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- PDB-6u9p: Wild-type MthK pore in ~150 mM K+ -

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Basic information

Entry
Database: PDB / ID: 6u9p
TitleWild-type MthK pore in ~150 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: 1.65 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 area6520 Å2
ΔGint-63 kcal/mol
Surface area15670 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
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 potassium chloride, 10 mM MOPS-KOH, pH 8.0) + 3.5-4.0 M 1,6-hexanediol, 100 mM MES-KOH, pH 6.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→44.05 Å / Num. obs: 11414 / % possible obs: 99.87 % / Redundancy: 23.2 % / Biso Wilson estimate: 22.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1037 / Rpim(I) all: 0.02178 / Rrim(I) all: 0.1061 / Net I/σ(I): 19.15
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.67 / Num. unique obs: 1096 / CC1/2: 0.653 / Rpim(I) all: 0.4666 / Rrim(I) all: 1.735 / % possible all: 98.92

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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: 1.65→44.05 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8366
RfactorNum. reflection% reflection
Rfree0.2075 1141 10.05 %
Rwork0.1829 --
obs0.1852 11408 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.89 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms637 0 13 30 680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192687
X-RAY DIFFRACTIONf_angle_d1.2721946
X-RAY DIFFRACTIONf_chiral_restr0.1039119
X-RAY DIFFRACTIONf_plane_restr0.0114111
X-RAY DIFFRACTIONf_dihedral_angle_d2.6884501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.710.32721460.29071096X-RAY DIFFRACTION98.92
1.69-1.730.29041420.2771264X-RAY DIFFRACTION100
1.73-1.780.25821220.22791255X-RAY DIFFRACTION100
1.78-1.830.24321500.22411245X-RAY DIFFRACTION99.86
1.83-1.890.19721320.19781256X-RAY DIFFRACTION100
1.89-1.960.20441450.17781230X-RAY DIFFRACTION100
1.96-2.040.22431400.18461267X-RAY DIFFRACTION100
2.04-2.130.161500.17191249X-RAY DIFFRACTION100
2.13-2.240.23121490.16211229X-RAY DIFFRACTION100
2.24-2.380.17251680.16671229X-RAY DIFFRACTION100
2.38-2.560.18531360.1521268X-RAY DIFFRACTION100
2.56-2.820.20051290.15261260X-RAY DIFFRACTION100
2.82-3.230.16951170.16121288X-RAY DIFFRACTION100
3.23-4.070.20181420.18181245X-RAY DIFFRACTION100
4.07-44.050.23191290.20321274X-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)
14.348079721451.520920671713.724831868764.542872775860.8705190055045.007526827320.0105343693152-0.57925259812-0.06646372496620.3626857804750.1119297798260.0871711278930.00766738861063-0.429995423673-0.09313498339150.2209603293280.08389718372280.006441054055980.2676245527680.009279558010510.2043302468167.6877023788414.77015742384.42575340469
22.00013572497-0.6033512703290.4086847420953.33070879725-0.01251288175533.052900664950.1464808902320.224754747718-0.158376135567-0.196508222521-0.0488227241515-0.06105623135830.4608089147860.108847409968-0.1064997014830.2405375426770.021885455513-0.02475006902630.192696967356-0.01559248017590.1827085536153.5416246993318.9358286142-12.7218867577
38.869815035461.016683733096.181685752032.15797246951.765773712127.72396658192-0.0468040709504-0.308203354072-0.3014718250050.08578267519750.1144329532910.09791061196670.0939298395978-0.223330911863-0.05447262961280.236353998743-0.00649760471392-0.001071081401820.1655858914750.04841106009530.179925131632-1.1792874576419.2567870297-1.61184490872
44.825844189532.98349546244-2.364786444423.770414433581.214943090044.879754212160.112496056624-1.520886983850.4467239110631.47173905694-0.174912228557-0.7890857312070.2189980697881.662786711560.06117909979090.897914453561-0.0305995764868-0.3530845697860.665501326087-0.05630483771220.62961884151912.852751995626.916060885510.0080264934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 18:34)
2X-RAY DIFFRACTION2(chain A and resid 35:73)
3X-RAY DIFFRACTION3(chain A and resid 74:90)
4X-RAY DIFFRACTION4(chain A and resid 91:99)

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