PDB-4wfe: Human TRAAK K+ channel in a K+ bound conductive conformation

ID or keywords:

Entry

Database: PDB / ID: 4wfe

Title

Human TRAAK K+ channel in a K+ bound conductive conformation

Components

(ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT ...) x 2
Potassium channel subfamily K member 4

Keywords

METAL TRANSPORT / Mechanosensitive ion channel / two-pore domain potassium ion channel / membrane protein

Function / homology

Function and homology information

TWIK related potassium channel (TREK) / cellular response to arachidonate / mechanosensitive potassium channel activity / temperature-gated cation channel activity / sensory perception of temperature stimulus / response to ultrasound / potassium channel complex / detection of mechanical stimulus involved in sensory perception of touch / cellular response to alkaline pH / Phase 4 - resting membrane potential ...
Similarity search - Function

Biological species

Homo sapiens (human)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Brohawn, S.G. / MacKinnon, R.

Citation

Journal: Nature / Year: 2014
Title: Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel.
Authors: Brohawn, S.G. / Campbell, E.B. / MacKinnon, R.

History

Deposition	Sep 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 17, 2014	Group: Database references
Revision 1.2	Dec 31, 2014	Group: Other
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords / struct_ncs_dom_lim Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_keywords.text / _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 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4wfe_validation.pdf.gz	477.4 KB	Display	wwPDB validaton report
Full document	4wfe_full_validation.pdf.gz	501.1 KB	Display
Data in XML	4wfe_validation.xml.gz	49.2 KB	Display
Data in CIF	4wfe_validation.cif.gz	69 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wf/4wfe ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wfe	HTTPS FTP

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Related structure data

Related structure data	4wffC 4wfgC 4wfhC 4i9wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4i9w-d 4wff-d 4wfg-d 4e3c-2 4wfh-d 2cge-d 5vrv-d 1r70-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (7) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #38 - Feb 2003 Potassium Channels similarity (2)

Deposited unit

A: Potassium channel subfamily K member 4

B: 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

159 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	80.795, 138.522, 96.843
Angle α, β, γ (deg.)	90.00, 95.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	D
2	2	F
1	3	E
2	3	G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	VAL	VAL	A	A	28 - 286	28 - 286
2	1	ARG	ARG	VAL	VAL	B	B	28 - 286	28 - 286
1	2	GLN	GLN	ASN	ASN	D	C	1 - 211	1 - 211
2	2	GLN	GLN	ASN	ASN	F	E	1 - 211	1 - 211
1	3	GLU	GLU	PRO	PRO	E	D	1 - 215	1 - 215
2	3	GLU	GLU	PRO	PRO	G	F	1 - 215	1 - 215

NCS ensembles :

ID
1
2
3

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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: 32569.650 Da / Num. of mol.: 2 / Mutation: N104Q, N108Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK4, TRAAK / Plasmid: PPICZ-B / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9NYG8

#1: Protein

Potassium channel subfamily K member 4 / TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium ...

Mass: 32569.650 Da / Num. of mol.: 2 / Mutation: N104Q, N108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: KCNK4, TRAAK / Plasmid: PPICZ-B / Production host:

Komagataella pastoris (fungus) / References: UniProt: Q9NYG8

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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, 200 molecules

#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#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.: 191 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.41 Å³/Da / Density % sol: 63.96 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 50 mM Tris pH 8.8, 200 mM CaCl2, 27-30% (vol/vol) PEG400, 4% (vol/vol) polypropylene glycol PH range: 8-9

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.5→48.2 Å / Num. obs: 69456 / % possible obs: 99.6 % / Redundancy: 3.8 % / R_sym value: 0.063 / Net I/σ(I): 22.6
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.9 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4I9W

4i9w

Resolution: 2.5→48.2 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.942 / SU B: 24.206 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2341	3686	5 %	RANDOM
R_work	0.19908	-	-	-
obs	0.20086	69456	99.59 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 89.526 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.11 Å²	0 Å²	3.03 Å²
2-	-	-3.19 Å²	0 Å²
3-	-	-	4.69 Å²

