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- PDB-4wfh: Human TRAAK K+ channel in a Tl+ bound nonconductive conformation -

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Basic information

Entry
Database: PDB / ID: 4wfh
TitleHuman TRAAK K+ channel in a Tl+ bound nonconductive conformation
Components
  • (ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT ...) x 2
  • Potassium channel subfamily K member 4
KeywordsMETAL TRANSPORT / Mechanosensitive ion channel / two-pore domain potassium ion channel / membrane protein
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / cellular response to arachidonate / temperature-gated cation channel activity / mechanosensitive potassium channel activity / sensory perception of temperature stimulus / potassium channel complex / detection of mechanical stimulus involved in sensory perception of touch / cellular response to alkaline pH / response to ultrasound / Phase 4 - resting membrane potential ...TWIK related potassium channel (TREK) / cellular response to arachidonate / temperature-gated cation channel activity / mechanosensitive potassium channel activity / sensory perception of temperature stimulus / potassium channel complex / detection of mechanical stimulus involved in sensory perception of touch / cellular response to alkaline pH / response to ultrasound / Phase 4 - resting membrane potential / potassium ion leak channel activity / cellular response to temperature stimulus / cellular response to acidic pH / node of Ranvier / outward rectifier potassium channel activity / cellular response to fatty acid / potassium channel activity / neuronal action potential / sensory perception of pain / potassium ion transmembrane transport / potassium ion transport / memory / cellular response to mechanical stimulus / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TRAAK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Two pore domain potassium channel, TRAAK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DECANE / THALLIUM (I) ION / Potassium channel subfamily K member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.01 Å
AuthorsBrohawn, S.G. / MacKinnon, R.
CitationJournal: Nature / Year: 2014
Title: Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel.
Authors: Brohawn, S.G. / Campbell, E.B. / MacKinnon, R.
History
DepositionSep 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _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_symmetry / _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 / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _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_conn.ptnr2_symmetry / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium channel subfamily K member 4
B: Potassium channel subfamily K member 4
D: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN
E: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN
F: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN
G: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,85817
Polymers158,1656
Non-polymers1,69311
Water3,315184
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.972, 138.755, 96.759
Angle α, β, γ (deg.)90.00, 94.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22F
13E
23G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGALAALAAA28 - 27328 - 273
21ARGARGALAALABB28 - 27328 - 273
12GLNGLNASNASNDC1 - 2111 - 211
22GLNGLNASNASNFE1 - 2111 - 211
13GLUGLUPROPROED1 - 2151 - 215
23GLUGLUPROPROGF1 - 2151 - 215

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel subfamily K member 4 / TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium ...TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium channel KT4.1 / Two pore K(+) channel KT4.1


Mass: 32569.650 Da / Num. of mol.: 2 / Mutation: N104Q, N108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK4, TRAAK / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9NYG8

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Antibody , 2 types, 4 molecules DFEG

