, 1 mM potassium chloride, 10 mM MOPS, pH 8.0) + 3.5-4.0 M 1,6-hexanediol, 100 mM MES-NaOH, 10 mM potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→31.9 Å / Num. obs: 8824 / % possible obs: 99.81 % / Redundancy: 24.9 % / Biso Wilson estimate: 23.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1446 / Rpim(I) all: 0.02937 / Rrim(I) all: 0.1476 / Net I/σ(I): 22.59
Reflection shellResolution: 1.8→1.868 Å / Redundancy: 25 % / Rmerge(I) obs: 3.326 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 838 / CC1/2: 0.613 / Rpim(I) all: 0.6733 / Rrim(I) all: 3.395 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LDC

3ldc


Resolution: 1.8→31.9 Å / SU ML: 0.1813 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6811
RfactorNum. reflection% reflection
Rfree0.2166 881 10.09 %
Rwork0.1941 --
obs0.1963 8820 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms637 0 13 30 680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094679
X-RAY DIFFRACTIONf_angle_d0.8014933
X-RAY DIFFRACTIONf_chiral_restr0.0565117
X-RAY DIFFRACTIONf_plane_restr0.0054109
X-RAY DIFFRACTIONf_dihedral_angle_d2.3308497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8680.3132890.3052836X-RAY DIFFRACTION98.7
1.86-1.920.26931300.27251203X-RAY DIFFRACTION99.78
1.92-1.980.2911470.24751191X-RAY DIFFRACTION100
1.98-2.060.21851260.22061199X-RAY DIFFRACTION100
2.06-2.160.27611710.20981177X-RAY DIFFRACTION100
2.16-2.270.23131290.18491198X-RAY DIFFRACTION100
2.27-2.410.22641570.18411198X-RAY DIFFRACTION100
2.41-2.60.18511300.16251198X-RAY DIFFRACTION99.92
2.6-2.860.19871210.15931219X-RAY DIFFRACTION100
2.86-3.280.16851100.16971210X-RAY DIFFRACTION100
3.28-4.130.20151350.18581207X-RAY DIFFRACTION100
4.13-31.90.2161280.20311223X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.782778143590.5911318298615.11058317663.92786725119-0.5074168504499.10422465534-0.0113316904638-0.52155270857-0.1424518260690.3437948252140.1915816248210.04246838006790.0642173600694-0.0507509856899-0.1352577502010.2230167284020.07145824143010.01841064543620.2675728192020.01192890968280.2230071208147.571211311314.63645529914.45531738955
22.15242206092-0.8343828951120.09955466855892.64340047502-0.4104048366762.767634671870.1424483588790.265033016817-0.216840127854-0.257213571827-0.0364073344182-0.05564081131390.4632232265350.153870698265-0.100143133560.2550030856590.0211739891268-0.03113868790110.193512143723-0.01871171732490.1874014763713.7746545852818.8682691782-12.6439057654
33.90225342179-0.7166185424792.800544737631.82879150815-0.6131187297727.48863760292-0.0136340295613-0.301561324437-0.3923140175140.07894055269020.176764209980.128125534850.232947822234-0.365838815547-0.1614688630550.238008721396-0.00531725321650.001458084352490.1951016918560.02960922713490.23611078773-2.2761226122819.047811929-3.14572741669
42.69784057234.125900204641.947583958346.959300477763.170815287925.75123963599-0.123841745893-1.257126674550.6690687394382.037848235230.320744892065-0.640544385315-0.7810633375360.768885868852-0.05012963274970.7236449175420.00225464132983-0.1917152084650.572627610968-0.1226048616250.57874825982812.098818822526.43387521899.72931965009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 18:34)
2X-RAY DIFFRACTION2(chain A and resid 35:72)
3X-RAY DIFFRACTION3(chain A and resid 73:88)
4X-RAY DIFFRACTION4(chain A and resid 89:99)

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