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- PDB-6v37: K2P2.1(TREK-1)I110D:RuR:ML335 bound channel structure -

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Basic information

Entry
Database: PDB / ID: 6v37
TitleK2P2.1(TREK-1)I110D:RuR:ML335 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 / positive regulation of cellular response to hypoxia / chemical synaptic transmission, postsynaptic / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / potassium channel inhibitor activity / astrocyte projection ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / chemical synaptic transmission, postsynaptic / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / potassium channel inhibitor activity / astrocyte projection / negative regulation of DNA biosynthetic process / outward rectifier potassium channel activity / cochlea development / calyx of Held / voltage-gated potassium channel activity / response to axon injury / response to mechanical stimulus / voltage-gated potassium channel complex / axon terminus / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / Schaffer collateral - CA1 synapse / memory / cellular response to hypoxia / postsynapse / G protein-coupled receptor signaling pathway / apical plasma membrane / axon / neuronal cell body / cell surface / endoplasmic reticulum / 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
: / DODECANE / HEXANE / : / Chem-Q6F / Chem-R2R / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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_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 1.2Oct 16, 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)71,21818
Polymers68,6122
Non-polymers2,60616
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-80 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.018, 118.735, 129.036
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
11chain C
21chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain CC40 - 406
211chain DD37 - 408

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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, 18 molecules

#2: Chemical ChemComp-R2R / ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)


Mass: 559.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H28N14O2Ru3 / 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-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#5: Chemical ChemComp-Q6F / N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl)amino]benzamide


Mass: 373.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14Cl2N2O3S
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M KCl, 1-3 mM CdCl2, 0.1 M 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: 2.8→46.5 Å / Num. obs: 25993 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.998 / Net I/σ(I): 13.6
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 2070 / CC1/2: 0.553

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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: 2.8→14.99 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 41.62
RfactorNum. reflection% reflection
Rfree0.3165 1146 4.6 %
Rwork0.2715 --
obs0.2735 24910 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 360.9 Å2 / Biso mean: 146.0202 Å2 / Biso min: 67.75 Å2
Refinement stepCycle: final / Resolution: 2.8→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 167 2 4341
Biso mean--155.45 116.68 -
Num. residues----534
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A23X-RAY DIFFRACTIONPOSITIONAL0.012
12B23X-RAY DIFFRACTIONPOSITIONAL0.012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.930.40651040.44932161226571
2.93-3.080.44311500.413330233173100
3.08-3.270.40351450.365330163161100
3.27-3.520.4061330.328230933226100
3.52-3.870.32011590.284630433202100
3.87-4.420.32191430.26230963239100
4.42-5.520.31131630.273831023265100
5.52-14.990.28981490.244332303379100

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