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- PDB-6pis: Mouse two pore domain K+ channel TRAAK (K2P4.1) - Fab complex str... -

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Basic information

Entry
Database: PDB / ID: 6pis
TitleMouse two pore domain K+ channel TRAAK (K2P4.1) - Fab complex structure
Components
  • ANTIBODY FAB FRAGMENT HEAVY CHAIN
  • ANTIBODY FAB FRAGMENT LIGHT CHAIN
  • Potassium channel subfamily K member 4
KeywordsION TRANSPORT / MEMBRANE PROTEIN / POTASSIUM ION CHANNEL
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / temperature-gated cation channel activity / mechanosensitive potassium channel activity / sensory perception of temperature stimulus / potassium channel complex / stabilization of membrane potential / detection of mechanical stimulus involved in sensory perception of touch / cellular response to alkaline pH / potassium ion leak channel activity ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / temperature-gated cation channel activity / mechanosensitive potassium channel activity / sensory perception of temperature stimulus / potassium channel complex / stabilization of membrane potential / detection of mechanical stimulus involved in sensory perception of touch / cellular response to alkaline pH / potassium ion leak channel activity / cellular response to temperature stimulus / outward rectifier potassium channel activity / cellular response to fatty acid / potassium channel activity / sensory perception of pain / potassium ion transmembrane transport / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TRAAK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Two pore domain potassium channel, TRAAK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Potassium channel subfamily K member 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Cricetulus migratorius (Armenian hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.77 Å
AuthorsBrohawn, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2019
Title: The mechanosensitive ion channel TRAAK is localized to the mammalian node of Ranvier.
Authors: Brohawn, S.G. / Wang, W. / Handler, A. / Campbell, E.B. / Schwarz, J.R. / MacKinnon, R.
History
DepositionJun 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Data collection / Derived calculations / Category: reflns_shell / struct_conn
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all / _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 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Potassium channel subfamily K member 4
B: Potassium channel subfamily K member 4
L: ANTIBODY FAB FRAGMENT LIGHT CHAIN
H: ANTIBODY FAB FRAGMENT HEAVY CHAIN
I: ANTIBODY FAB FRAGMENT HEAVY CHAIN
M: ANTIBODY FAB FRAGMENT LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,81012
Polymers162,5766
Non-polymers2356
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.450, 154.510, 202.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12L
22M
13H
23I

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUAA28 - 28428 - 284
21ARGARGLEULEUBB28 - 28428 - 284
12ASPASPASNASNLC1 - 2111 - 211
22ASPASPASNASNMF1 - 2111 - 211
13GLNGLNPROPROHD1 - 2241 - 224
23GLNGLNPROPROIE1 - 2241 - 224

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Potassium channel subfamily K member 4 / TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK


Mass: 33725.898 Da / Num. of mol.: 2 / Mutation: N107Q, N110Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnk4, Traak / Production host: Komagataella pastoris (fungus) / References: UniProt: O88454
#2: Antibody ANTIBODY FAB FRAGMENT LIGHT CHAIN


Mass: 23526.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cricetulus migratorius (Armenian hamster)
#3: Antibody ANTIBODY FAB FRAGMENT HEAVY CHAIN


Mass: 24035.871 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cricetulus migratorius (Armenian hamster)
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM Sodium Citrate pH 5.5 500 mM KCl 12% PEG4000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→122.91 Å / Num. obs: 26117 / % possible obs: 98.7 % / Redundancy: 13.384 % / Biso Wilson estimate: 118.358 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.483 / Rrim(I) all: 0.502 / Χ2: 0.983 / Net I/σ(I): 3.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured obsNum. possibleNum. unique obs% possible allMean I/σ(I) obsCC1/2Rmerge(I) obsRrim(I) all
2.6-2.675.068235295194464389.4
2.67-2.748.98437075025486796.9
2.74-2.8212.06586484921486398.8
2.82-2.9113.961665804799476999.4
2.91-314.829680664611459099.50.180.184
3-3.1114.929666004489446199.40.360.326
3.11-3.2214.985651394368434799.50.530.4577.8368.112
3.22-3.3614.987622424165415399.70.890.7584.764.928
3.36-3.514.949594683996397899.51.260.9273.1513.263
3.5-3.6814.94574593861384699.61.790.922.1962.274
3.68-3.8714.883544133661365699.92.550.9591.3981.448
3.87-4.1114.83514323472346899.93.530.9760.9350.968
4.11-4.3914.767482883275327099.85.130.990.5770.598
4.39-4.7514.59144677306330621007.230.9910.3770.39
4.75-5.214.46441005283528351008.560.9920.3250.337
5.2-5.8114.39936876256125611009.40.9920.290.3
5.81-6.7114.137324862298229810011.040.9940.2310.239
6.71-8.2213.596266071957195710017.040.9970.1320.137
8.22-11.6212.949199161538153810024.460.9980.0860.089
11.62-122.9111.751105769189009825.720.9970.0710.074

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.91 Å122.91 Å
Translation7.91 Å122.91 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSMarch 15, 2019data reduction
XSCALEMarch 15, 2019data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFE

4wfe


Resolution: 2.77→122.91 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.851 / SU B: 22.79 / SU ML: 0.436 / Cross valid method: THROUGHOUT / ESU R Free: 0.679 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2863 1287 4.9 %RANDOM
Rwork0.24843 ---
obs0.2503 24830 44.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---1.55 Å20 Å2
3---1.79 Å2
Refinement stepCycle: 1 / Resolution: 2.77→122.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10244 0 6 0 10250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01410517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179484
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.64614339
X-RAY DIFFRACTIONr_angle_other_deg0.7081.62922142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.50951313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.19222.692442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9151536
X-RAY DIFFRACTIONr_chiral_restr0.0440.21399
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211635
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022069
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7678.3895288
X-RAY DIFFRACTIONr_mcbond_other4.7668.3895287
X-RAY DIFFRACTIONr_mcangle_it7.92212.5746589
X-RAY DIFFRACTIONr_mcangle_other7.92112.5746590
X-RAY DIFFRACTIONr_scbond_it4.4068.5165229
X-RAY DIFFRACTIONr_scbond_other4.4028.5165227
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.61612.6997750
X-RAY DIFFRACTIONr_long_range_B_refined11.79199.44211812
X-RAY DIFFRACTIONr_long_range_B_other11.7999.44411813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A70660.09
12B70660.09
21L63310.08
22M63310.08
31H64110.06
32I64110.06
LS refinement shellResolution: 2.77→2.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 8 -
Rwork0.502 105 -
obs--2.65 %

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