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- PDB-4hyo: Crystal Structure of MthK Pore -

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Basic information

Entry
Database: PDB / ID: 4hyo
TitleCrystal Structure of MthK Pore
ComponentsCalcium-gated potassium channel mthK
KeywordsMETAL TRANSPORT / transmembrane ion channel family / potassium channel
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
: / Regulator of K+ conductance, N-terminal / 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. / RCK N-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain ...: / Regulator of K+ conductance, N-terminal / 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. / RCK N-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
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 / molecular replacement / Resolution: 1.65 Å
AuthorsPosson, D.J. / McCoy, J.G. / Nimigean, C.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: The voltage-dependent gate in MthK potassium channels is located at the selectivity filter.
Authors: Posson, D.J. / McCoy, J.G. / Nimigean, C.M.
History
DepositionNov 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
C: Calcium-gated potassium channel mthK
D: Calcium-gated potassium channel mthK
E: Calcium-gated potassium channel mthK
F: Calcium-gated potassium channel mthK
G: Calcium-gated potassium channel mthK
H: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,95528
Polymers81,2248
Non-polymers1,73120
Water4,792266
1
A: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
C: Calcium-gated potassium channel mthK
D: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,71416
Polymers40,6124
Non-polymers1,10212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-61 kcal/mol
Surface area15530 Å2
MethodPISA
2
E: Calcium-gated potassium channel mthK
F: Calcium-gated potassium channel mthK
G: Calcium-gated potassium channel mthK
H: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,24112
Polymers40,6124
Non-polymers6298
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-55 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.035, 63.452, 63.477
Angle α, β, γ (deg.)90.030, 89.990, 89.990
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Calcium-gated potassium channel mthK


Mass: 10152.961 Da / Num. of mol.: 8 / Fragment: unp residues 11-101 / Mutation: S68H, V77C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: mthK, MTH_1520 / Plasmid: pqe82 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3.5-4.0M 1,6-hexanediol, 100mM MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 3.2 % / Av σ(I) over netI: 18.73 / Number: 257675 / Rmerge(I) obs: 0.042 / Χ2: 0.83 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 79424 / % possible obs: 96.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.555099.110.0270.6843.3
2.823.5598.410.0340.8233.4
2.462.8297.710.040.9083.2
2.242.4697.110.0490.8773.3
2.082.2496.610.0640.9653.1
1.962.089610.0860.8933.4
1.861.9695.610.1280.8273.2
1.781.869510.210.7823.2
1.711.7894.210.2840.7613.4
1.651.7193.810.3970.7363
ReflectionResolution: 1.65→50 Å / Num. obs: 79424 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.042 / Χ2: 0.826 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.7130.39777520.736193.8
1.71-1.783.40.28477870.761194.2
1.78-1.863.20.2177690.782195
1.86-1.963.20.12878920.827195.6
1.96-2.083.40.08679750.893196
2.08-2.243.10.06478860.965196.6
2.24-2.463.30.04980150.877197.1
2.46-2.823.20.0480530.908197.7
2.82-3.553.40.03481120.823198.4
3.55-503.30.02781830.684199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å44.86 Å
Translation2.5 Å44.86 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LDC

