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- PDB-2fy8: Crystal structure of MthK rck domain in its ligand-free gating-ri... -

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Basic information

Entry
Database: PDB / ID: 2fy8
TitleCrystal structure of MthK rck domain in its ligand-free gating-ring form
ComponentsCalcium-gated potassium channel mthK
KeywordsTRANSPORT PROTEIN / Transport / Ionic channel / Alternative initiation / Transmembrane / Ion transport / Potassium / Potassium transport / Membrane / gating ring / closed conformation / partially open conformation / transition state
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Potassium channel domain ...Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsYe, S. / Jiang, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Crystal Structures of a Ligand-free MthK Gating Ring: Insights into the Ligand Gating Mechanism of K(+) Channels.
Authors: Ye, S. / Li, Y. / Chen, L. / Jiang, Y.
History
DepositionFeb 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: 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

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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


Theoretical massNumber of molelcules
Total (without water)203,5768
Polymers203,5768
Non-polymers00
Water93752
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

A: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
C: Calcium-gated potassium channel mthK
D: Calcium-gated potassium channel mthK


Theoretical massNumber of molelcules
Total (without water)203,5768
Polymers203,5768
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
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

E: Calcium-gated potassium channel mthK
F: Calcium-gated potassium channel mthK
G: Calcium-gated potassium channel mthK
H: Calcium-gated potassium channel mthK


Theoretical massNumber of molelcules
Total (without water)203,5768
Polymers203,5768
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)174.141, 180.965, 252.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is an octamer. There are two tetramers in an asymmetric unit. The first octamer can be generated from the first tetramer (polypeptide chain A, B, C and D) by the operation: ROTATION MATRIX -1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.000 TRANSLATION VECTOR 0.00000 0.00000 126.374 The first octamer has the 422 symmetry, representing the closed conformation of mthK gating ring. The second octamer can be generated from the second tetramer (polypeptide chain E, F, G and H) by the operation: ROTATION MATRIX -1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.000 TRANSLATION VECTOR 0.00000 0.00000 126.374 The second octamer is an asymmetric, parcially open mthK gating ring, which might represent a gating ring conformation in transition state.

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Components

#1: Protein
Calcium-gated potassium channel mthK


Mass: 25447.000 Da / Num. of mol.: 8 / Fragment: soluble isoform, residues 107-336 / Mutation: D184N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mthK / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: O27564
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 4.89 Å3/Da / Density % sol: 74.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.6 M Na/K PO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 95903 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 20.9
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1.3 / Num. unique all: 7334 / Rsym value: 0.824 / % possible all: 75.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LNQ (MONOMER)

