PDB-4j9u: Crystal Structure of the TrkH/TrkA potassium transport complex

ID or keywords:

Entry

Database: PDB / ID: 4j9u

Title

Crystal Structure of the TrkH/TrkA potassium transport complex

Components

Potassium uptake protein TrkA
Trk system potassium uptake protein TrkH

Keywords

TRANSPORT PROTEIN / RCK domain / potassium transport /

membrane protein /

Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS

Function / homology

Function and homology information

potassium ion transmembrane transporter activity / potassium:chloride symporter activity /

potassium ion binding /

potassium channel activity / potassium ion transmembrane transport /

nucleotide binding / protein homodimerization activity / identical protein binding /

plasma membrane
Similarity search - Function

Biological species

Vibrio parahaemolyticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.8 Å

Authors

Cao, Y. / Jin, X. / Huang, H. / Levin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)

Citation

Journal: Nature / Year: 2013
Title: Gating of the TrkH ion channel by its associated RCK protein TrkA.
Authors: Cao, Y. / Pan, Y. / Huang, H. / Jin, X. / Levin, E.J. / Kloss, B. / Zhou, M.

History

Deposition	Feb 17, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4j9u.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb4j9u.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	4j9u.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/j9/4j9u ftp://data.pdbj.org/pub/pdb/validation_reports/j9/4j9u	HTTPS FTP

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Related structure data

Related structure data	4j9vC C: citing same article (ref.)
Similar structure data	10688 9999 21543 21412 0460 6vi0-d 6ait-d 6l8s-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NYCOMPS-GO.1008

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#38 - Feb 2003 Potassium Channels similarity (7) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Trk system potassium uptake protein TrkH

B: Trk system potassium uptake protein TrkH

C: Trk system potassium uptake protein TrkH

D: Trk system potassium uptake protein TrkH

E: Potassium uptake protein TrkA

F: Potassium uptake protein TrkA

G: Potassium uptake protein TrkA

H: Potassium uptake protein TrkA

hetero molecules

453 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Trk system potassium uptake protein TrkH

B: Trk system potassium uptake protein TrkH

E: Potassium uptake protein TrkA

F: Potassium uptake protein TrkA

G: Potassium uptake protein TrkA

H: Potassium uptake protein TrkA

hetero molecules

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

2

C: Trk system potassium uptake protein TrkH

D: Trk system potassium uptake protein TrkH

E: Potassium uptake protein TrkA

F: Potassium uptake protein TrkA

G: Potassium uptake protein TrkA

H: Potassium uptake protein TrkA

hetero molecules

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

Unit cell

Length a, b, c (Å)	133.725, 146.627, 163.672
Angle α, β, γ (deg.)	90.000, 99.320, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

The biological assembly is an hexamer generated from the chains A, B, E, F, G, and H.

#1: Protein	Trk system potassium uptake protein TrkH Mass: 53104.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: trkH, VP0032 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87TN7
#2: Protein	Potassium uptake protein TrkA Mass: 50193.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VP3045 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87KD2
#3: Chemical	ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM Mass: 2044.535 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Br₁₂Ta₆
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.83 Å³/Da / Density % sol: 67.9 %
Crystal grow	Temperature: 298 K / Method: microbatch / pH: 6.75 Details: 37.5% PEG 400, 400 mM ammonium sulfate, 100 mM HEPES, pH 6.75, microbatch, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25 / Wavelength: 1.2515 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2009

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.2515 Å / Relative weight: 1

Reflection

Resolution: 3.8→50 Å / Num. obs: 61373 / % possible obs: 99.7 % / Redundancy: 7.2 % / R_merge(I) obs: 0.144 / Χ²: 1.25 / Net I/σ(I): 8.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
3.8-3.87	6.3	0.814	3040	0.756	1	98.7
3.87-3.94	6.4	0.691	3019	0.817	1	99
3.94-4.01	6.6	0.562	3007	0.793	1	99.4
4.01-4.09	6.7	0.465	3075	0.808	1	99.5
4.09-4.18	6.9	0.36	3061	0.867	1	99.4
4.18-4.28	6.9	0.325	3015	0.905	1	99.4
4.28-4.39	7	0.28	3080	0.978	1	99.8
4.39-4.5	7.2	0.251	3058	1.016	1	99.8
4.5-4.64	7.2	0.209	3062	1.064	1	100
4.64-4.79	7.4	0.191	3066	1.071	1	100
4.79-4.96	7.5	0.175	3097	1.089	1	100
4.96-5.16	7.6	0.169	3052	1.03	1	100
5.16-5.39	7.6	0.178	3071	1.032	1	100
5.39-5.67	7.6	0.185	3092	1.136	1	100
5.67-6.03	7.5	0.182	3063	1.226	1	100
6.03-6.49	7.5	0.154	3084	1.408	1	99.9
6.49-7.15	7.5	0.121	3095	1.654	1	99.9
7.15-8.18	7.4	0.096	3097	2.033	1	100
8.18-10.29	7.1	0.083	3103	2.352	1	99.7
10.29-50	7.4	0.097	3136	2.599	1	98.7

