PDB-3um7: Crystal structure of the human two pore domain K+ ion channel TRA...

ID or keywords:

Entry

Database: PDB / ID: 3um7

Title

Crystal structure of the human two pore domain K+ ion channel TRAAK (K2P4.1)

Components

Potassium channel subfamily K member 4

Keywords

METAL 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 / temperature-gated cation channel activity / sensory perception of temperature stimulus / 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)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 3.31 Å

Authors

Brohawn, S.G. / MacKinnon, R.

Citation

Journal: Science / Year: 2012
Title: Crystal structure of the human K2P TRAAK, a lipid- and mechano-sensitive K+ ion channel.
Authors: Brohawn, S.G. / del Marmol, J. / MacKinnon, R.

History

Deposition	Nov 12, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3um7.cif.gz	206.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3um7.ent.gz	171.6 KB	Display	PDB format
PDBx/mmJSON format	3um7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/um/3um7 ftp://data.pdbj.org/pub/pdb/validation_reports/um/3um7	HTTPS FTP

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Related structure data

Similar structure data	4xdl-1 4twk-d 4ruf-d 3vmp-d 6wm0-d 3vmn-d 2wq7-d 3cvu-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 (8) #38 - Feb 2003 Potassium Channels similarity (2)

Deposited unit

A: Potassium channel subfamily K member 4

B: Potassium channel subfamily K member 4

hetero molecules

67.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.938, 130.852, 132.779
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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: KCNK4, TRAAK / Plasmid: pPICZ-B / Production host: Pichia pastoris (fungus) / References: UniProt: Q9NYG8
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
Sequence details	THE DEPOSITED SEQUENCE CORRESPONDS TO THE SEQUENCE OF THE ISOFORM 2 OF THE UNP ENTRY Q9NYG8.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 5.69 Å³/Da / Density % sol: 78.37 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 21-24% PEG400, 1 mM Fos-choline-12, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97833 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 5, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97833 Å / Relative weight: 1

Reflection

Redundancy: 3.6 % / Av σ(I) over netI: 25.57 / Number: 41830 / R_merge(I) obs: 0.089 / Χ²: 1.84 / D res high: 4.2 Å / D res low: 40 Å / Num. obs: 11492 / % possible obs: 98.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
10.3	40	90.1	1	0.059	3.089	3.3
8.2	10.3	98.5	1	0.063	3.004	3.5
7.17	8.2	97.7	1	0.076	2.501	3.6
6.52	7.17	98.6	1	0.103	2.1	3.6
6.05	6.52	99	1	0.163	1.775	3.7
5.7	6.05	99	1	0.247	1.857	3.7
5.41	5.7	97.8	1	0.312	1.654	3.7
5.18	5.41	99	1	0.305	1.611	3.7
4.98	5.18	99.1	1	0.338	1.626	3.7
4.81	4.98	99	1	0.339	1.526	3.7
4.66	4.81	98.9	1	0.485	1.471	3.7
4.52	4.66	99.6	1	0.766	1.437	3.7
4.4	4.52	99.1	1	0.798	1.423	3.7
4.3	4.4	99.4	1	0.943	1.428	3.7
4.2	4.3	99.3	1		1.272	3.7

Reflection

Resolution: 3.3→40 Å / Num. obs: 17761 / % possible obs: 73.4 % / Redundancy: 3.7 % / R_merge(I) obs: 0.056 / Χ²: 1.494 / Net I/σ(I): 11.7

Reflection shell

Resolution (Å)	Redundancy (%)	Num. unique all	Χ²	Diffraction-ID	% possible all	R_merge(I) obs
3.3-3.36	4.5	25	1.448	1	2.1
3.36-3.42	4.5	88	1.398	1	7.4	0.948
3.42-3.48	4.4	162	1.357	1	13.9	0.684
3.48-3.55	4.2	267	1.372	1	22.1	0.761
3.55-3.63	4.3	366	1.288	1	30.8
3.63-3.72	4.1	518	1.45	1	43.2
3.72-3.81	4	754	1.364	1	63.8	0.901
3.81-3.91	3.7	1140	1.258	1	94.8	0.997
3.91-4.03	3.7	1194	1.419	1	99.8	0.833
4.03-4.16	3.7	1190	1.327	1	100	0.446
4.16-4.31	3.7	1203	1.376	1	100	0.355
4.31-4.48	3.7	1196	1.475	1	99.9	0.212
4.48-4.68	3.7	1215	1.488	1	99.9	0.162
4.68-4.93	3.7	1202	1.465	1	99.8	0.102
4.93-5.24	3.7	1196	1.459	1	99.4	0.09
5.24-5.64	3.7	1207	1.519	1	99.3	0.094
5.64-6.21	3.6	1214	1.78	1	99	0.093
6.21-7.1	3.6	1218	1.931	1	98.5	0.057
7.1-8.94	3.6	1248	1.812	1	98.3	0.03
8.94-50	3.3	1158	1.342	1	86.9	0.019

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Phasing

Phasing

Method:

