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- PDB-7lj5: Human TRAAK K+ channel FHIEG mutant A198E in a K+ bound conductiv... -

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Basic information

Entry
Database: PDB / ID: 7lj5
TitleHuman TRAAK K+ channel FHIEG mutant A198E in a K+ bound conductive conformation
Components
  • (ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT ...) x 2
  • Isoform 2 of Potassium channel subfamily K member 4
KeywordsMETAL TRANSPORT/Immune System / Potassium Ion Channel / METAL TRANSPORT / METAL TRANSPORT-Immune System complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / Isoform 2 of Potassium channel subfamily K member 4
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRietmeijer, R.A. / Brohawn, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM123496 United States
CitationJournal: Neuron / Year: 2021
Title: Physical basis for distinct basal and mechanically gated activity of the human K + channel TRAAK.
Authors: Rietmeijer, R.A. / Sorum, B. / Li, B. / Brohawn, S.G.
History
DepositionJan 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 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: Isoform 2 of Potassium channel subfamily K member 4
B: Isoform 2 of Potassium channel subfamily K member 4
D: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN
E: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN
F: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN
G: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,67516
Polymers158,2816
Non-polymers39410
Water4,468248
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)80.160, 136.980, 95.740
Angle α, β, γ (deg.)90.000, 94.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isoform 2 of Potassium channel subfamily K member 4 / TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium ...TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium channel KT4.1 / Two pore K(+) channel KT4.1


Mass: 32627.686 Da / Num. of mol.: 2 / Mutation: A198E, N104Q, N108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK4, TRAAK / Details (production host): pPICz / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: Q9NYG8-2

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Antibody , 2 types, 4 molecules DFEG

#2: Antibody ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN


Mass: 23038.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN


Mass: 23474.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Non-polymers , 3 types, 258 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 50mM Tris pH 8.8, 64-200 mM CaCl2, 27-33 vol vol PEG400

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Data collection

DiffractionMean temperature: 77 K / Ambient temp details: lN2 jet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 29, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.26→95.45 Å / Num. obs: 57752 / % possible obs: 93.8 % / Redundancy: 27.2 % / CC1/2: 0.971 / Net I/σ(I): 10.2
Reflection shellResolution: 2.26→2.504 Å / Redundancy: 12.88 % / Rmerge(I) obs: 2.827 / Mean I/σ(I) obs: 1.508 / Num. unique obs: 2875 / CC1/2: 0.5782 / Rpim(I) all: 0.567 / Rrim(I) all: 2.884 / % possible all: 12

