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

ID or keywords:

Entry

Database: PDB / ID: 4wfg

Title

Human TRAAK K+ channel in a Tl+ 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

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

Biological species

Homo sapiens (human)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 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	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.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.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.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 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4wfg_validation.pdf.gz	480.8 KB	Display	wwPDB validaton report
Full document	4wfg_full_validation.pdf.gz	504.2 KB	Display
Data in XML	4wfg_validation.xml.gz	49.4 KB	Display
Data in CIF	4wfg_validation.cif.gz	68.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wf/4wfg ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wfg	HTTPS FTP

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Related structure data

Related structure data	4wfeC 4wffC 4wfhC 4i9wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4i9w-d 4wfe-d 4wfh-d 4wff-d 2cge-d 4e3c-2 3t0e-d 1ko7-2 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

160 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)	80.798, 138.760, 96.317
Angle α, β, γ (deg.)	90.00, 94.52, 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 / 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 / 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, 201 molecules

#4: Chemical	ChemComp-TL / THALLIUM (I) ION Mass: 204.383 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Tl
#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.: 190 / 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: 3.4 Å³/Da / Density % sol: 63.86 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 50 MM TRIS PH 8.8, 200 MM CA(NO3)2, 27-30%(VOL/VOL) PEG400, 52 MM TRICHLOROETHANOL PH range: 8-9

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9781 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9781 Å / Relative weight: 1
Reflection	Resolution: 3→48 Å / Num. obs: 40099 / % possible obs: 99.6 % / Redundancy: 5.6 % / Net I/σ(I): 14.7
Reflection shell	Resolution: 3→3.05 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.9 / % possible all: 99.7

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Processing

Software

Name: REFMAC / Version: 5.8.0073 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4I9w

4i9w

Resolution: 3→48 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.916 / SU B: 43.04 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2363	2130	5 %	RANDOM
R_work	0.2022	-	-	-
obs	0.20395	40099	99.5 %	-

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: 108.712 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.97 Å²	0 Å²	2.89 Å²
2-	-	-3.86 Å²	0 Å²
3-	-	-	4.32 Å²

Refinement step

Cycle: 1 / Resolution: 3→48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10398	0	11	190	10599

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.02	10670
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9942
X-RAY DIFFRACTION	r_angle_refined_deg	0.898	1.95	14534
X-RAY DIFFRACTION	r_angle_other_deg	0.611	3	22938
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.614	5	1341
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.162	23.704	405
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.275	15	1692
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.281	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	1661
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	11903
X-RAY DIFFRACTION	r_gen_planes_other	0.002	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	3.946	5.232	5394
X-RAY DIFFRACTION	r_mcbond_other	3.946	5.232	5393
X-RAY DIFFRACTION	r_mcangle_it	6.02	7.85	6725
X-RAY DIFFRACTION	r_mcangle_other	6.02	7.85	6726
X-RAY DIFFRACTION	r_scbond_it	4.474	5.599	5276
X-RAY DIFFRACTION	r_scbond_other	4.473	5.6	5277
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.88	8.254	7810
X-RAY DIFFRACTION	r_long_range_B_refined	10.525	50.417	44033
X-RAY DIFFRACTION	r_long_range_B_other	10.515	50.371	43965
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	12887	0.15
1	2	B	12887	0.15
2	1	D	10978	0.12
2	2	F	10978	0.12
3	1	E	11345	0.11
3	2	G	11345	0.11

LS refinement shell

Resolution: 3→3.078 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.379	172	-
R_work	0.386	2940	-
obs	-	-	99.17 %