Refinement step

Cycle: 1 / Resolution: 2.5→48.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10398	0	9	191	10598

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	10670
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9942
X-RAY DIFFRACTION	r_angle_refined_deg	1.058	1.954	14546
X-RAY DIFFRACTION	r_angle_other_deg	0.665	3	22938
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.54	5	1341
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.082	23.704	405
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.159	15	1692
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.186	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1661
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	11951
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2417
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.367	4.556	5394
X-RAY DIFFRACTION	r_mcbond_other	4.365	4.556	5393
X-RAY DIFFRACTION	r_mcangle_it	6.43	6.829	6725
X-RAY DIFFRACTION	r_mcangle_other	6.43	6.83	6726
X-RAY DIFFRACTION	r_scbond_it	5.8	4.985	5276
X-RAY DIFFRACTION	r_scbond_other	5.799	4.985	5277
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	8.401	7.305	7822
X-RAY DIFFRACTION	r_long_range_B_refined	11.99	44.008	44128
X-RAY DIFFRACTION	r_long_range_B_other	11.987	43.978	44061
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	12575	0.18
1	2	B	12575	0.18
2	1	D	10873	0.13
2	2	F	10873	0.13
3	1	E	11235	0.12
3	2	G	11235	0.12

LS refinement shell

Resolution: 2.499→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	243	-
R_work	0.378	5036	-
obs	-	-	97.2 %

Refinement TLS params.

