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- PDB-7ljb: Human TRAAK K+ channel mutant G158D in a K+ bound conductive conf... -

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Basic information

Entry
Database: PDB / ID: 7ljb
TitleHuman TRAAK K+ channel mutant G158D 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: 2.97 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
Citation
Journal: 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.
#1: Journal: Biorxiv / 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 / citation_author / database_2
Item: _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 / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.journal_id_ISSN / _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 1.4Nov 6, 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: 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)158,63615
Polymers158,2816
Non-polymers3559
Water3,621201
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)80.140, 137.310, 96.300
Angle α, β, γ (deg.)90.000, 94.720, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22F
13E
23G

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 - 28328 - 283
21ARGARGLEULEUBB28 - 28328 - 283
12GLNGLNASNASNDC1 - 2111 - 211
22GLNGLNASNASNFE1 - 2111 - 211
13GLUGLUPROPROED1 - 2151 - 215
23GLUGLUPROPROGF1 - 2151 - 215

NCS ensembles :
ID
1
2
3

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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: G158D, 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, 210 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / 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.: 201 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
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: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 26, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.97→48.03 Å / Num. obs: 31745 / % possible obs: 93.6 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.207 / Net I/σ(I): 8.5
Reflection shellResolution: 2.97→3.232 Å / Redundancy: 6.22 % / Rmerge(I) obs: 2.023 / Mean I/σ(I) obs: 1.234 / Num. unique obs: 1984 / CC1/2: 0.5668 / Rpim(I) all: 0.597 / Rrim(I) all: 2.109 / % possible all: 21.23

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFF

4wff


Resolution: 2.97→48.03 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.888 / SU B: 45.647 / SU ML: 0.381 / SU R Cruickshank DPI: 0.4568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1575 5 %RANDOM
Rwork0.1958 ---
obs0.1981 30170 74.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 254.61 Å2 / Biso mean: 99.553 Å2 / Biso min: 40.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20.08 Å2
2--0.94 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 2.97→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10376 0 9 201 10586
Biso mean--104.16 79.97 -
Num. residues----1347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310647
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179704
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.63814515
X-RAY DIFFRACTIONr_angle_other_deg1.2171.56522547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07751337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20222.455448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.462151690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7791542
X-RAY DIFFRACTIONr_chiral_restr0.060.21419
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022233
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A71590.15
12B71590.15
21D61970.12
22F61970.12
31E60420.14
32G60420.14
LS refinement shellResolution: 2.971→3.048 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 7 -
Rwork0.339 179 -
all-186 -
obs--5.88 %
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)
13.5791-1.2393-3.21260.56720.68614.75010.37450.40650.0833-0.1181-0.25120.0867-0.47780.4658-0.12340.4553-0.0820.04270.51250.130.285344.985-5.6259.733
20.22470.10.82160.14740.84888.09880.00840.4765-0.0126-0.17260.03820.10070.70470.5378-0.04661.45220.1276-0.05621.3494-0.10340.630549.975-19.924-21.071
39.10540.1848-2.21914.30870.30974.3507-0.21050.6613-0.5564-0.2970.1671-0.13970.893-0.37470.04340.76320.1402-0.09410.87250.0060.487546.139-15.966-7.228
43.382-0.3516-2.72710.8491-0.49784.7710.25110.70010.1788-0.2838-0.09750.0462-0.41290.2482-0.15360.4809-0.02550.04470.53660.06480.214848.663-10.0866.65
56.57732.5004-0.00248.4327-2.26940.7596-0.55430.71450.04520.50780.6203-0.2903-0.0535-0.0184-0.0660.9910.0028-0.06230.9773-0.01240.712991.968-4.061-4.538
66.36020.3568-0.11112.9151-0.93824.05960.29570.11621.0902-0.03330.009-0.7776-1.04230.8239-0.30470.8851-0.12720.1230.92090.1190.607865.234-1.7325.25
74.0054-1.12070.53863.498-0.11086.4784-0.00960.4120.2509-0.6323-0.30730.1609-0.7867-0.1550.31690.29690.0482-0.05290.07570.02730.126914.28616.2727.233
84.26522.66664.895.26415.15037.0154-0.24560.68820.2212-0.91250.20.0241-0.62240.81490.04570.36940.0369-0.08420.29870.02140.286313.10845.46945.799
93.59281.73163.47935.21693.54376.6363-0.18930.41110.3783-0.42070.14170.0078-0.52640.59690.04760.4417-0.0127-0.0080.20540.06020.311113.77946.58346.057
104.4048-0.68721.1784.57382.19726.7347-0.0786-0.17370.08130.3093-0.04310.1196-0.13810.40190.12180.09870.02130.07140.09250.05610.146825.4056.76245.383
111.1563-1.3766-1.53046.69823.07072.34830.0537-0.4315-0.00610.1841-0.0416-0.1428-0.04790.4313-0.01210.1394-0.0077-0.0030.25270.06230.102620.86119.83849.655
128.2786-3.80281.3394.0454-0.41313.77980.3409-0.29360.19210.0321-0.14150.03260.20.1173-0.19940.2962-0.0607-0.03760.0874-0.06960.2257.29336.58658.087
136.0039-0.17190.28794.4933-1.1793.16730.1082-0.2135-0.68870.0845-0.1682-0.34490.14460.05970.05990.120.00320.02130.01660.02540.347530.049-35.17542.86
148.1623.26294.42554.17771.50564.26830.35450.5527-0.6586-0.6365-0.0155-0.14550.37020.0744-0.3390.41910.0688-0.10960.11190.05230.61699.316-63.28244.224
158.46686.25293.51247.03461.94446.01190.40930.2867-0.40480.27380.10710.26530.683-0.1232-0.51640.64520.0985-0.20750.19310.01780.839912.825-71.49847.418
166.82561.70130.78365.3363-0.63333.4436-0.02740.3594-0.07570.00310.03250.3690.18010.0036-0.0050.18380.03980.07960.08880.0470.089612.335-25.8731.136
173.49611.9375-0.72523.0156-0.72170.42080.0476-0.007-0.5644-0.0292-0.0375-0.0120.1156-0.1093-0.010.19360.0138-0.00430.12210.01920.3375.297-44.20341.441
183.5506-1.52492.69895.5912-5.11768.4554-0.0698-0.5621-0.19330.10410.28910.23450.4059-0.0835-0.21930.1969-0.0307-0.07550.23970.05810.5676-3.186-55.60550.684
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 - 284
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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