PDB-4l11: Structure of the C-linker/CNBHD of agERG channels

ID or keywords:

Entry

Database: PDB / ID: 4l11

Title

Structure of the C-linker/CNBHD of agERG channels

Components

AGAP007709-PA

Keywords

METAL TRANSPORT / CNBHD / CNBD / KCNH / cyclic nucleotide binding domain /

ion transport

Function / homology

Function and homology information

regulation of monoatomic ion transmembrane transport /

voltage-gated potassium channel activity / plasma membrane => GO:0005886 / potassium ion transmembrane transport /

regulation of membrane potential
Similarity search - Function

Biological species

Anopheles gambiae (African malaria mosquito)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Brelidze, T.I.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of the C-terminal region of an ERG channel and functional implications.
Authors: Brelidze, T.I. / Gianulis, E.C. / Dimaio, F. / Trudeau, M.C. / Zagotta, W.N.

History

Deposition	Jun 1, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 26, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2013	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4l11.cif.gz	93.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4l11.ent.gz	71.9 KB	Display	PDB format
PDBx/mmJSON format	4l11.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/l1/4l11 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/4l11	HTTPS FTP

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Related structure data

Related structure data	3uknS S: Starting model for refinement
Similar structure data	3ry4-d 4yii-d 2w46-d 1h9v-d 6asb-1 4uyr-d 4jrg-d 2g3k-11 5ocl-4 4uht-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	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (5) #183 - Mar 2015 Phototropin similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (5) #251 - Nov 2020 Adenylyl Cyclase similarity (6) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (1) #207 - Mar 2017 Photoactive Yellow Protein similarity (1)

Deposited unit

A: AGAP007709-PA

23.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	51.400, 51.400, 162.031
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	AGAP007709-PA Mass: 23298.578 Da / Num. of mol.: 1 / Fragment: C-linker/CNBHD (unp residues 535-734) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Gene: AGAP007709, AgaP_AGAP007709, ERG / Plasmid: pMALc2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q7QJX3
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

AGAP007709-PA

Mass: 23298.578 Da / Num. of mol.: 1 / Fragment: C-linker/CNBHD (unp residues 535-734)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Anopheles gambiae (African malaria mosquito)
Gene: AGAP007709, AgaP_AGAP007709, ERG / Plasmid: pMALc2T / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q7QJX3

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 9 mM Urea, 18.2% (w/v) PEG 3350, 7.3 % (v/v) Tacsimate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2010
Radiation	Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.55→40.51 Å / Num. obs: 8662 / % possible obs: 100 % / Redundancy: 12.1 % / R_merge(I) obs: 0.082 / Net I/σ(I): 17
Reflection shell	Resolution: 2.55→2.69 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
BOS		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.4_486)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UKN

3ukn

Resolution: 2.55→34.351 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 26.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2562	405	4.76 %
R_work	0.2193	-	-
obs	0.2209	8511	98.32 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 71.287 Å² / k_sol: 0.345 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.55→34.351 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1517	0	0	18	1535

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	1553
X-RAY DIFFRACTION	f_angle_d	1.333	2119
X-RAY DIFFRACTION	f_dihedral_angle_d	16.116	538
X-RAY DIFFRACTION	f_chiral_restr	0.089	244
X-RAY DIFFRACTION	f_plane_restr	0.004	276