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 3.8→49.791 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.7828 / SU ML: 0.45 / σ(F): 1.37 / Phase error: 28.68 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2801	3127	5.1 %	RANDOM
R_work	0.2318	-	-	-
obs	0.2342	61260	99.47 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 539.5 Å² / B_iso mean: 89.6396 Å² / B_iso min: 13.53 Å²

Refinement step

Cycle: LAST / Resolution: 3.8→49.791 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28063	0	504	0	28567

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	29486
X-RAY DIFFRACTION	f_angle_d	1.242	42460
X-RAY DIFFRACTION	f_chiral_restr	0.075	4646
X-RAY DIFFRACTION	f_plane_restr	0.005	4935
X-RAY DIFFRACTION	f_dihedral_angle_d	21.454	10677

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.8-3.8594	0.3278	141	0.2911	2576	2717	97
3.8594-3.9226	0.3142	148	0.2765	2617	2765	99
3.9226-3.9903	0.3248	121	0.2606	2615	2736	99
3.9903-4.0628	0.311	137	0.242	2638	2775	99
4.0628-4.1409	0.2857	148	0.2227	2606	2754	100
4.1409-4.2254	0.2567	125	0.2101	2659	2784	99
4.2254-4.3172	0.2473	154	0.1991	2646	2800	100
4.3172-4.4176	0.2455	143	0.2001	2610	2753	100
4.4176-4.528	0.2601	139	0.1959	2609	2748	100
4.528-4.6503	0.2149	136	0.1833	2670	2806	100
4.6503-4.787	0.2504	153	0.1835	2635	2788	100
4.787-4.9414	0.2284	134	0.1881	2681	2815	100
4.9414-5.1179	0.2358	126	0.1921	2661	2787	100
5.1179-5.3225	0.2605	151	0.1964	2625	2776	100
5.3225-5.5645	0.2567	133	0.2151	2667	2800	100
5.5645-5.8574	0.2953	163	0.227	2650	2813	100
5.8574-6.2238	0.2881	161	0.2443	2611	2772	100
6.2238-6.7033	0.3236	147	0.2248	2680	2827	100
6.7033-7.3759	0.3091	149	0.23	2653	2802	100
7.3759-8.4387	0.2469	137	0.2107	2686	2823	100
8.4387-10.6149	0.2298	130	0.2075	2677	2807	100
10.6149-49.7951	0.3651	151	0.3376	2661	2812	97