MIRAS

Phasing set

ID
1
2
3

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 17850

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
11.85-100	55.2	0.873	503
9.51-11.85	45.7	0.904	506
8.32-9.51	44.1	0.903	509
7.55-8.32	44.8	0.909	520
6.96-7.55	47	0.898	567
6.49-6.96	54	0.869	610
6.1-6.49	59.1	0.823	633
5.78-6.1	63.1	0.814	677
5.5-5.78	66.8	0.812	703
5.26-5.5	71.4	0.828	753
5.05-5.26	70.8	0.87	771
4.86-5.05	74.3	0.87	799
4.69-4.86	77.4	0.898	820
4.54-4.69	80.3	0.889	870
4.4-4.54	77.8	0.884	878
4.27-4.4	83.4	0.903	920
4.15-4.27	92.3	0.874	924
4.05-4.15	89.7	0.827	952
3.95-4.05	90.3	0.769	977
3.86-3.95	90.4	0.762	1007
3.77-3.86	88.2	0.71	938
3.69-3.77	88.1	0.671	639
3.61-3.69	87.7	0.619	504
3.31-3.61	90.4	0.56	870

Phasing MIR

Resolution: 4→31.07 Å / FOM acentric: 0.375 / FOM centric: 0.337 / Reflection acentric: 11354 / Reflection centric: 1821

Phasing MIR der

Native set-ID: 1 / Resolution: 4→31.07 Å

ID	R cullis acentric	R cullis centric	Der set-ID	Reflection acentric	Reflection centric
ISO_1	0	0	1	11313	1670
ISO_2	0.2	0.159	2	9512	713
ISO_3	0.395	0.337	3	9317	710

Phasing MIR der shell

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
15.6	31.07	ISO_1	0	0	87	43
11.8	15.6	ISO_1	0	0	222	78
9.87	11.8	ISO_1	0	0	292	80
8.66	9.87	ISO_1	0	0	353	89
7.81	8.66	ISO_1	0	0	404	78
7.17	7.81	ISO_1	0	0	443	79
6.66	7.17	ISO_1	0	0	482	80
6.25	6.66	ISO_1	0	0	509	85
5.9	6.25	ISO_1	0	0	562	80
5.61	5.9	ISO_1	0	0	596	87
5.36	5.61	ISO_1	0	0	617	91
5.14	5.36	ISO_1	0	0	643	87
4.94	5.14	ISO_1	0	0	679	87
4.76	4.94	ISO_1	0	0	706	94
4.61	4.76	ISO_1	0	0	722	89
4.46	4.61	ISO_1	0	0	753	86
4.33	4.46	ISO_1	0	0	761	85
4.21	4.33	ISO_1	0	0	786	90
4.1	4.21	ISO_1	0	0	857	96
4	4.1	ISO_1	0	0	839	86
15.6	31.07	ISO_2	0.139	0.084	85	18
11.8	15.6	ISO_2	0.09	0.094	220	36
9.87	11.8	ISO_2	0.093	0.085	285	35
8.66	9.87	ISO_2	0.105	0.098	348	42
7.81	8.66	ISO_2	0.093	0.094	393	36
7.17	7.81	ISO_2	0.101	0.104	437	38
6.66	7.17	ISO_2	0.135	0.171	473	39
6.25	6.66	ISO_2	0.184	0.251	502	42
5.9	6.25	ISO_2	0.26	0.309	551	37
5.61	5.9	ISO_2	0.327	0.428	583	41
5.36	5.61	ISO_2	0.367	0.497	605	44
5.14	5.36	ISO_2	0.395	0.572	630	44
4.94	5.14	ISO_2	0.449	0.676	662	36
4.76	4.94	ISO_2	0.461	0.596	691	48
4.61	4.76	ISO_2	0.484	0.653	701	46
4.46	4.61	ISO_2	0.567	0.651	738	40
4.33	4.46	ISO_2	0.591	0.883	746	44
4.21	4.33	ISO_2	0.672	0.874	766	42
4.1	4.21	ISO_2	0.748	0.697	96	5
4	4.1	ISO_2	0	0	0	0
15.6	31.07	ISO_3	0.238	0.215	84	18
11.8	15.6	ISO_3	0.23	0.229	220	36
9.87	11.8	ISO_3	0.222	0.204	288	35
8.66	9.87	ISO_3	0.253	0.273	348	42
7.81	8.66	ISO_3	0.261	0.254	395	36
7.17	7.81	ISO_3	0.262	0.274	437	38
6.66	7.17	ISO_3	0.342	0.416	474	38
6.25	6.66	ISO_3	0.408	0.428	501	42
5.9	6.25	ISO_3	0.481	0.532	551	37
5.61	5.9	ISO_3	0.563	0.61	583	41
5.36	5.61	ISO_3	0.575	0.806	605	44
5.14	5.36	ISO_3	0.579	0.768	629	43
4.94	5.14	ISO_3	0.617	0.834	661	36
4.76	4.94	ISO_3	0.601	0.853	687	48
4.61	4.76	ISO_3	0.644	0.899	699	46
4.46	4.61	ISO_3	0.7	1.276	732	40
4.33	4.46	ISO_3	0.729	1.278	740	44
4.21	4.33	ISO_3	0.823	1.069	646	42
4.1	4.21	ISO_3	0.662	0.786	37	4
4	4.1	ISO_3	0	0	0	0