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	0.3255	0.154	-0.318	0.1476	-0.165	0.1447	-0.2682	0.2004	0.5896	0.1963	-0.1268	-0.0215	-0.9377	-0.2614	0.0011	0.8471	-0.0622	0.0072	0.3489	0.0476	0.6612	4.3657	-31.9422	19.3274
2	0.6871	-0.0516	-0.5582	0.4054	0.0402	0.404	0.8874	2.6945	-0.7391	-1.073	-1.6119	0.1428	0.038	-2.5056	-0.0138	0.9616	-0.2891	0.0264	0.9108	-0.2613	0.8464	14.2099	-27.6092	16.0195
3	0.2411	-0.1883	-0.2657	0.1102	0.1764	0.2305	-0.2091	-0.3353	-0.6903	-1.7852	2.0645	-1.7876	0.7584	0.978	-0.002	1.2676	-0.0738	0.002	0.8443	0.0915	1.4158	23.4353	-25.7582	19.0485
4	0.3844	0.36	-0.2205	0.2912	-0.135	0.21	0.331	-0.1116	-0.8393	1.3997	-0.5001	-0.3675	1.1924	-0.9035	-0.0011	1.252	-0.0852	-0.048	0.5379	0.1771	0.8321	14.7909	-28.4127	27.5113
5	0.9551	0.1092	0.2313	0.0338	0.0721	0.2156	0.9469	1.6768	0.8745	0.2145	0.9496	2.9669	1.2535	0.3313	-0.0176	1.4981	0.5258	0.0514	0.509	0.1238	1.1724	1.646	-27.7391	24.7003
6	0.4911	0.3589	0.2011	0.669	0.1222	0.077	-0.3891	0.8512	0.546	-0.4239	-0.6617	0.7194	2.5789	-1.1516	-0.0113	1.0582	0.0634	0.3328	1.0001	-0.0218	1.7893	7.5249	-20.6947	18.6755
7	0.1385	-0.009	-0.1084	-0.0392	-0.0025	0.0944	0.1281	0.6673	-0.2214	-0.2566	0.8422	0.0718	0.0107	-1.1531	-0.0006	1.2332	-0.2436	0.2721	0.7406	0.2621	1.1161	16.2297	-17.8011	27.435
8	-0.006	0.0075	-0.0165	0.113	0.1276	0.1112	-0.1339	0.3471	-0.6354	-2.1038	-0.581	1.4592	-1.4988	-0.2214	-0.0047	0.7441	0.0726	-0.1514	0.2914	0.0097	0.8364	23.6635	-15.8045	19.7926
9	0.7396	0.3323	0.5407	0.6686	0.2331	0.4032	0.1527	-0.0705	-0.9801	-0.6516	-0.1368	-0.286	0.5074	0.3385	-0.002	0.6757	0.1065	-0.0412	0.3601	-0.077	0.7919	32.3232	-10.9532	13.4844
10	0.1291	-0.2382	0.3034	1.6317	-0.0047	0.516	0.5104	-0.3304	0.2063	0.677	-0.1496	0.0771	0.8887	-0.0405	0.0011	0.636	-0.0403	0.0505	0.2918	0.0596	0.3775	26.685	-7.9655	19.0444
11	0.2149	-0.0607	0.1897	0.0145	-0.0672	0.1091	-0.2479	-0.138	-1.2864	2.297	-0.746	0.5356	-0.0177	-0.7908	-0.0012	0.8016	-0.0639	-0.0825	1.3377	0.1029	0.6614	9.0038	-10.8484	4.5982
12	0.7786	1.0707	1.2664	1.6601	0.0512	1.5876	0.0592	-0.2776	-0.2152	0.3176	-0.1726	0.4636	0.4372	-0.5008	0.0004	0.4772	0.019	-0.0283	0.4796	-0.0287	0.4424	16.3735	-4.0723	5.6823
13	1.6842	1.319	-0.1945	1.3734	0.7185	1.0505	0.0754	-0.0368	0.2583	0.164	0.1663	0.1679	0.1159	0.3092	0	0.5504	-0.0569	0.0025	0.5953	-0.1243	0.4071	18.5549	-5.9576	-2.3275
14	0.3179	-0.0712	-0.2974	0.0969	-0.04	0.2555	-0.1249	0.0561	0.1254	0.0263	0.2299	-0.2337	-0.2874	0.7574	0.0003	0.5906	0.041	0.0405	0.4783	0.0885	0.5914	25.864	7.1921	8.8986
15	0.2024	0.3555	-0.1888	0.2845	-0.2045	0.1006	-0.9784	0.5636	0.2496	-1.0004	0.6256	0.1641	-1.2879	-0.3511	0.0002	0.725	0.0307	-0.1122	0.5555	0.0033	0.5595	14.8292	3.3641	3.1252
16	0.4281	-0.2207	-0.1395	0.3761	0.3924	0.3153	0.7883	-0.9782	-0.1596	0.8741	-0.5513	1.0278	2.037	-2.0172	0.002	0.9169	-0.2333	-0.0971	0.7003	0.018	0.7096	14.7114	-15.3919	4.6209
17	0.7268	0.1629	0.9305	0.449	-0.1163	1.6955	-0.1885	0.4257	-0.06	0.3888	0.3866	0.4305	-0.2796	0.052	-0	0.5156	0.0008	0.0525	0.3339	0.0163	0.3396	25.623	1.3381	18.3376
18	0.5232	-0.1883	0.0594	0.0793	0.2451	0.5563	-0.2007	-0.2649	0.0047	0.5286	-0.2034	-0.2531	-0.3475	-0.3787	-0.0013	0.4609	0.048	-0.0047	0.4147	0.0289	0.365	35.5759	1.7905	11.8148
19	0.4632	-0.1971	0.3828	2.4627	-0.8766	0.5331	-0.7719	0.8758	0.666	-0.1331	1.617	1.139	0.0799	1.8519	0.0374	0.532	-0.0613	-0.0604	0.7519	-0.0972	0.2983	25.4283	-1.5687	0.4251
20	0.3472	-0.0439	-0.2971	-0.011	0.0351	0.2219	0.446	0.8141	0.3029	2.442	0.5144	-0.1494	-0.3655	-1.4103	-0.0012	0.7232	0.1323	0.0714	0.551	0.1767	0.647	18.9048	7.9495	0.1874

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 537:544)
2	X-RAY DIFFRACTION	2	(chain A and resid 545:551)
3	X-RAY DIFFRACTION	3	(chain A and resid 552:560)
4	X-RAY DIFFRACTION	4	(chain A and resid 561:571)
5	X-RAY DIFFRACTION	5	(chain A and resid 572:575)
6	X-RAY DIFFRACTION	6	(chain A and resid 576:584)
7	X-RAY DIFFRACTION	7	(chain A and resid 585:594)
8	X-RAY DIFFRACTION	8	(chain A and resid 595:600)
9	X-RAY DIFFRACTION	9	(chain A and resid 601:611)
10	X-RAY DIFFRACTION	10	(chain A and resid 612:630)
11	X-RAY DIFFRACTION	11	(chain A and resid 631:636)
12	X-RAY DIFFRACTION	12	(chain A and resid 637:655)
13	X-RAY DIFFRACTION	13	(chain A and resid 656:673)
14	X-RAY DIFFRACTION	14	(chain A and resid 674:680)
15	X-RAY DIFFRACTION	15	(chain A and resid 681:690)
16	X-RAY DIFFRACTION	16	(chain A and resid 691:697)
17	X-RAY DIFFRACTION	17	(chain A and resid 698:713)
18	X-RAY DIFFRACTION	18	(chain A and resid 714:723)
19	X-RAY DIFFRACTION	19	(chain A and resid 724:728)
20	X-RAY DIFFRACTION	20	(chain A and resid 729:734)

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