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- PDB-4i9w: Human two pore domain K+ channel TRAAK (K2P4.1) - Fab complex str... -

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Basic information

Entry
Database: PDB / ID: 4i9w
TitleHuman two pore domain K+ channel TRAAK (K2P4.1) - Fab complex structure
Components
  • (ANTIBODY FAB FRAGMENT ...) x 2
  • Potassium channel subfamily K member 4
KeywordsMETAL TRANSPORT / POTASSIUM ION CHANNEL
Function / homology
Function and homology information


mechanosensitive potassium channel activity / TWIK related potassium channel (TREK) / detection of mechanical stimulus involved in sensory perception of touch / sensory perception of temperature stimulus / temperature-gated cation channel activity / Phase 4 - resting membrane potential / potassium channel complex / cellular response to alkaline pH / stabilization of membrane potential / potassium ion leak channel activity ...mechanosensitive potassium channel activity / TWIK related potassium channel (TREK) / detection of mechanical stimulus involved in sensory perception of touch / sensory perception of temperature stimulus / temperature-gated cation channel activity / Phase 4 - resting membrane potential / potassium channel complex / cellular response to alkaline pH / stabilization of membrane potential / potassium ion leak channel activity / cellular response to temperature stimulus / outward rectifier potassium channel activity / cellular response to fatty acid / potassium channel activity / potassium ion transmembrane transport / sensory perception of pain / potassium ion transport / memory / cellular response to mechanical stimulus / identical protein binding / 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 speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBrohawn, S.G. / Mackinnon, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Domain-swapped chain connectivity and gated membrane access in a Fab-mediated crystal of the human TRAAK K+ channel.
Authors: Brohawn, S.G. / Campbell, E.B. / Mackinnon, R.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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 4
B: Potassium channel subfamily K member 4
D: ANTIBODY FAB FRAGMENT LIGHT CHAIN
E: ANTIBODY FAB FRAGMENT HEAVY CHAIN
F: ANTIBODY FAB FRAGMENT LIGHT CHAIN
G: ANTIBODY FAB FRAGMENT HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,47313
Polymers160,1976
Non-polymers2767
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.887, 138.905, 97.461
Angle α, β, γ (deg.)90.00, 94.87, 90.00
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
11ARGARGARGARGAA28 - 28428 - 284
21ARGARGARGARGBB28 - 28428 - 284
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 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: 33585.805 Da / Num. of mol.: 2 / Fragment: UNP residues 1-300 / Mutation: N104Q, N108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: K2P4.1, KCNK4, TRAAK / Plasmid: pPICZ-B / Production host: Pichia pastoris (fungus) / References: UniProt: Q9NYG8

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Antibody , 2 types, 4 molecules DFEG

#2: Antibody ANTIBODY 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 ANTIBODY 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, 160 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE DEPOSITED SEQUENCE CORRESPONDS TO THE SEQUENCE OF THE ISOFORM 2 OF THE UNP ENTRY Q9NYG8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM Tris pH 8.5, 200 mM CaCl2, 27-30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.75→48.6 Å / Num. all: 55431 / Num. obs: 55209 / % possible obs: 99.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allDiffraction-ID% possible allRmerge(I) obs
2.75-2.83.92631195.8
2.8-2.854.12750199.9
2.85-2.94.227561100
2.9-2.964.2279911000.85
2.96-3.034.2275811000.687
3.03-3.14.3274811000.583
3.1-3.174.3274211000.442
3.17-3.264.2277711000.345
3.26-3.364.3278811000.289
3.36-3.464.3274211000.219
3.46-3.594.3272511000.164
3.59-3.734.3280111000.139
3.73-3.94.3275811000.12
3.9-4.114.2275811000.091
4.11-4.364.22782199.90.07
4.36-4.74.2277111000.059
4.7-5.174.12776199.90.055
5.17-5.924.12771199.90.053
5.92-7.464.12807199.90.046
7.46-504.12769197.30.031