Phasing MIR shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
15.6-31.07	0.825	0.677	118	64
11.8-15.6	0.869	0.671	226	89
9.87-11.8	0.807	0.567	292	92
8.66-9.87	0.773	0.536	353	99
7.81-8.66	0.776	0.55	405	87
7.17-7.81	0.763	0.485	443	89
6.66-7.17	0.722	0.512	483	85
6.25-6.66	0.645	0.46	510	98
5.9-6.25	0.573	0.417	563	90
5.61-5.9	0.511	0.415	596	100
5.36-5.61	0.446	0.347	617	97
5.14-5.36	0.4	0.261	645	93
4.94-5.14	0.307	0.225	679	92
4.76-4.94	0.282	0.212	706	97
4.61-4.76	0.229	0.151	722	93
4.46-4.61	0.191	0.126	753	91
4.33-4.46	0.169	0.118	761	92
4.21-4.33	0.137	0.128	786	91
4.1-4.21	0.015	0.005	857	96
4-4.1	0	0	839	86

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.6.0117	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MIRAS / Resolution: 3.31→31.2 Å / Cor.coef. F_o:F_c: 0.881 / Cor.coef. F_o:F_c free: 0.887 / WR_factor R_free: 0.312 / WR_factor R_work: 0.291 / Occupancy max: 1 / Occupancy min: 1 / SU B: 45.286 / SU ML: 0.481 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3228	880	5 %	RANDOM
R_work	0.3169	-	-	-
obs	0.3172	16792	75.4 %	-

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 max: 396.94 Å² / B_iso mean: 175.4904 Å² / B_iso min: 21.36 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.5 Å²	0 Å²	0 Å²
2-	-	1.45 Å²	0 Å²
3-	-	-	0.04 Å²

Refinement step

Cycle: LAST / Resolution: 3.31→31.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3740	0	5	0	3745

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	3829
X-RAY DIFFRACTION	r_angle_refined_deg	1.172	1.953	5264
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.988	5	497
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.889	22.406	133
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.874	15	538
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.784	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	634
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	2840

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.315-3.4	0.298	1	0.416	80	1671	4.847
3.4-3.492	0.285	14	0.394	205	1609	13.611
3.492-3.592	0.381	26	0.403	355	1540	24.74
3.592-3.701	0.351	21	0.43	578	1485	40.337
3.701-3.82	0.407	45	0.439	987	1437	71.816
3.82-3.952	0.377	80	0.429	1237	1322	99.622
3.952-4.099	0.44	71	0.4	1180	1255	99.681
4.099-4.263	0.353	57	0.372	1176	1236	99.757
4.263-4.449	0.317	69	0.329	1089	1164	99.485
4.449-4.661	0.333	58	0.289	1072	1137	99.384
4.661-4.908	0.324	62	0.266	1004	1071	99.533
4.908-5.197	0.316	48	0.257	934	990	99.192
5.197-5.545	0.314	40	0.317	898	950	98.737
5.545-5.974	0.378	47	0.349	821	882	98.413
5.974-6.52	0.442	25	0.338	768	812	97.66
6.52-7.25	0.249	34	0.283	684	731	98.222
7.25-8.297	0.268	42	0.235	585	644	97.36
8.297-9.987	0.213	25	0.22	502	540	97.593
9.987-13.451	0.266	15	0.26	391	424	95.755
13.451-31.2	0.381	8	0.421	171	292	61.301

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	0.5684	-1.9287	0.618	9.1283	-2.3207	4.9836	0.0471	-0.2387	0.2621	-1.0187	0.2368	-1.0043	-0.6848	0.1647	-0.2839	0.6976	-0.1572	0.2479	0.768	-0.0163	1.2778	11.7176	41.332	21.893
2	0.2186	-0.1778	-0.6839	9.8989	-0.5564	2.56	0.1242	0.0452	0.1195	1.1841	-0.1564	-0.1926	-0.6337	0.1231	0.0323	0.9148	-0.0209	0.0895	0.8119	-0.0273	0.9231	1.6702	23.9668	36.4737
3	0.7783	2.3312	-0.6057	10.2055	0.3119	3.5145	0.1117	-0.0512	-0.0265	-1.3506	-0.3184	1.4585	-1.1783	-0.3774	0.2067	0.9511	0.1123	-0.464	0.6477	0.1152	1.6884	-10.3532	43.7959	17.3734
4	3.5831	-0.1594	-1.5178	8.9712	1.6694	3.0875	-0.2715	0.2894	0.0727	-2.1516	0.1258	0.7059	0.1376	-0.1365	0.1457	1.339	-0.1512	-0.0536	0.7523	0.0091	0.603	-2.7609	19.316	14.838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 106
2	X-RAY DIFFRACTION	2	A	112 - 290
3	X-RAY DIFFRACTION	3	B	25 - 106
4	X-RAY DIFFRACTION	4	B	112 - 290

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-Aug 12, 2020. Covid-19 info

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi