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- PDB-6v3i: K2P2.1(TREK-1)I110D:RuR bound channel structure -

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Basic information

Entry
Database: PDB / ID: 6v3i
TitleK2P2.1(TREK-1)I110D:RuR 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 / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity / negative regulation of DNA biosynthetic process / cochlea development / voltage-gated potassium channel activity / calyx of Held / response to axon injury / voltage-gated potassium channel complex / axon terminus / response to mechanical stimulus / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / memory / cellular response to hypoxia / 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 / : / PENTANE / N-OCTANE / Chem-R2R / 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn_type.id

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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)70,71619
Polymers68,6122
Non-polymers2,10417
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-84 kcal/mol
Surface area30510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.945, 120.303, 127.818
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 83 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 - 320
141(chain A and (resid 46 through 75 or (resid 76...A45 - 320
151(chain A and (resid 46 through 75 or (resid 76...A45 - 320
161(chain A and (resid 46 through 75 or (resid 76...A45 - 320
211(chain B and (resid 46 through 83 or resid 86...B46 - 83
221(chain B and (resid 46 through 83 or resid 86...B86 - 90
231(chain B and (resid 46 through 83 or resid 86...B92 - 93
241(chain B and (resid 46 through 83 or resid 86...B95 - 96
251(chain B and (resid 46 through 83 or resid 86...B37 - 316
261(chain B and (resid 46 through 83 or resid 86...B37 - 316
271(chain B and (resid 46 through 83 or resid 86...B37 - 316
281(chain B and (resid 46 through 83 or resid 86...B37 - 316
291(chain B and (resid 46 through 83 or resid 86...B233 - 253
2101(chain B and (resid 46 through 83 or resid 86...B268
2111(chain B and (resid 46 through 83 or resid 86...B270
2121(chain B and (resid 46 through 83 or resid 86...B0
2131(chain B and (resid 46 through 83 or resid 86...B37 - 316
2141(chain B and (resid 46 through 83 or resid 86...B37 - 316
2151(chain B and (resid 46 through 83 or resid 86...B312 - 31

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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 , 8 types, 19 molecules

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


Mass: 559.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H28N14O2Ru3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-LNK / PENTANE / Pentane


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
#8: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#9: Water ChemComp-HOH / water / 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

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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: 3.81 Å3/Da / Density % sol: 67.69 %
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: 3.39→46.6 Å / Num. obs: 15118 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
3.4-3.676.730530.1281100
9-46.745.69050.999198.8

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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→15 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 44.46
RfactorNum. reflection% reflection
Rfree0.3278 653 4.57 %
Rwork0.2755 --
obs0.2778 14286 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 723.68 Å2 / Biso mean: 193.6429 Å2 / Biso min: 122.23 Å2
Refinement stepCycle: final / Resolution: 3.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 135 2 4207
Biso mean--206.24 125.85 -
Num. residues----526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1732X-RAY DIFFRACTIONPOSITIONAL1.391
12B1732X-RAY DIFFRACTIONPOSITIONAL1.391
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 (%)
3.39-3.650.47481050.46382219232479
3.65-4.010.3991370.372928162953100
4.01-4.580.33191120.289428232935100
4.58-5.710.29981560.287128372993100
5.71-150.32121430.244729383081100

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