3ldc


Resolution: 1.65→44.864 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.9103 / SU ML: 0.14 / σ(F): 2.14 / Phase error: 16.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 3966 5.05 %random
Rwork0.1637 ---
obs0.1646 78558 94.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.56 Å2 / Biso mean: 22.7799 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5120 0 104 266 5490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015556
X-RAY DIFFRACTIONf_angle_d1.1737528
X-RAY DIFFRACTIONf_chiral_restr0.074928
X-RAY DIFFRACTIONf_plane_restr0.005880
X-RAY DIFFRACTIONf_dihedral_angle_d12.0811820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6492-1.66940.23591270.18972214234177
1.6694-1.69050.19221390.20012440257989
1.6905-1.71270.17931200.18142600272091
1.7127-1.73620.171330.17042451258492
1.7362-1.7610.1811500.16192722287293
1.761-1.78730.20511390.1632585272494
1.7873-1.81520.14021500.16572657280793
1.8152-1.8450.17251490.16042589273893
1.845-1.87680.15561400.14872664280494
1.8768-1.91090.21081440.13922613275795
1.9109-1.94770.1991270.14092625275295
1.9477-1.98740.19361460.15282697284395
1.9874-2.03060.15741340.14592717285195
2.0306-2.07790.22791420.15772694283696
2.0779-2.12980.21391530.14482707286096
2.1298-2.18740.12331480.1412694284296
2.1874-2.25180.14151400.15462674281496
2.2518-2.32450.19711410.14462733287497
2.3245-2.40750.2481300.15942732286297
2.4075-2.50390.21531440.15442716286097
2.5039-2.61790.18791530.13352721287497
2.6179-2.75590.13981530.14732786293998
2.7559-2.92850.17891480.16192697284598
2.9285-3.15460.1721480.16692759290798
3.1546-3.47190.12251410.17442759290098
3.4719-3.97410.20031490.16592774292399
3.9741-5.00580.16781440.17152791293599
5.0058-44.8810.22681340.20592781291599
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)
17.2609-4.53161.60376.0042-1.57794.8483-0.1388-0.0872-0.1190.0839-0.03770.42570.3782-0.4220.14770.1486-0.02120.02250.167-0.07830.1428-6.46697.5377-14.9454
21.3819-0.0015-0.18031.73270.96473.0076-0.0607-0.41630.17050.19670.1388-0.1497-0.04760.1298-0.04940.10650.0289-0.01360.1402-0.02660.09310.49944.8296-19.533
36.1743-2.15221.56663.0575-0.94142.9221-0.2171-0.4106-0.32280.35460.11210.16890.0839-0.04310.0820.14910.0220.03140.15540.00560.0673.5255-2.7365-18.8038
45.9509-0.76433.82177.9182-2.72843.10740.38170.34320.6497-0.3939-0.2121.939-0.8664-1.6053-0.20730.53790.36460.01420.7852-0.0030.5593-11.884912.8463-27.1238
56.63973.9188-2.24895.4096-1.73394.9164-0.15610.10760.0884-0.0088-0.05020.4069-0.3166-0.44910.16670.1320.0134-0.01870.1729-0.07780.1464-6.4678-7.7988-49.214
61.3613-0.04050.06281.63330.87223.3246-0.06840.4107-0.1275-0.17920.1252-0.1646-0.01270.1775-0.03630.1056-0.03310.01190.1456-0.0260.091210.7809-4.7677-44.6223
75.81422.3369-1.22633.2712-0.92772.535-0.23240.35560.3369-0.41030.09160.1827-0.0917-0.08010.10030.1555-0.0217-0.03650.15350.00850.06582.68192.4269-45.4298
86.18550.6487-3.6778.0891-2.29842.65560.237-0.3133-0.50170.5432-0.14041.84330.8138-1.6848-0.14360.5768-0.38210.00730.89750.02960.5143-11.9214-13.0954-37.0471
95.80531.10973.75993.83251.47615.1749-0.1443-0.16710.03060.38370.19490.4071-0.0094-0.4443-0.06410.14790.02080.01280.14230.10970.1759-6.477816.9896-39.7728
101.641-0.1433-0.0532.2006-0.62861.3044-0.0740.09610.44590.0136-0.0634-0.1765-0.19380.15860.10540.1105-0.0155-0.03430.09530.02860.155311.012912.6068-36.1325
115.39661.83832.2792.47251.21023.3925-0.218-0.29340.39450.06380.10990.145-0.3959-0.25480.09380.15530.0435-0.02550.0743-0.00920.16481.566112.9059-29.9845
126.17195.13351.18795.38324.10259.11210.57320.648-0.4754-0.91030.12441.68060.6763-1.7935-0.40860.5412-0.0221-0.36780.52830.05810.8224-11.92294.8466-45.0233
136.2923-1.7068-4.2234.57551.76365.6121-0.19070.197-0.205-0.35560.18130.43820.0573-0.4565-0.02030.1367-0.0204-0.01420.14770.09250.1627-6.4696-17.2545-24.4117
141.63770.33220.10092.1334-0.51971.4637-0.0781-0.0988-0.4340.0041-0.0365-0.17480.21860.16250.08780.11210.01660.03530.0950.02390.15111.0073-12.8568-28.0349
156.3176-1.176-2.69891.80020.67073.505-0.19250.3029-0.3239-0.05650.1160.13460.3838-0.25380.08460.1564-0.04170.01950.0779-0.00220.17291.57-13.157-34.1825
165.5807-3.9448-1.56383.13612.19674.040.5107-0.27510.40710.9043-0.11071.6947-0.5908-1.8338-0.30490.5468-0.00650.36170.54340.02820.8683-11.9222-5.1252-19.1305