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFE

4wfe


Resolution: 2.26→95.45 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.898 / SU B: 20.721 / SU ML: 0.231 / SU R Cruickshank DPI: 0.5584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.558 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 2846 4.9 %RANDOM
Rwork0.22 ---
obs0.2216 54920 60.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 204.69 Å2 / Biso mean: 69.498 Å2 / Biso min: 22.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20.4 Å2
2--1.45 Å20 Å2
3----2.33 Å2
Refinement stepCycle: final / Resolution: 2.26→95.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10402 0 10 248 10660
Biso mean--80.21 54.75 -
Num. residues----1351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310673
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179733
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.63814550
X-RAY DIFFRACTIONr_angle_other_deg1.2031.56522614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40351341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85222.455448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.516151695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.71542
X-RAY DIFFRACTIONr_chiral_restr0.0570.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022237
LS refinement shellResolution: 2.264→2.345 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4434 --
Rwork0.3276 406 -
obs--4.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3973-0.6323-2.48270.21450.56384.050.29350.33510.0596-0.1627-0.11990.0687-0.36260.4214-0.17350.3875-0.00370.05840.45770.0160.419445.2307-5.52759.586
20.5751-0.30961.34030.2463-0.52516.77330.33860.6724-0.2106-0.4711-0.36860.18391.13390.53050.031.54660.0907-0.07151.212-0.18740.733450.3543-20.0323-21.2043
36.73370.4732-1.85023.13250.58986.1902-0.210.3984-0.8092-0.55950.19940.3450.9522-0.17960.01070.62970.0632-0.01820.6115-0.0460.452145.5415-15.4035-7.0243
42.0574-0.1065-2.01820.5652-0.30514.09260.24560.46250.0673-0.3506-0.11350.028-0.32590.3627-0.13210.3146-0.01820.02570.4340.00660.316948.7242-9.87476.521
57.29198.38894.224112.85942.13435.67490.2692-0.31810.10780.9210.4950.4345-0.0632-0.1003-0.76431.13550.07160.08061.3286-0.09871.13592.0179-3.2825-5.4911
64.40650.5783-1.01685.06311.64796.82930.27140.08150.9574-0.1025-0.0629-0.7633-0.86370.6123-0.20860.6154-0.10120.06720.80350.08630.482665.5551-2.93475.0422
73.187-0.59490.11372.5928-0.26094.15710.07830.28670.2361-0.4359-0.19710.0444-0.4948-0.28680.11880.16690.0596-0.03320.06430.01860.173914.620116.425927.2567
83.70921.93264.51484.18573.68716.6485-0.1610.51860.1698-0.65980.1633-0.1382-0.66220.8545-0.00230.2483-0.09290.02560.2180.02990.307913.188445.378845.6527
92.0731.0663.29773.98373.36326.9758-0.22930.41690.1842-0.40630.1537-0.1201-0.74820.75860.07570.2607-0.03250.07430.25760.0810.299713.835646.55745.9457
102.31750.1311-0.03854.52522.3714.5782-0.0086-0.20440.19530.0989-0.14120.0729-0.11910.12430.14980.0114-0.0133-0.01420.03850.02370.233525.91476.978645.411
111.1625-1.3446-1.41574.33742.32841.90080.0292-0.2610.0432-0.05510.0146-0.0627-0.06390.2457-0.04380.05530.0012-0.05950.0884-0.00890.262721.090720.006249.6877
126.5096-3.45610.62183.8746-0.50062.32550.0821-0.11530.16150.14660.0197-0.1383-0.11090.2863-0.10180.0851-0.0207-0.02540.0414-0.01130.23567.307636.473258.115
133.7073-0.37881.03484.5042-1.2793.08190.1656-0.3349-0.2630.1724-0.1381-0.12860.09620.0657-0.02740.0195-0.0179-0.01390.04280.01640.278230.4472-35.022143.0201
147.98992.62464.01053.31130.85414.99220.41550.3882-0.5725-0.3402-0.00670.07080.5410.0946-0.40870.24810.0494-0.09160.05880.05890.45059.9527-63.07644.0194
1512.53187.01672.83335.77673.29164.62240.14790.1735-0.77510.0530.24730.01710.45890.1074-0.39520.42520.0271-0.17480.07780.09550.641613.3505-71.446247.2194
164.46151.70590.00674.8791-1.61492.34550.01130.1761-0.0225-0.05420.04110.15510.1624-0.0093-0.05240.03590.0019-0.01380.01190.02160.160612.8592-25.6331.0134
173.10931.4994-0.53613.7042-1.09490.9241-0.0009-0.1918-0.3126-0.09510.07090.05860.1482-0.1752-0.070.0301-0.0352-0.04370.06890.01760.29775.7225-44.04441.356
183.8843-0.9071.36664.4229-4.77618.2258-0.0418-0.5182-0.23930.10090.27390.28330.4789-0.4637-0.23220.1645-0.0345-0.06360.1110.01230.367-2.8781-55.545850.4428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 148
2X-RAY DIFFRACTION2A149 - 219
3X-RAY DIFFRACTION3A220 - 286
4X-RAY DIFFRACTION4B28 - 175
5X-RAY DIFFRACTION5B176 - 197
6X-RAY DIFFRACTION6B198 - 287
7X-RAY DIFFRACTION7D1 - 105
8X-RAY DIFFRACTION8D106 - 157
9X-RAY DIFFRACTION9D158 - 211
10X-RAY DIFFRACTION10E1 - 80
11X-RAY DIFFRACTION11E81 - 137
12X-RAY DIFFRACTION12E138 - 217
13X-RAY DIFFRACTION13F1 - 105
14X-RAY DIFFRACTION14F106 - 188
15X-RAY DIFFRACTION15F189 - 211
16X-RAY DIFFRACTION16G1 - 80
17X-RAY DIFFRACTION17G81 - 172
18X-RAY DIFFRACTION18G173 - 216

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