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- PDB-8ctv: Crystal structure of a K+ selective NaK mutant (NaK2K) -Tl+ complex -

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Basic information

Entry
Database: PDB / ID: 8ctv
TitleCrystal structure of a K+ selective NaK mutant (NaK2K) -Tl+ complex
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / Potassium ion channel / thallium ion / Tl+
Function / homology
Function and homology information


potassium channel activity / membrane
Similarity search - Function
Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THALLIUM (I) ION / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus m1550 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM12345 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM141697 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM118217 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)DP2OD028805 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Kinship FoundationSSP-2018-3240 United States
New York Community Trust338034 United States
CitationJournal: To Be Published
Title: Direct visualization of electric field-stimulated ion conduction in a potassium channel
Authors: Lee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,78919
Polymers21,2812
Non-polymers2,50817
Water57632
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)47,34236
Polymers42,5624
Non-polymers4,78032
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 area12130 Å2
ΔGint-283 kcal/mol
Surface area16950 Å2
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)47,81540
Polymers42,5624
Non-polymers5,25336
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 area14270 Å2
ΔGint-325 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.123, 69.123, 91.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-204-

TL

21A-205-

TL

31A-206-

TL

41A-207-

TL

51B-205-

TL

61B-206-

TL

71B-207-

TL

81B-208-

TL

91B-209-

NA

101A-319-

HOH

111A-323-

HOH

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Components

#1: Protein Potassium channel protein


Mass: 10640.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus m1550 (bacteria) / Gene: bcere0011_5790 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: C2R3K4
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Tl / Feature type: SUBJECT OF INVESTIGATION
#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.: 32 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NaK2K protein was mixed with 50mM MES pH 6.5/100mM potassium citrate/200mM TlNO3/56%-68% MPD while 50mM MES pH 6.5/100mM potassium citrate/200mM KNO3/56%-68% MPD was used for the reservoir. ...Details: NaK2K protein was mixed with 50mM MES pH 6.5/100mM potassium citrate/200mM TlNO3/56%-68% MPD while 50mM MES pH 6.5/100mM potassium citrate/200mM KNO3/56%-68% MPD was used for the reservoir. Crystal is transferred to 100mM TlNO3/50mM MES (pH 6.0 or 6.5)/60%-70% MPD

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Data collection

DiffractionMean temperature: 289 K / Ambient temp details: room temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9781 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 22504 / % possible obs: 99.8 % / Redundancy: 21.3 % / Biso Wilson estimate: 20.28 Å2 / Rsym value: 0.115 / Net I/σ(I): 32.272
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2.904 / Num. unique obs: 648 / CC1/2: 0.731 / Rsym value: 0.741 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3235refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: room temperature NaK2K structure

Resolution: 2.1→48.88 Å / SU ML: 0.1922 / Cross valid method: FREE R-VALUE / σ(F): 1.73 / Phase error: 17.2478 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1811 2296 10.2 %
Rwork0.1678 20204 -
obs0.1692 22500 90.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 66 32 1578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561729
X-RAY DIFFRACTIONf_angle_d0.84192379
X-RAY DIFFRACTIONf_chiral_restr0.0454293
X-RAY DIFFRACTIONf_plane_restr0.0059287
X-RAY DIFFRACTIONf_dihedral_angle_d19.842603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.2135790.2487674X-RAY DIFFRACTION48.12
2.15-2.20.27651000.2549874X-RAY DIFFRACTION62.48
2.2-2.250.24411090.22971010X-RAY DIFFRACTION72.43
2.25-2.310.24461430.19651166X-RAY DIFFRACTION84.51
2.31-2.380.22591420.21241290X-RAY DIFFRACTION91.5
2.38-2.460.17331310.19551349X-RAY DIFFRACTION95.42
2.46-2.540.18681530.17291313X-RAY DIFFRACTION96.26
2.54-2.650.16021540.1621405X-RAY DIFFRACTION99.87
2.65-2.770.1631670.14941415X-RAY DIFFRACTION99.87
2.77-2.910.17361700.15851354X-RAY DIFFRACTION100
2.91-3.090.18461380.15571411X-RAY DIFFRACTION100
3.09-3.330.1591640.14811392X-RAY DIFFRACTION99.62
3.33-3.670.14971560.14741388X-RAY DIFFRACTION100
3.67-4.20.17151360.13881416X-RAY DIFFRACTION99.94
4.2-5.290.15911730.1451379X-RAY DIFFRACTION99.49
5.29-48.880.19811810.18921368X-RAY DIFFRACTION99.49
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)
13.591775819250.507199862783-0.2448879033263.259158189111.041868817790.91594911027-0.119489686647-0.454222904007-0.5878155769230.46331404959-0.1201287691630.02009442462190.724060318169-0.1054274918510.1975810129270.288277250152-0.01595241634160.1332362254160.1254410107080.03206306213080.36398029922-3.38266625677-15.477576094720.1504416729
23.56690138979-0.1554625409491.220309058523.20584343131-0.1768614583864.6466429569-0.092305403935-0.682825425899-0.2570577138820.851946219995-0.1335804289350.1892968477360.406810009103-0.08624251847930.1823737049170.326761351606-0.04706941500390.143648482240.2217682019740.01392571063390.317039580116-6.16962380957-10.04477685226.5397304926
36.911124535362.11700643641-4.040985833297.15932172698-0.01451000840332.64957177960.00311126288513-0.3757202116460.09562356926310.2026377358960.0584998042932-0.149572016627-0.06018180908860.0890771395678-0.06373497085081.10867805526-0.09545069966470.003492259583670.7347087984790.1530278089070.63195594326318.130098054-11.989780833640.6568343371
44.15154822383-0.4056215243752.227541012033.71602983049-0.2996274617355.55394440088-0.0741883671277-0.263830301637-0.03759994967890.135000620602-0.1239536546880.4909180797970.313907736686-0.2850475129130.1820515218280.260790631427-0.07247663932570.09678848356060.2453803230830.1202451793920.415462297547-15.9816327727-11.7596866916-26.1661206242
50.4615882292560.293899092217-0.5650929180490.641774681581-0.757297799981.070844293860.205788495196-0.943426407653-0.2660463227180.972779558481-0.04418570944990.2335232286930.364191832142-0.301980920607-0.06588034318190.687583117328-0.03750598756490.2374326495580.5473683630750.236820646924-0.135149031736-8.92513842743-7.29270414014-12.2679146257
62.66167052274-1.072918103960.7423975258492.7539263217-0.3768326665321.551338662120.147565165474-0.401491602221-0.2242847864550.208534680456-0.1195352514840.00863661908990.3615387224780.0952057061302-0.02958073427370.293655887274-0.02206712884870.04485577161890.2553390008030.09209774155590.173947593601-5.92033862081-10.4197453855-24.3469937753
74.86460278759-3.949509790251.023860464874.74571685156-2.760790414683.393582765560.1104033244210.09789004049590.416572842583-0.1731201071170.164572071624-0.0408781800433-0.365944584972-0.183328731258-0.234420417440.2971014759880.06758825348690.05191594574880.172340228489-0.01824876841430.316466291295-19.748858369910.8989036388-37.7862931983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 113 )
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 45 )
5X-RAY DIFFRACTION5chain 'B' and (resid 46 through 73 )
6X-RAY DIFFRACTION6chain 'B' and (resid 74 through 101 )
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 113 )

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