178.3422-1.78044.70254.7713-1.57065.4632-0.18250.09250.1475-0.2720.2027-0.464-0.13160.4267-0.03230.1303-0.02970.01890.1313-0.08160.15753.263848.73857.3118
181.44390.1728-0.0983.23980.67141.6926-0.0796-0.1480.39330.0276-0.0650.1893-0.184-0.14940.1080.10110.0129-0.03330.0965-0.02970.1417-13.960544.10454.3064
195.8951-1.43822.20622.7875-1.13173.256-0.22990.33010.4017-0.08930.1043-0.0793-0.40180.18770.12420.1528-0.0372-0.01890.06890.01250.1495-5.85944.9273-2.9001
205.594-3.6163-0.74574.3092-2.56954.86470.5596-0.5172-0.40490.8545-0.0626-1.54550.69342.0581-0.25240.53540.0033-0.38650.5589-0.00820.81448.674836.528812.6544
218.27162.03-4.22124.7539-1.56215.2081-0.2027-0.1299-0.01250.30780.2262-0.41440.12650.3771-0.04590.13470.0274-0.01380.1427-0.07990.16623.276914.4592-8.0247
221.3980.19280.19463.3230.92711.5479-0.05920.1371-0.4013-0.0447-0.09610.17320.1988-0.14050.11030.1112-0.01680.03330.0938-0.03210.1473-13.597119.0231-5.5267
235.5841.3164-1.59992.7602-0.68582.798-0.1316-0.2911-0.39410.14220.0994-0.02620.28930.10030.01320.15080.02890.02440.05590.01140.157-7.084518.35582.2931
244.6033.29890.68452.5893-0.57795.36180.44610.41830.2387-0.95920.1041-1.2383-0.32662.0126-0.36370.47930.05790.36640.58410.01850.79318.728726.5455-13.2795
255.7612-3.856-1.59215.37211.48934.4446-0.124-0.21450.1362-0.0449-0.0302-0.4073-0.36050.43620.1090.1468-0.0176-0.01930.17430.09810.14033.284423.908416.7806
261.60730.05860.31651.2604-0.53082.0101-0.0649-0.4466-0.10040.23620.12380.1651-0.0454-0.1811-0.03780.11780.03520.01790.16020.02920.0971-14.19127.521912.3929
275.433-2.2465-1.46123.20961.00792.1878-0.225-0.43070.27310.36730.124-0.2367-0.04430.12850.06250.14770.0257-0.03970.1653-0.0040.0714-4.745733.672712.6964
284.96491.2066-3.03355.40952.47663.8930.41980.4499-0.6276-0.3742-0.4122-2.10860.88721.7204-0.09410.48240.33990.00980.89650.07880.57618.737618.6434.6341
296.29854.21761.62175.10561.66194.0355-0.18410.1394-0.2383-0.044-0.0137-0.42360.30920.46110.14230.13880.01750.01840.17920.1040.15183.287639.2647-17.4761
301.1921-0.0054-0.31241.4689-0.7733.0576-0.06680.40920.1485-0.18750.1180.16410.0004-0.1934-0.0290.1079-0.0308-0.01640.15050.03150.0964-13.966536.2314-12.8764
317.18052.80831.14453.841.11812.8384-0.23940.4747-0.241-0.38790.097-0.11420.0980.09760.10380.1425-0.01470.0350.15230.00110.0738-5.861229.0356-13.6914
325.1791.9774.15343.70672.43253.58750.2786-0.32770.59650.2277-0.323-1.8034-0.90761.8053-0.05330.5061-0.3421-0.00240.82090.0690.58468.744644.5124-5.3352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 18:33)A18 - 33
2X-RAY DIFFRACTION2(chain A and resid 34:67)A34 - 67
3X-RAY DIFFRACTION3(chain A and resid 68:90)A68 - 90
4X-RAY DIFFRACTION4(chain A and resid 91:99)A91 - 99
5X-RAY DIFFRACTION5(chain B and resid 18:33)B18 - 33
6X-RAY DIFFRACTION6(chain B and resid 34:68)B34 - 68
7X-RAY DIFFRACTION7(chain B and resid 69:90)B69 - 90
8X-RAY DIFFRACTION8(chain B and resid 91:99)B91 - 99
9X-RAY DIFFRACTION9(chain C and resid 18:33)C18 - 33
10X-RAY DIFFRACTION10(chain C and resid 34:70)C34 - 70
11X-RAY DIFFRACTION11(chain C and resid 71:90)C71 - 90
12X-RAY DIFFRACTION12(chain C and resid 91:99)C91 - 99
13X-RAY DIFFRACTION13(chain D and resid 18:33)D18 - 33
14X-RAY DIFFRACTION14(chain D and resid 34:70)D34 - 70
15X-RAY DIFFRACTION15(chain D and resid 71:90)D71 - 90
16X-RAY DIFFRACTION16(chain D and resid 91:99)D91 - 99
17X-RAY DIFFRACTION17(chain E and resid 18:33)E18 - 33
18X-RAY DIFFRACTION18(chain E and resid 34:68)E34 - 68
19X-RAY DIFFRACTION19(chain E and resid 69:90)E69 - 90
20X-RAY DIFFRACTION20(chain E and resid 91:99)E91 - 99
21X-RAY DIFFRACTION21(chain F and resid 18:33)F18 - 33
22X-RAY DIFFRACTION22(chain F and resid 34:66)F34 - 66
23X-RAY DIFFRACTION23(chain F and resid 67:90)F67 - 90
24X-RAY DIFFRACTION24(chain F and resid 91:99)F91 - 99
25X-RAY DIFFRACTION25(chain G and resid 18:33)G18 - 33
26X-RAY DIFFRACTION26(chain G and resid 34:70)G34 - 70
27X-RAY DIFFRACTION27(chain G and resid 71:90)G71 - 90
28X-RAY DIFFRACTION28(chain G and resid 91:99)G91 - 99
29X-RAY DIFFRACTION29(chain H and resid 18:33)H18 - 33
30X-RAY DIFFRACTION30(chain H and resid 34:68)H34 - 68
31X-RAY DIFFRACTION31(chain H and resid 69:90)H69 - 90
32X-RAY DIFFRACTION32(chain H and resid 91:99)H91 - 99

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