1lnq


Resolution: 2.79→47.19 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 24.095 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.357 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25408 1923 2 %RANDOM
Rwork0.21201 ---
obs0.21286 93976 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.098 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--2.2 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.79→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13799 0 0 52 13851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.97718854
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2951768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68823.494664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19152552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.44615160
X-RAY DIFFRACTIONr_chiral_restr0.0960.22176
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.25906
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.29479
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2404
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2208
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5141.58997
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.899214238
X-RAY DIFFRACTIONr_scbond_it1.29835395
X-RAY DIFFRACTIONr_scangle_it2.2754.54616
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.794→2.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 111 -
Rwork0.342 4968 -
obs--100 %
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)
11.9433-0.7998-0.72283.5548-0.5592.57580.0982-0.077-0.0925-0.0884-0.08860.02320.4533-0.3288-0.0096-0.0327-0.1734-0.0051-0.042-0.0041-0.1195-24.193429.692358.2617
24.5002-3.5106-3.748714.758217.338724.07920.559-0.49220.3753-0.5861-0.0748-0.2024-0.65-0.324-0.4842-0.2014-0.1560.08850.1462-0.0391-0.0491-30.794149.921272.7497
39.45054.4444-0.19819.16092.55342.53810.4877-1.03590.09690.4205-0.31960.11640.1535-0.2477-0.1681-0.2356-0.21350.03480.36090.0627-0.104-36.851141.70180.3986
46.92890.65090.80014.2636-0.59156.5705-0.07120.3766-0.30360.0617-0.00150.09490.149-0.32170.0727-0.3119-0.23350.03070.1439-0.0291-0.0814-53.388331.153371.1923
51.90830.8453-0.28862.52720.36112.45490.13360.15380.2471-0.0323-0.03750.0713-0.0414-0.0942-0.0961-0.10820.04940.0219-0.0270.061-0.08-15.258752.455143.4982
616.4815-18.028-7.188222.90585.72515.71150.27290.9302-0.2367-0.0618-0.02070.16480.6089-0.0239-0.2522-0.00830.1209-0.05320.0428-0.0568-0.198-5.454832.249930.8477
74.91-3.41922.923914.79752.54335.97190.06580.11420.0216-0.26630.3589-0.29440.140.1125-0.4247-0.00270.0499-0.00860.15190.0738-0.2575-1.281440.773522.3651
85.55660.5085-0.17423.1809-0.61217.71850.35340.44560.35410.131-0.02960.1447-0.4747-0.7919-0.32380.03490.16320.03360.07680.1029-0.2746-17.05551.651411.8304
92.15240.19480.40782.3389-0.68951.86860.11850.2167-0.1753-0.1075-0.05550.0440.33310.1573-0.0630.03070.1291-0.0024-0.0545-0.0568-0.1444.893829.599238.6594
1022.9495-14.9311-0.568212.9784-1.93971.648-0.3490.60030.6890.19850.0896-0.4966-0.1541-0.23210.2593-0.09580.0353-0.02560.04290.0357-0.1329-9.63949.739731.9304
114.0371-2.52372.091311.2595-5.37810.1028-0.2608-0.092-0.1095-0.0520.39670.2261-0.02510.1378-0.1359-0.0426-0.03390.0110.19420.0329-0.267-17.085341.379526.0012
127.70823.8213-2.56345.09890.368610.10250.02850.2859-0.7347-0.14330.0087-0.27871.03950.3776-0.03720.16590.0826-0.0763-0.0725-0.0314-0.2756-7.691230.88249.2873
132.0441-0.14070.93432.68150.31831.8311-0.01180.13660.2901-0.0252-0.0775-0.03930.09140.19770.0893-0.14960.09250.07030.01920.051-0.065919.354152.448547.837
143.531-6.7194.981625.4799-14.588415.17360.3690.1809-0.444-0.456-0.48470.25820.66620.89070.1156-0.1420.24670.02390.0953-0.0324-0.137431.945732.35957.7152
157.0025-1.6046-0.439622.4051-0.74983.3225-0.4269-0.4716-0.11160.25180.7703-0.55-0.17180.3663-0.3435-0.25720.14110.09540.3066-0.0122-0.107640.477540.898862.0068
164.642-0.068-4.17478.09262.309510.60410.27120.2250.6112-0.4798-0.03380.3013-0.74410.0449-0.2374-0.31330.11230.13290.05670.08170.114751.213852.298346.5914