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ORS and 3UM7

1ors

3um7


Resolution: 2.75→48.6 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.938 / SU B: 26.458 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.574 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23564 2797 5.1 %RANDOM
Rwork0.20085 ---
all0.20264 55623 --
obs0.20264 55167 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.435 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å22.14 Å2
2---3.14 Å20 Å2
3---3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10384 0 7 153 10544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0210656
X-RAY DIFFRACTIONr_bond_other_d0.0020.029942
X-RAY DIFFRACTIONr_angle_refined_deg1.011.95414526
X-RAY DIFFRACTIONr_angle_other_deg0.6313.00222916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85851339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47623.704405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.556151690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.81542
X-RAY DIFFRACTIONr_chiral_restr0.0580.21657
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111937
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022415
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A126500.16
12B126500.16
21D111730.1
22F111730.1
31E115560.1
32G115560.1
LS refinement shellResolution: 2.753→2.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 182 -
Rwork0.353 3621 -
obs--93.05 %
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)
15.2353-1.8326-3.81560.77050.83975.54050.49050.5780.3063-0.2312-0.2237-0.0555-0.64910.1825-0.26680.6862-0.02940.0720.63240.04810.469544.2638-5.835210.0949
20.192-0.056-0.96060.0680.252520.95-0.13550.4332-0.111-0.1925-0.18520.16151.7380.55440.32071.79480.17610.04851.4679-0.27790.842449.9514-20.4152-20.7751
311.0447-0.4460.95938.34562.07666.3241-0.25041.1276-0.9392-1.01380.11270.14560.6545-0.19730.13781.01060.18470.05451.019-0.08040.491945.6677-16.7534-6.5944
44.1415-0.7554-3.35350.8928-0.49656.14280.3680.51110.3128-0.3794-0.1671-0.1038-0.50560.4696-0.2010.67380.01160.08670.68340.0350.438147.8751-10.15547.3275
54.91996.9123-1.52799.7345-2.1480.4773-0.27210.26840.1331-0.16370.38730.21150.0742-0.0346-0.11522.05320.16720.15952.8239-0.16962.489692.1494-4.5589-4.8015
610.73671.57141.7345.3336-0.553311.48560.46360.5841.0563-0.1438-0.2034-1.4844-0.99631.4941-0.26021.0123-0.11390.25051.09350.14740.880864.3697-2.72715.5236
74.9707-1.88130.34025.72510.57566.8137-0.15760.36430.5483-0.8795-0.41880.3346-1.0354-0.38980.57640.6970.0668-0.1970.3793-0.02970.433414.178316.475927.0642
86.08191.8995.88715.46154.55667.8447-0.02070.71760.2317-1.0109-0.1420.2048-0.59180.65360.16270.75420.0699-0.05610.54810.050.548412.927546.38746.1371
94.75031.71154.02898.57456.24539.89010.04690.65950.3312-0.8346-0.12620.3286-0.97050.79180.07930.82720.0146-0.02550.54480.02750.563213.411247.4646.1141
103.7021-0.11490.33426.47473.9756.0873-0.1815-0.2260.36090.0524-0.05720.2687-0.06780.23180.23870.2760.0146-0.01530.37670.0120.340824.93616.527145.2737
111.2721-1.9957-1.85817.69934.16473.08890.1308-0.21920.0981-0.5325-0.15110.2606-0.39480.21250.02030.440.0155-0.08760.4158-0.02820.41519.325122.13749.2691
1210.6113-5.09610.19456.09560.7592.64910.149-0.43340.1460.04510.02440.5565-0.2011-0.058-0.17350.4526-0.04750.00170.4796-0.07270.66477.320437.127258.2597
136.0445-0.48490.64975.0217-1.9473.3605-0.0421-0.3184-0.5190.1648-0.0378-0.12820.15590.23370.07990.27150.06580.01930.3238-0.0080.435129.7276-34.984342.2411
1414.63634.8635.99126.27391.24035.35940.24740.8775-1.696-0.80710.33380.10970.76560.1914-0.58110.74340.0657-0.08190.47230.1251.32988.7948-63.206843.9358
153.5465-3.32454.52343.2791-4.07736.12261.91350.2177-1.9214-1.358-0.18912.01292.79150.4665-1.72441.89120.0716-0.43830.44270.12352.89911.8761-72.055646.6511
167.26771.6417-0.73825.3443-1.62373.6715-0.00530.2725-0.1663-0.12220.11290.59090.1454-0.1935-0.10760.29590.0053-0.04190.3736-0.00740.401211.7732-25.240531.1338
174.08172.8877-1.2754.0148-1.08791.4521-0.0953-0.2203-0.9212-0.05170.0310.14690.2863-0.23130.06430.33440.0389-0.01660.46570.08030.87385.0051-45.085342.0354
186.4534-1.56472.74897.9991-7.780511.1556-0.3454-0.7646-0.6252-0.15580.10430.26660.7256-0.55630.2410.4482-0.023-0.00380.56730.09091.1785-3.5392-55.61750.5203
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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