#2: Antibody ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN


Mass: 23038.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN


Mass: 23474.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 195 molecules

#4: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Tl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 50 MM TRIS PH 8.8, 200 MM CA(NO3)2, 27-30% (VOL/VOL) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9781 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 3→48.2 Å / Num. obs: 39746 / % possible obs: 100 % / Redundancy: 10.5 % / Net I/σ(I): 11.3
Reflection shellResolution: 3→3.05 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 0.6 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementResolution: 3.01→48.2 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.917 / SU B: 47.469 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 2098 5 %RANDOM
Rwork0.20321 ---
obs0.20502 39746 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 112.451 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å23.38 Å2
2---3.27 Å20 Å2
3---3.22 Å2
Refinement stepCycle: 1 / Resolution: 3.01→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10302 0 20 184 10506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0210580
X-RAY DIFFRACTIONr_bond_other_d0.0010.029860
X-RAY DIFFRACTIONr_angle_refined_deg0.9081.95514415
X-RAY DIFFRACTIONr_angle_other_deg0.608322756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70751328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47523.731402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.735151676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.321541
X-RAY DIFFRACTIONr_chiral_restr0.0530.21642
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111839
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022392
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9235.2645345
X-RAY DIFFRACTIONr_mcbond_other4.9225.2645344
X-RAY DIFFRACTIONr_mcangle_it7.5637.8926662
X-RAY DIFFRACTIONr_mcangle_other7.5627.8936663
X-RAY DIFFRACTIONr_scbond_it5.6375.6745235
X-RAY DIFFRACTIONr_scbond_other5.6375.6765236
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6868.3427754
X-RAY DIFFRACTIONr_long_range_B_refined13.56850.71943753
X-RAY DIFFRACTIONr_long_range_B_other13.56950.72143754
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A122650.14
12B122650.14
21D111820.1
22F111820.1
31E114730.1
32G114730.1
LS refinement shellResolution: 3.01→3.088 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 130 -
Rwork0.371 2602 -
obs--87.73 %
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)
14.1055-1.0816-3.64610.3710.61585.1570.46350.45580.0716-0.1477-0.22390.121-0.50480.3811-0.23970.5772-0.03750.17530.40510.0620.793644.264-5.83510.095
20.3435-0.15570.03640.1686-0.91111.64790.03310.6231-0.2077-0.2798-0.29160.14621.17680.2640.25851.51270.1330.07171.1618-0.21771.015749.951-20.415-20.775
37.9924-0.5254-1.4147.0066-0.0514.1332-0.41320.9908-0.7603-0.80160.19240.06531.025-0.48180.22090.8520.132-0.07020.8238-0.11460.73845.668-16.753-6.594
44.0644-0.4037-3.87860.8048-0.88996.30130.51340.43510.1694-0.2245-0.29210.0446-0.5480.3513-0.22130.5471-0.05680.12330.4533-0.02280.695647.875-10.1557.327
53.9721.21471.736210.8047-3.75712.5272-0.59030.15390.0662-0.12550.74290.2507-0.2523-0.198-0.15261.36460.0550.07151.6981-0.17891.492792.149-4.559-4.801
67.15371.25242.35012.962-1.23268.80840.68860.27180.9910.1049-0.2106-1.014-1.33281.0909-0.47790.8679-0.08470.23050.86880.0661.098164.37-2.7275.524
73.8983-1.71571.0125.85090.14267.3612-0.15170.32750.432-0.9641-0.35240.3129-0.9861-0.36640.50410.40270.0779-0.07220.0621-0.00050.520114.17816.47627.064
86.39194.28826.73846.28465.96989.0235-0.18020.68510.3258-1.1856-0.17390.1891-0.64360.9050.3540.58470.1849-0.09040.34610.04610.879612.92746.38746.137
94.38652.38623.16537.18495.20827.82040.0550.58130.3764-0.6427-0.22860.1252-0.62850.45330.17360.6150.0911-0.02320.16860.0430.868813.41147.4646.114
103.4398-0.75920.22376.84834.53888.1152-0.3318-0.15250.22060.38890.00260.2396-0.1010.48930.32920.0773-0.00950.0630.06710.05260.504324.9366.52745.274
111.1341-1.6062-1.55967.53723.29772.39270.1424-0.31240.0139-0.2428-0.3040.4007-0.24230.26630.16160.19230.0283-0.02040.2149-0.04550.590319.32522.13749.269
1210.1407-5.317-0.1726.57341.12852.70470.1589-0.42140.07710.1387-0.11860.6478-0.2445-0.1585-0.04030.2398-0.04-0.01740.0564-0.08550.81977.3237.12758.26
135.81660.0860.11757.6275-2.7713.28420.0265-0.2783-0.48230.2843-0.0619-0.43580.02910.09550.03540.03860.00330.06760.02120.00720.626429.728-34.98442.241
145.41132.66112.62122.69081.17023.4780.09530.5331-0.2636-0.32080.0493-0.15570.37810.0416-0.14460.49380.0927-0.04230.26710.11480.82998.795-63.20743.936
150.24790.94090.36896.0902-0.50053.31720.3524-0.1418-0.05180.3699-0.17430.42631.6169-0.011-0.1781.0146-0.1322-0.14850.49530.07741.540611.876-72.05646.651
166.67352.6313-0.7937.3077-0.96073.4119-0.03120.3637-0.0561-0.15290.22930.6071-0.0178-0.193-0.1980.0750.04810.04340.06240.04870.430511.773-25.2431.134
174.36343.141-1.35725.7205-1.19130.9337-0.0506-0.0185-0.7631-0.01830.01970.06020.1605-0.18650.0310.0497-0.05450.02460.07410.07180.9675.005-45.08542.035
183.1725-0.63411.91495.3415-4.72628.8657-0.2105-0.3566-0.02630.10420.21630.24930.2779-0.37-0.00580.2491-0.04810.00350.37770.02750.746-3.539-55.61750.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 148
2X-RAY DIFFRACTION2A149 - 219
3X-RAY DIFFRACTION3A220 - 286
4X-RAY DIFFRACTION4B28 - 175
5X-RAY DIFFRACTION5B176 - 197
6X-RAY DIFFRACTION6B198 - 274
7X-RAY DIFFRACTION7D1 - 105
8X-RAY DIFFRACTION8D106 - 157
9X-RAY DIFFRACTION9D158 - 211
10X-RAY DIFFRACTION10E1 - 80
11X-RAY DIFFRACTION11E81 - 137
12X-RAY DIFFRACTION12E138 - 217
13X-RAY DIFFRACTION13F1 - 105
14X-RAY DIFFRACTION14F106 - 188
15X-RAY DIFFRACTION15F189 - 211
16X-RAY DIFFRACTION16G1 - 80
17X-RAY DIFFRACTION17G81 - 172
18X-RAY DIFFRACTION18G173 - 216

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