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- PDB-4ruf: Human K2P4.1 (TRAAAK) potassium channel, W262S mutant -

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Basic information

Entry
Database: PDB / ID: 4ruf
TitleHuman K2P4.1 (TRAAAK) potassium channel, W262S mutant
ComponentsPotassium channel subfamily K member 4
KeywordsMETAL TRANSPORT / TRAAK POTASSIUM ION CHANNEL
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Potassium channel subfamily K member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLolicato, M. / Minor, D.L.Jr.
CitationJournal: Neuron / Year: 2014
Title: Transmembrane Helix Straightening and Buckling Underlies Activation of Mechanosensitive and Thermosensitive K2P Channels.
Authors: Lolicato, M. / Riegelhaupt, P.M. / Arrigoni, C. / Clark, K.A. / Minor, D.L.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 22, 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_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
Revision 1.4Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2088
Polymers66,9732
Non-polymers2356
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-98 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.053, 127.982, 130.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: 33486.672 Da / Num. of mol.: 2 / Fragment: UNP residues 1-300 / Mutation: W262S, N104Q, N108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK4, TRAAK / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: Q9NYG8
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 5.49 Å3/Da / Density % sol: 77.58 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG400, 10mM Sarcosine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.4→48.31 Å / Num. obs: 38349 / % possible obs: 100 %
Reflection shellResolution: 3.4→3.67 Å / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I9W

4i9w


Resolution: 3.4→14.993 Å / SU ML: 0.7 / σ(F): 0.12 / Phase error: 46.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3283 1911 4.98 %
Rwork0.2971 --
obs0.2988 38347 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→14.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 6 0 3923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034017
X-RAY DIFFRACTIONf_angle_d0.8525472
X-RAY DIFFRACTIONf_dihedral_angle_d18.2292392
X-RAY DIFFRACTIONf_chiral_restr0.026638
X-RAY DIFFRACTIONf_plane_restr0.006683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.48410.43871180.42422638X-RAY DIFFRACTION100
3.4841-3.57710.5012950.44282697X-RAY DIFFRACTION100
3.5771-3.68080.52081250.47342582X-RAY DIFFRACTION98
3.6808-3.79780.47661270.41842584X-RAY DIFFRACTION99
3.7978-3.93120.44751120.41192622X-RAY DIFFRACTION99
3.9312-4.08550.40851270.37632636X-RAY DIFFRACTION99
4.0855-4.26740.40451850.3472543X-RAY DIFFRACTION98
4.2674-4.48660.38471290.33032575X-RAY DIFFRACTION98
4.4866-4.75930.32631540.29612558X-RAY DIFFRACTION98
4.7593-5.11320.3511750.26172541X-RAY DIFFRACTION98
5.1132-5.60320.27391460.28252601X-RAY DIFFRACTION100
5.6032-6.35920.3711450.32082609X-RAY DIFFRACTION100
6.3592-7.81810.33141230.28552648X-RAY DIFFRACTION100
7.8181-14.99360.24191500.2152604X-RAY DIFFRACTION100

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