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

ID	L11 (°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)
1	4.1271	-0.8324	-3.167	0.1954	0.6998	4.1527	0.3469	0.4883	0.2629	-0.1759	-0.0773	-0.0532	-0.4606	0.2365	-0.2697	0.4453	-0.0081	0.0073	0.3255	0.0229	0.198	44.264	-5.835	10.095
2	0.0926	-0.039	0.2626	0.0492	-0.143	10.7291	0.0196	0.2911	-0.0991	-0.1845	-0.1178	0.0961	1.1777	0.3974	0.0981	1.1996	0.0984	0.0088	1.0154	-0.1318	0.6019	49.951	-20.415	-20.775
3	6.5806	-2.0182	0.0023	7.5213	-0.0405	5.0254	-0.276	0.7046	-0.9643	-0.6096	0.0295	0.0124	0.6529	-0.412	0.2466	0.7431	0.0787	-0.0364	0.6968	-0.0989	0.2426	45.668	-16.753	-6.594
4	3.658	-0.4669	-2.831	0.8391	-0.3424	4.7794	0.2949	0.5342	0.2711	-0.3633	-0.1461	-0.1968	-0.4185	0.3595	-0.1488	0.4237	-0.012	0.0196	0.4371	0.013	0.1551	47.875	-10.155	7.327
5	6.8196	-0.4233	2.128	6.7662	-2.1746	1.2944	-0.4016	0.1593	0.042	0.1812	0.4287	-0.0981	-0.1427	-0.1224	-0.0271	0.7329	0.0441	0.0381	0.8331	-0.0508	0.6789	92.149	-4.559	-4.801
6	7.8797	1.7662	0.5321	5.3606	-0.7045	8.4625	0.2522	0.2398	1.1051	-0.1227	0.0205	-1.2525	-0.9475	1.0674	-0.2727	0.7692	-0.1169	0.1634	0.785	0.1263	0.6897	64.37	-2.727	5.524
7	4.186	-1.5405	0.3648	4.8935	0.8562	5.4052	-0.0147	0.2037	0.3999	-0.7825	-0.3872	0.1024	-0.7801	-0.2217	0.4019	0.3618	0.042	-0.156	0.097	0.0159	0.1084	14.178	16.476	27.064
8	3.8694	1.5698	3.9932	4.3122	3.6486	6.6767	-0.0305	0.4816	0.1986	-0.7385	-0.039	0.0404	-0.4487	0.5588	0.0695	0.3614	0.0458	-0.1135	0.2028	0.0158	0.2275	12.927	46.387	46.137
9	3.0823	0.9891	2.9256	6.0073	4.4804	7.0974	0.0681	0.4571	0.338	-0.4496	0.0027	0.0934	-0.5693	0.5303	-0.0709	0.3661	-0.0123	-0.0401	0.2943	0.0216	0.2445	13.411	47.46	46.114
10	3.8647	-1.2636	0.2321	5.8685	3.6021	5.7482	-0.1131	-0.2491	0.2202	0.0848	-0.0676	0.1655	-0.0202	0.2779	0.1807	0.036	-0.0015	-0.0259	0.1123	0	0.045	24.936	6.527	45.274
11	1.1132	-1.5507	-1.4147	5.0774	2.6921	2.064	0.0424	-0.1736	0.1448	-0.0715	-0.0139	0.0641	-0.1608	0.1886	-0.0285	0.1308	-0.0197	-0.0976	0.1561	0.0044	0.1379	19.325	22.137	49.269
12	7.6443	-3.9168	-0.2566	4.3804	0.738	1.7	0.0616	-0.1988	0.1813	0.2376	0.0444	0.2397	-0.0951	0.036	-0.1059	0.2045	-0.0401	-0.0422	0.1937	-0.0516	0.2537	7.32	37.127	58.26
13	4.7242	-0.2192	0.7292	4.9178	-1.6681	3.0705	0.0475	-0.201	-0.4321	0.1581	-0.0299	-0.16	0.1352	0.1887	-0.0176	0.0361	0.0397	-0.0398	0.0789	-0.0022	0.1874	29.728	-34.984	42.241
14	9.6515	3.1939	3.9994	4.5866	1.0844	3.7123	0.2694	0.6416	-0.7173	-0.4655	0.0589	-0.0608	0.6313	0.082	-0.3282	0.378	0.0654	-0.1061	0.2119	0.1127	0.6773	8.795	-63.207	43.936
15	0.1157	-0.0386	0.0444	4.4974	-0.4254	4.3994	0.2072	0.0375	-0.3325	0.1361	0.3077	-0.0038	1.117	-0.0478	-0.5149	0.8648	0.1036	-0.342	0.2617	0.0014	1.5079	11.876	-72.056	46.651
16	5.8586	2.3487	-0.4411	5.8869	-1.2992	3.3117	0.0178	0.2034	-0.0887	-0.1204	0.0106	0.3929	0.0716	-0.1716	-0.0284	0.0591	0.0134	-0.0614	0.0958	0.0104	0.104	11.773	-25.24	31.134
17	3.0449	2.2611	-1.2337	3.455	-1.0553	1.0118	-0.0633	-0.1592	-0.7367	-0.0909	-0.0477	-0.0371	0.2292	-0.1408	0.111	0.1423	0.0026	-0.1012	0.1996	0.0517	0.4465	5.005	-45.085	42.035
18	4.5737	-1.637	1.3929	6.2993	-6.3869	7.874	-0.2651	-0.4103	-0.5214	-0.018	0.2276	0.2556	0.4402	-0.4647	0.0374	0.2192	-0.0771	-0.0903	0.2755	0.0275	0.5857	-3.539	-55.617	50.52

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	28 - 148
2	X-RAY DIFFRACTION	2	A	149 - 219
3	X-RAY DIFFRACTION	3	A	220 - 286
4	X-RAY DIFFRACTION	4	B	28 - 175
5	X-RAY DIFFRACTION	5	B	176 - 197
6	X-RAY DIFFRACTION	6	B	198 - 286
7	X-RAY DIFFRACTION	7	D	1 - 105
8	X-RAY DIFFRACTION	8	D	106 - 157
9	X-RAY DIFFRACTION	9	D	158 - 211
10	X-RAY DIFFRACTION	10	E	1 - 80
11	X-RAY DIFFRACTION	11	E	81 - 137
12	X-RAY DIFFRACTION	12	E	138 - 217
13	X-RAY DIFFRACTION	13	F	1 - 105
14	X-RAY DIFFRACTION	14	F	106 - 188
15	X-RAY DIFFRACTION	15	F	189 - 211
16	X-RAY DIFFRACTION	16	G	1 - 80
17	X-RAY DIFFRACTION	17	G	81 - 172
18	X-RAY DIFFRACTION	18	G	173 - 216

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