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	1.3698	-0.8012	0.273	4.5378	-1.7192	2.0849	0.2362	-0.0157	-0.3193	0.2124	-0.2734	-0.3863	0.7412	0.3443	0.0376	0.2722	-0.0035	-0.0599	0.3945	0.0167	0.2771	34.5254	22.0277	125.2155
2	1.721	-0.2677	-0.233	4.3855	1.2533	1.1901	0.1337	-0.0121	-0.4858	-0.4401	-0.2365	0.8567	0.6068	-0.2083	-0.0379	0.3206	-0.1198	-0.1961	0.4465	-0.1236	0.5116	-6.8032	21.6637	118.8828
3	0.3356	1.2642	0.2818	5.5216	-0.2543	1.95	0.0761	-0.2804	0.3185	0.8425	-0.155	-0.5874	-0.7847	-0.0081	0.1007	0.8791	-0.0096	-0.1085	0.4736	-0.155	0.3288	11.6072	119.3178	141.1715
4	1.6338	-1.9763	0.0458	2.9919	-0.4308	1.2564	0.2962	0.3193	0.4869	-0.7561	-0.2801	0.2075	-0.4309	-0.0134	-0.0254	0.9457	0.0751	-0.0432	0.389	0.0217	0.3712	11.2116	119.0749	99.3435
5	3.6118	-0.26	0.2371	1.8391	-0.536	2.894	0.1072	0.08	0.2202	-0.0514	-0.239	0.3011	-0.2641	-0.0313	0.0848	0.5009	0.0175	-0.012	0.4075	-0	0.3917	13.4235	67.5524	95.1046
6	1.0129	-0.0451	-0.4079	1.9903	-0.703	1.1879	0.4439	0.9463	0.4898	-0.484	-0.5582	-0.6597	0.1864	1.059	0.1096	0.8834	0.3227	0.1818	1.3983	0.2205	0.7129	23.4736	68.1117	69.4593
7	2.1163	-0.4259	-1.0291	2.2596	-2.2415	3.8414	0.24	-0.2479	0.0133	0.0825	-0.154	-0.0021	-0.0918	0.3508	-0.0323	0.3716	-0.0648	-0.0547	0.5825	-0.0291	0.6392	38.1555	73.95	124.9768
8	1.8432	-0.4259	0.0354	3.031	-0.2692	1.2728	0.0722	0.2156	-0.1689	-0.2136	-0.0183	-0.1831	-0.0422	0.4255	-0.1504	0.5956	-0.0504	0.0701	1.2251	-0.0784	0.8665	64.7992	75.3645	119.8189
9	3.2548	0.6845	-0.2399	2.7674	0.8544	3.3461	0.1419	-0.1842	0.113	0.0156	-0.2239	-0.1066	-0.3706	-0.0287	0.0614	0.529	0.0055	0.0568	0.4728	-0.0923	0.3876	12.0862	68.6445	147.2748
10	1.0266	-0.028	-0.5716	2.2811	0.36	0.7201	0.1284	-1.1898	0.0528	0.8076	-0.1593	0.1976	0.1861	-0.4208	0.0061	1.1457	-0.1381	0.2315	1.4823	-0.2344	0.679	1.8045	69.3955	172.9066
11	1.8467	0.8145	-0.2055	2.61	1.9465	3.5098	0.0841	0.2253	-0.167	-0.1903	-0.2634	0.2714	-0.1654	-0.2169	0.1177	0.3736	0.062	-0.0354	0.6435	-0.0572	0.6536	-12.9025	72.35	117.4345
12	0.8887	-0.2137	-0.6624	2.9385	0.4509	1.72	0.1349	-0.1255	-0.0781	0.2634	-0.5187	0.3881	0.023	-1.2957	-0.0347	0.6592	0.0267	0.0324	1.5598	-0.2663	1.0679	-39.6137	70.3974	124.1699

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A	A	1 - 502
2	X-RAY DIFFRACTION	2	chain B	B	1 - 502
3	X-RAY DIFFRACTION	3	chain C	C	1 - 502
4	X-RAY DIFFRACTION	4	chain D	D	1 - 502
5	X-RAY DIFFRACTION	5	chain E and not (resseq 138:230 or resseq 366:456)	E	0
6	X-RAY DIFFRACTION	6	chain E and (resseq 138:230 or resseq 366:456)	E	138 - 230
7	X-RAY DIFFRACTION	6	chain E and (resseq 138:230 or resseq 366:456)	E	366 - 456
8	X-RAY DIFFRACTION	7	chain F and not (resseq 138:230 or resseq 366:456)	F	0
9	X-RAY DIFFRACTION	8	chain F and (resseq 138:230 or resseq 366:456)	F	138 - 230
10	X-RAY DIFFRACTION	8	chain F and (resseq 138:230 or resseq 366:456)	F	366 - 456
11	X-RAY DIFFRACTION	9	chain G and not (resseq 138:230 or resseq 366:456)	G	0
12	X-RAY DIFFRACTION	10	chain G and (resseq 138:230 or resseq 366:456)	G	138 - 230
13	X-RAY DIFFRACTION	10	chain G and (resseq 138:230 or resseq 366:456)	G	366 - 456
14	X-RAY DIFFRACTION	11	chain H and not (resseq 138:230 or resseq 366:456)	H	0
15	X-RAY DIFFRACTION	12	chain H and (resseq 138:230 or resseq 366:456)	H	138 - 230
16	X-RAY DIFFRACTION	12	chain H and (resseq 138:230 or resseq 366:456)	H	366 - 456

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