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- PDB-6v36: K2P2.1(TREK-1)I110D apo channel structure -

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Basic information

Entry
Database: PDB / ID: 6v36
TitleK2P2.1(TREK-1)I110D apo channel structure
ComponentsPotassium channel subfamily K member 2
KeywordsMEMBRANE PROTEIN / potassium channel / TREK-1 / K2P channel / mouse
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
: / : / N-OCTANE / UNDECANE / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPope, L. / Lolicato, M. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)NIH-R01-MH093603 United States
CitationJournal: Cell Chem Biol / Year: 2020
Title: Polynuclear Ruthenium Amines Inhibit K2PChannels via a "Finger in the Dam" Mechanism.
Authors: Pope, L. / Lolicato, M. / Minor Jr., D.L.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)69,83916
Polymers68,6122
Non-polymers1,22714
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-80 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.192, 120.400, 128.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 46 through 75 or (resid 76...
21(chain B and (resid 46 through 84 or resid 86...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 46 through 75 or (resid 76...A46 - 75
121(chain A and (resid 46 through 75 or (resid 76...A76
131(chain A and (resid 46 through 75 or (resid 76...A45 - 321
141(chain A and (resid 46 through 75 or (resid 76...A45 - 321
151(chain A and (resid 46 through 75 or (resid 76...A45 - 321
161(chain A and (resid 46 through 75 or (resid 76...A45 - 321
211(chain B and (resid 46 through 84 or resid 86...B46 - 84
221(chain B and (resid 46 through 84 or resid 86...B86 - 88
231(chain B and (resid 46 through 84 or resid 86...B90 - 93
241(chain B and (resid 46 through 84 or resid 86...B99 - 100
251(chain B and (resid 46 through 84 or resid 86...B102 - 112
261(chain B and (resid 46 through 84 or resid 86...B126 - 133
271(chain B and (resid 46 through 84 or resid 86...B135 - 184
281(chain B and (resid 46 through 84 or resid 86...B186 - 190
291(chain B and (resid 46 through 84 or resid 86...B192 - 1931
2101(chain B and (resid 46 through 84 or resid 86...B233 - 268
2111(chain B and (resid 46 through 84 or resid 86...B270268
2121(chain B and (resid 46 through 84 or resid 86...B270
2131(chain B and (resid 46 through 84 or resid 86...B272 - 294
2141(chain B and (resid 46 through 84 or resid 86...B296
2151(chain B and (resid 46 through 84 or resid 86...B298 - 300
2161(chain B and (resid 46 through 84 or resid 86...B303 - 310
2171(chain B and (resid 46 through 84 or resid 86...B312 - 314
2181(chain B and (resid 46 through 84 or resid 86...B316

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel subfamily K member 2


Mass: 34305.867 Da / Num. of mol.: 2 / Mutation: I110D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus) / References: UniProt: P97438*PLUS

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Non-polymers , 5 types, 17 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M KCl, 1-3 mM CdCl2, HEPES pH 7-8, 20-26% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.4→46.7 Å / Num. obs: 14468 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 9.6
Reflection shellResolution: 3.4→3.67 Å / Num. unique obs: 1096 / CC1/2: 0.128

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RUE

4rue


Resolution: 3.4→14.98 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 46.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3179 742 5.13 %
Rwork0.2858 13726 -
obs0.2876 14468 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 459.12 Å2 / Biso mean: 218.5154 Å2 / Biso min: 116.46 Å2
Refinement stepCycle: final / Resolution: 3.4→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 54 3 4091
Biso mean--186.2 162.74 -
Num. residues----518
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1712X-RAY DIFFRACTIONPOSITIONAL0.308
12B1712X-RAY DIFFRACTIONPOSITIONAL0.308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.660.45251310.42012366249785
3.66-4.020.3611310.351728292960100
4.02-4.590.321470.27127922939100
4.59-5.720.3441660.31928232989100
5.72-14.980.29871670.263929163083100

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