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	4.2915	-1.1235	-3.7239	0.3471	0.7346	5.1726	0.4151	0.4098	0.1537	-0.127	-0.1425	0.0644	-0.511	0.3281	-0.2726	0.5513	-0.0489	0.1909	0.3256	0.0815	0.6008	44.264	-5.835	10.095
2	0.5369	-0.3237	0.3128	0.2791	-0.9466	11.1008	0.126	0.7721	-0.2249	-0.3153	-0.4534	0.1776	0.9828	0.5889	0.3274	1.553	0.0758	0.1229	1.1377	-0.2229	0.9076	49.951	-20.415	-20.775
3	7.3772	-0.8321	-1.6433	7.7051	-1.3747	5.5835	-0.2576	0.801	-0.8072	-0.7418	0.1161	0.1273	0.986	-0.5867	0.1415	0.8071	0.0511	-0.0544	0.7405	-0.1023	0.5816	45.668	-16.753	-6.594
4	4.2062	-0.5715	-3.592	1.1668	-0.9029	5.8726	0.4473	0.4573	0.2438	-0.2544	-0.1785	-0.0069	-0.5321	0.3732	-0.2688	0.4675	-0.07	0.1208	0.4712	-0.0185	0.484	47.875	-10.155	7.327
5	2.79	-1.414	2.4654	8.1678	-3.98	3.1981	-0.5098	0.0033	-0.0658	0.2011	0.7452	0.1257	-0.3719	-0.3023	-0.2355	1.3127	0.0685	0.0626	1.5139	-0.1381	1.4456	92.149	-4.559	-4.801
6	7.8051	2.0643	0.7468	4.6078	-2.3005	6.6046	0.4954	0.0804	0.8497	-0.0344	-0.2391	-1.06	-0.9038	1.2097	-0.2563	0.7989	-0.1381	0.1922	0.9136	0.0854	0.8877	64.37	-2.727	5.524
7	4.4083	-1.4975	0.7015	5.8656	0.2457	6.8217	-0.1675	0.3709	0.3609	-0.8357	-0.4002	0.2766	-0.9592	-0.3429	0.5677	0.397	0.0541	-0.0807	0.0771	0.01	0.3855	14.178	16.476	27.064
8	6.0968	3.2539	6.1701	5.8882	5.3152	9.1882	-0.0382	0.6044	0.1561	-1.0939	-0.0852	-0.0468	-0.7314	0.8283	0.1234	0.5771	0.1023	-0.0243	0.1931	0.0504	0.6288	12.927	46.387	46.137
9	5.2532	1.5577	4.144	6.6416	5.1708	7.9362	0.0639	0.6582	0.4101	-0.5866	-0.1503	0.0161	-0.7061	0.5501	0.0864	0.6138	0.0123	0.0619	0.1715	0.0502	0.6461	13.411	47.46	46.114
10	3.7908	-0.8106	0.4644	6.2133	3.7005	7.0208	-0.19	-0.1204	0.1782	0.3498	-0.0452	0.2633	-0.1052	0.3674	0.2353	0.1066	0.0148	0.1014	0.0673	0.0424	0.3541	24.936	6.527	45.274
11	1.3972	-1.8229	-1.7867	6.8867	3.5792	2.6437	0.1806	-0.3448	0.0303	-0.304	-0.2578	0.188	-0.2767	0.2439	0.0771	0.2398	0.0359	0.0282	0.223	0.0033	0.3404	19.325	22.137	49.269
12	9.5398	-4.7834	-0.0673	6.0617	0.8805	2.1218	0.0679	-0.5066	0.1082	0.0423	-0.0022	0.4759	-0.1055	-0.0904	-0.0657	0.3039	-0.0659	0.0295	0.1272	-0.0608	0.6124	7.32	37.127	58.26
13	6.3499	-0.1711	0.0291	6.0538	-2.2867	3.2788	0.089	-0.212	-0.4868	0.284	-0.0617	-0.3335	0.0088	0.0959	-0.0273	0.1012	0.0212	0.0714	0.0274	-0.0091	0.4867	29.728	-34.984	42.241
14	13.318	5.5032	6.1924	5.4432	2.4838	6.056	0.2926	0.588	-1.0705	-0.5295	0.0979	-0.2011	0.6497	0.0936	-0.3904	0.477	0.0845	-0.0287	0.1068	0.1515	1.0959	8.795	-63.207	43.936
15	0.1351	-0.6954	0.1942	3.9355	-0.8479	2.7905	0.0867	-0.0438	-0.1538	-0.0348	0.0106	0.7506	1.2945	-0.0222	-0.0973	0.9643	-0.1182	-0.0949	0.3668	0.0248	1.5131	11.876	-72.056	46.651
16	6.559	2.6453	-0.2578	7.3212	-1.3303	3.4697	-0.0507	0.2953	-0.0828	-0.0195	0.2011	0.5403	-0.0038	-0.1772	-0.1504	0.1178	0.042	0.0535	0.0771	0.0524	0.2876	11.773	-25.24	31.134
17	3.7808	2.6455	-1.3556	5.6402	-1.187	1.1374	-0.0479	-0.0535	-0.8174	0.0043	0.002	0.0299	0.1353	-0.2132	0.0459	0.0653	-0.0253	0.0416	0.0997	0.0693	0.7504	5.005	-45.085	42.035
18	2.4311	-0.5567	1.5845	4.1774	-4.2615	6.6182	-0.1623	-0.3031	-0.1036	0.0077	0.2615	0.2216	0.3745	-0.4602	-0.0992	0.3378	-0.0268	-0.0003	0.4265	0.0454	0.7016	-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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