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- PDB-7lj4: Human TRAAK K+ channel FHEIG mutant A270P in a K+ bound conductiv... -

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Basic information

Entry
Database: PDB / ID: 7lj4
TitleHuman TRAAK K+ channel FHEIG mutant A270P 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 / homology: / 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: 2.782 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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)158,61116
Polymers158,2176
Non-polymers39410
Water3,387188
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)80.280, 136.880, 95.580
Angle α, β, γ (deg.)90.000, 94.240, 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
11ARGARGVALVALAA28 - 28628 - 286
21ARGARGVALVALBB28 - 28628 - 286
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: 32595.686 Da / Num. of mol.: 2 / Mutation: A270P, 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, 198 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.: 188 / 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: 3.3 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 50 mM Tris pH 8.8, 64-200 mM CaCl2, 27-33%(v/v) PEG400

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen 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: Oct 29, 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: 2.782→47.66 Å / Num. obs: 32708 / % possible obs: 63.22 % / Redundancy: 13.2 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.3906 / Rpim(I) all: 0.1116 / Rrim(I) all: 0.4065 / Net I/σ(I): 4.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.233-47.6596.460.12118.50520430.98310.0350.12699.41
6.518-8.2336.980.16413.38520440.98440.0460.17100
5.683-6.5186.20.20210.10120460.98250.060.211100
5.165-5.6836.710.2189.8620440.98110.0620.22799.95
4.789-5.1656.910.2279.62120430.9830.0640.236100
4.508-4.7896.990.2379.14520440.98230.0660.246100
4.277-4.5087.050.2857.67720460.98240.0790.296100
4.092-4.2776.010.336.20820440.97960.0990.344100
3.929-4.0926.450.4255.28320440.97070.1230.44397.37
3.78-3.9296.710.5734.26120430.95950.1630.59692.05
3.637-3.786.850.634.03220440.95010.1770.65481.78
3.501-3.6376.960.6753.7920460.94840.1880.70173.69
3.37-3.5017.040.9482.89620440.89210.2630.98465.83
3.236-3.377.071.2062.30220440.84120.3331.25255.14
3.087-3.2366.121.5021.75720450.7250.4451.56841.75
2.782-3.0876.632.1671.32320440.55360.6172.25415.03

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Processing

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

4wfe


Resolution: 2.782→47.66 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.853 / SU B: 45.432 / SU ML: 0.404 / SU R Cruickshank DPI: 0.4575 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1619 4.9 %RANDOM
Rwork0.2145 ---
obs0.21668 31089 63.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 235.86 Å2 / Biso mean: 70.366 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.2 Å2
2--2.05 Å2-0 Å2
3----2.1 Å2
Refinement stepCycle: final / Resolution: 2.782→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10398 0 10 188 10596
Biso mean--66.62 39.85 -
Num. residues----1351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310671
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179735
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.63914550
X-RAY DIFFRACTIONr_angle_other_deg1.2491.56522620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28851341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17222.422446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.983151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.531542
X-RAY DIFFRACTIONr_chiral_restr0.0620.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022235
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73350.16
12B73350.16
21D62330.12
22F62330.12
31E62370.11
32G62370.11
LS refinement shellResolution: 2.782→2.881 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4617 --
Rwork0.3992 211 -
obs--4.09 %
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)
12.6096-0.5352-2.56180.3450.07613.97650.26330.3184-0.0715-0.1901-0.19430.1483-0.24370.458-0.0690.4571-0.06470.03020.54340.020.521245.6118-5.51039.4513
20.2353-0.07360.04760.10860.62057.69690.01020.5724-0.1695-0.1367-0.16020.16130.80570.39410.151.57830.1502-0.11921.4433-0.24020.913950.7053-19.6775-21.4899
36.72322.4866-1.69042.11831.12175.57850.05120.5383-0.5418-0.34270.18920.01790.8399-0.3121-0.24041.07990.1794-0.13880.8812-0.01260.785746.0807-15.4621-7.1827
42.4293-0.414-2.210.6811-0.37814.06630.36120.6127-0.0362-0.2721-0.22580.1518-0.44730.2734-0.13540.4547-0.0272-0.0050.6116-0.01840.445949.097-9.83176.334
52.88931.49772.39516.591-0.93323.0055-0.450.4352-0.04730.52770.5165-0.0108-0.2870.2291-0.06650.83710.01940.02730.8401-0.05130.507992.9207-4.2233-5.1264
64.64610.3261-0.50533.47841.64966.34480.3117-0.0570.7989-0.1381-0.2045-0.6416-0.99750.5017-0.10720.8564-0.08280.01050.88540.17790.628866.0072-3.03674.9891
73.1168-0.9698-0.61752.88460.24855.01250.03420.3670.203-0.5502-0.20170.0521-0.6602-0.36030.16740.26870.0295-0.01310.08160.03520.344314.745316.31227.1179
84.24152.8033.86693.69343.91116.4443-0.21220.59350.2934-0.85950.2816-0.0698-1.07781.0653-0.06940.4543-0.07620.04020.30940.08790.483913.25845.287645.7234
92.85390.95943.73813.33733.84037.4356-0.2780.49730.2147-0.28180.2473-0.1809-0.74290.96050.03070.5106-0.08120.05170.35240.13890.460813.828146.496946.0367
103.68360.4947-0.2454.62792.82775.6428-0.0849-0.05320.26680.2680.13270.2331-0.17670.2047-0.04780.09020.01860.02840.02720.05580.362925.94076.889445.2217
110.9328-1.0762-1.08634.34272.3182.1505-0.0069-0.2580.08410.27530.0617-0.1560.01280.3079-0.05480.12070.020.01610.14460.05680.346421.273119.915149.6088
126.5469-3.22771.70964.0295-1.08442.75430.2453-0.14920.16950.099-0.0958-0.05540.0380.3164-0.14960.2535-0.0589-0.00790.1436-0.00450.34627.442436.392658.122
134.3037-0.17790.37333.8858-1.27073.98070.2169-0.3684-0.46020.1826-0.1158-0.22510.09490.0144-0.10110.1551-0.02970.00080.03880.01450.453630.783-35.058542.7908
147.55382.66353.69013.44451.04093.8260.49920.726-0.4063-0.3081-0.0877-0.04340.5040.2368-0.41150.45650.0865-0.08720.15730.08180.542210.1401-63.135843.8873
157.33226.02141.0477.57712.46495.45210.60380.2272-0.37810.30560.10430.4210.785-0.1322-0.70810.64880.0077-0.22460.08760.08390.960513.6522-71.512746.9568
165.95761.7370.49645.5209-0.65532.23890.06840.1810.01180.16850.02840.19980.29930.0521-0.09680.2219-0.00010.03570.06280.05750.22513.1428-25.713730.9128
172.89881.498-0.50183.1806-0.60210.85310.0593-0.1686-0.3836-0.1025-0.0489-0.0190.2024-0.1717-0.01050.1299-0.00880.01330.10670.02070.44065.9855-44.151741.1124
182.1873-1.00071.17044.1523-4.25998.88960.0093-0.3187-0.13960.02390.11860.17880.4754-0.0518-0.12790.1962-0.0553-0.04550.2662-0.0040.5391-2.6216-55.654850.2806
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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