172.75990.0288-0.47162.15871.0672.16040.0070.06920.10090.0035-0.05820.1983-0.4184-0.24630.05110.15820.110.0637-0.16650.043-0.131-10.7442-25.951851.9769
1821.12315.40515.35991.5672.472722.71930.19390.56540.19350.1996-0.0019-0.5686-0.73820.3707-0.19190.4456-0.07450.1358-0.3552-0.0248-0.13148.4659-16.063266.0111
1922.11279.16874.283415.1262-0.46382.32870.52410.13670.49430.8971-0.12780.17440.1744-0.1565-0.39640.57060.04240.2057-0.3827-0.0196-0.1579-0.2876-8.661571.365
206.2834-1.1362-1.1555.06831.68695.63460.15620.14210.2679-0.3765-0.13290.4726-0.1888-0.0933-0.02320.36650.03930.2124-0.50930.10160.0494-10.2285.182657.5131
213.62190.13570.71822.18920.70583.21160.14670.0756-0.093-0.12440.0917-0.2638-0.26290.2838-0.23830.0249-0.1040.0764-0.1152-0.0083-0.144512.8035-38.30441.4622
2217.875911.517411.736311.98418.53297.91210.12010.03370.5119-0.7033-0.06470.50810.0399-0.3889-0.05540.1401-0.0062-0.0237-0.05340.0213-0.1968-6.4768-51.144730.2344
2310.42381.28584.54832.6606-2.10939.99420.37680.8691-0.0240.2666-0.0823-0.29710.2744-0.0717-0.29450.12110.10150.06080.00410.0182-0.20822.4876-57.274723.5059
246.0606-2.43670.22356.5254-0.27855.7304-0.04350.45440.2322-0.59640.4666-0.7689-0.55651.0176-0.4231-0.0701-0.1630.19520.255-0.0996-0.262813.5608-44.376810.0988
253.4094-0.5966-0.82163.72840.02382.40140.10270.0493-0.0482-0.26090.09080.3432-0.0341-0.2344-0.1935-0.1218-0.0241-0.0513-0.02950.0405-0.1095-10.1262-58.946239.9409
269.17089.95161.173316.2935-2.01976.14990.28230.1867-0.38560.0971-0.1287-0.9077-0.5850.4298-0.15360.0368-0.08120.1096-0.08-0.0212-0.120110.6966-46.60131.3947
2725.09140.2925-8.69815.4720.40958.38930.54080.7288-0.2071-0.1372-0.0217-0.0342-0.49240.1682-0.51910.2040.04330.042-0.0255-0.0012-0.30472.7958-41.024723.4539
286.046-2.99712.85785.8081.70278.2375-0.1097-0.171-0.46070.17530.45160.18970.5896-0.4988-0.34190.0848-0.06040.04980.13330.1001-0.3018-7.2406-54.21189.0656
293.40261.6947-0.21982.9746-1.51575.57520.00230.0297-0.2644-0.1161-0.0857-0.26370.050.69280.0834-0.151-0.00540.0042-0.0431-0.0211-0.02910.9762-74.34951.6252
303.03054.7466-4.37168.1409-9.975520.15870.17330.4408-0.28780.3717-0.11180.2513-0.1318-0.3287-0.0615-0.04070.01740.0522-0.19480.03630.0779-7.1336-83.715366.7385
313.6613-2.6239-6.18815.63360.405114.78560.7842-0.66450.72510.8347-0.4002-1.3197-0.67420.6447-0.384-0.1241-0.0341-0.0818-0.2038-0.08870.49043.781-91.403769.8431
323.4851.45970.15036.56431.52873.108-0.1689-0.0947-0.025-0.6209-0.0282-0.61260.0323-0.00690.1971-0.15380.03210.1111-0.22130.01730.11677.3693-104.795554.3879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA115 - 2309 - 124
2X-RAY DIFFRACTION2AA231 - 244125 - 138
3X-RAY DIFFRACTION3AA245 - 261139 - 155
4X-RAY DIFFRACTION4AA262 - 336156 - 230
5X-RAY DIFFRACTION5BB115 - 2309 - 124
6X-RAY DIFFRACTION6BB231 - 244125 - 138
7X-RAY DIFFRACTION7BB245 - 261139 - 155
8X-RAY DIFFRACTION8BB262 - 336156 - 230
9X-RAY DIFFRACTION9CC115 - 2309 - 124
10X-RAY DIFFRACTION10CC231 - 244125 - 138
11X-RAY DIFFRACTION11CC245 - 261139 - 155
12X-RAY DIFFRACTION12CC262 - 336156 - 230
13X-RAY DIFFRACTION13DD115 - 2309 - 124
14X-RAY DIFFRACTION14DD231 - 244125 - 138
15X-RAY DIFFRACTION15DD245 - 261139 - 155
16X-RAY DIFFRACTION16DD262 - 336156 - 230
17X-RAY DIFFRACTION17EE115 - 2309 - 124
18X-RAY DIFFRACTION18EE231 - 244125 - 138
19X-RAY DIFFRACTION19EE245 - 261139 - 155
20X-RAY DIFFRACTION20EE262 - 336156 - 230
21X-RAY DIFFRACTION21FF115 - 2309 - 124
22X-RAY DIFFRACTION22FF231 - 244125 - 138
23X-RAY DIFFRACTION23FF245 - 261139 - 155
24X-RAY DIFFRACTION24FF262 - 336156 - 230
25X-RAY DIFFRACTION25GG115 - 2309 - 124
26X-RAY DIFFRACTION26GG231 - 244125 - 138
27X-RAY DIFFRACTION27GG245 - 261139 - 155
28X-RAY DIFFRACTION28GG262 - 336156 - 230
29X-RAY DIFFRACTION29HH115 - 2309 - 124
30X-RAY DIFFRACTION30HH231 - 244125 - 138
31X-RAY DIFFRACTION31HH245 - 261139 - 155
32X-RAY DIFFRACTION32HH262 - 336156 - 230

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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