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- PDB-6v3c: K2P2.1(TREK-1)I110D:Ru360 bound channel structure -

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Basic information

Entry
Database: PDB / ID: 6v3c
TitleK2P2.1(TREK-1)I110D:Ru360 bound channel structure
ComponentsPotassium channel subfamily K member 2
KeywordsMEMBRANE PROTEIN / K channel / TREK-1 / Mus musculus
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
: / HEXANE / : / PENTANE / N-OCTANE / Chem-RU3 / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.2Oct 23, 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

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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)70,19617
Polymers68,6122
Non-polymers1,58415
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-69 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.737, 120.708, 127.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
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 , 7 types, 17 molecules

#2: Chemical ChemComp-RU3 / ruthenium(6+) formate azanide tetraamino(formato-kappaO)oxidoruthenate(1-) (1/1/4/1)


Mass: 436.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H18N8O5Ru2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#6: Chemical ChemComp-LNK / PENTANE


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
#7: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.79 Å3/Da / Density % sol: 67.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M KCl, 1-3 mM CdCl2, 0.1 M HEPES 7-8, 20-25% 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: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.51→46.4 Å / Num. obs: 12595 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 10.8
Reflection shellResolution: 3.51→3.85 Å / Num. unique obs: 530 / CC1/2: 0.149

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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: 3.51→14.98 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 44.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3245 576 4.57 %
Rwork0.3019 12019 -
obs0.3029 12595 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 327.88 Å2 / Biso mean: 203.5724 Å2 / Biso min: 119.59 Å2
Refinement stepCycle: final / Resolution: 3.51→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 67 2 4022
Biso mean--166.92 127.24 -
Num. residues----511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.51-3.850.43751150.43052349246475
3.85-4.40.37761390.360231723311100
4.4-5.50.31991590.332832023361100
5.5-14.980.30891630.27232963459100

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