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- PDB-6cq6: K2P2.1(TREK-1) apo structure -

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Basic information

Entry
Database: PDB / ID: 6cq6
TitleK2P2.1(TREK-1) apo structure
ComponentsPotassium channel subfamily K member 2
KeywordsTRANSPORT PROTEIN / TREK-1 ion channel K2P
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / cellular response to arachidonate / mechanosensitive potassium channel activity / negative regulation of DNA biosynthetic process / positive regulation of cellular response to hypoxia / detection of mechanical stimulus involved in sensory perception of touch / chemical synaptic transmission, postsynaptic / stabilization of membrane potential / cardiac ventricle development ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / cellular response to arachidonate / mechanosensitive potassium channel activity / negative regulation of DNA biosynthetic process / positive regulation of cellular response to hypoxia / detection of mechanical stimulus involved in sensory perception of touch / chemical synaptic transmission, postsynaptic / stabilization of membrane potential / cardiac ventricle development / negative regulation of cardiac muscle cell proliferation / ligand-gated channel activity / potassium ion leak channel activity / node of Ranvier / outward rectifier potassium channel activity / glutamate secretion / astrocyte projection / regulation of synaptic transmission, GABAergic / cochlea development / voltage-gated potassium channel activity / response to axon injury / neuronal action potential / voltage-gated potassium channel complex / chloride transmembrane transport / calyx of Held / regulation of membrane potential / postsynaptic density membrane / sarcolemma / potassium ion transport / Schaffer collateral - CA1 synapse / memory / cellular response to hypoxia / apical plasma membrane / G protein-coupled receptor signaling pathway / protein heterodimerization activity / neuronal cell body / dendrite / cell surface / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TREK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DECANE / : / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLolicato, M. / Minor, D.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) United States
American Heart Association United States
CitationJournal: Nature / Year: 2017
Title: K2P2.1 (TREK-1)-activator complexes reveal a cryptic selectivity filter binding site.
Authors: Lolicato, M. / Arrigoni, C. / Mori, T. / Sekioka, Y. / Bryant, C. / Clark, K.A. / Minor, D.L.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 28, 2018ID: 5VK5
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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_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 / _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_conn.ptnr2_symmetry
Revision 1.5Nov 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 2
B: Potassium channel subfamily K member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,31819
Polymers68,6082
Non-polymers1,71017
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-66 kcal/mol
Surface area31510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.718, 120.417, 126.440
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 2 / Outward rectifying potassium channel protein TREK-1 / TREK-1 K(+) channel subunit / Two pore ...Outward rectifying potassium channel protein TREK-1 / TREK-1 K(+) channel subunit / Two pore potassium channel TPKC1


Mass: 34303.938 Da / Num. of mol.: 2
Mutation: K65R, Q66E, T67K, I69L, A70R, Q71A, A73P, N76S, S77D, T78Q, S281A, E287A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnk2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P97438
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22
Has protein modificationY

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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: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22-25% PEG400, 100mM HEPES pH=8.0, 1mM CdCl2, 200mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 3.1→15 Å / Num. obs: 18913 / % possible obs: 97 % / Redundancy: 6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 0.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2574

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHASERphasing
Aimlessdata scaling
Cootmodel building
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RUE

4rue


Resolution: 3.1→14.965 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.75
RfactorNum. reflection% reflection
Rfree0.3022 905 4.89 %
Rwork0.2604 --
obs0.2622 18506 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→14.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 74 0 4363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034453
X-RAY DIFFRACTIONf_angle_d0.5396029
X-RAY DIFFRACTIONf_dihedral_angle_d6.0982539
X-RAY DIFFRACTIONf_chiral_restr0.038707
X-RAY DIFFRACTIONf_plane_restr0.004726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29230.44231270.39522574X-RAY DIFFRACTION87
3.2923-3.54340.39671700.35382942X-RAY DIFFRACTION100
3.5434-3.89430.29691750.28652939X-RAY DIFFRACTION100
3.8943-4.44480.31541580.24452984X-RAY DIFFRACTION100
4.4448-5.5520.30641420.25833019X-RAY DIFFRACTION100
5.552-14.9650.26691330.24093143X-RAY DIFFRACTION100

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