PDB-6mvx: NavAb Voltage-gated Sodium Channel, I217C, in Complex with Class ...

ID or keywords:

Entry

Database: PDB / ID: 6mvx

Title

NavAb Voltage-gated Sodium Channel, I217C, in Complex with Class 1C Anti-arrhythmic Flecainide

Components

Ion transport protein

Keywords

MEMBRANE PROTEIN / Ion channel Voltage-gated Sodium Channel

Function / homology

Function and homology information

voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function

Biological species

Arcobacter butzleri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.455 Å

Authors

Lenaeus, M.J. / Catterall, W.A.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Fenestrations control resting-state block of a voltage-gated sodium channel.
Authors: Gamal El-Din, T.M. / Lenaeus, M.J. / Zheng, N. / Catterall, W.A.

History

Deposition	Oct 28, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 5, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 19, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Jan 2, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 11, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mvx.cif.gz	355.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6mvx.ent.gz	290.6 KB	Display	PDB format
PDBx/mmJSON format	6mvx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6mvx_validation.pdf.gz	811.8 KB	Display	wwPDB validaton report
Full document	6mvx_full_validation.pdf.gz	825.7 KB	Display
Data in XML	6mvx_validation.xml.gz	32.1 KB	Display
Data in CIF	6mvx_validation.cif.gz	42.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mv/6mvx ftp://data.pdbj.org/pub/pdb/validation_reports/mv/6mvx	HTTPS FTP

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Related structure data

Related structure data	6mvvC 6mvwC 6mvyC 3rvyS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	21446 4mtf-d 6c1p-d 6c1k-1 6mvw-d 21425 5vb8-1 4mvu-d 4mtg-d 4ms2-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	#243 - Mar 2020 Voltage-gated Sodium Channels similarity (3)

Deposited unit

A: Ion transport protein

B: Ion transport protein

C: Ion transport protein

D: Ion transport protein

hetero molecules

134 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	177.525, 177.687, 192.923
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Ion transport protein Mass: 33105.094 Da / Num. of mol.: 4 / Mutation: I217C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria) Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-K4D / Flecainide / N-{[(2R)-piperidin-2-yl]methyl}-2,5-bis(2,2,2-trifluoroethoxy)benzamide Mass: 414.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₀F₆N₂O₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.74 Å³/Da / Density % sol: 78.59 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1.8 M Ammonium Sulfate 100 mM Sodium Acetate, pH 5.0 100 uM Flecainide

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.455→50 Å / Num. obs: 39868 / % possible obs: 99.9 % / Redundancy: 6.3 % / R_merge(I) obs: 0.157 / Net I/σ(I): 8.75
Reflection shell	Resolution: 3.455→3.579 Å / Num. unique all: 3883 / CC_1/2: 0.431

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3RVY, tetramer

3rvy

Resolution: 3.455→29.855 Å / Cross valid method: FREE R-VALUE / σ(F): 411.8 / Phase error: 26.26

	R_factor	Num. reflection	% reflection
R_free	0.2629	2006	5.03 %
R_work	0.2302	-	-
obs	0.236	39852	99.17 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.455→29.855 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6509	0	78	0	6587

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6761
X-RAY DIFFRACTION	f_angle_d	0.67	9256
X-RAY DIFFRACTION	f_dihedral_angle_d	4.034	3831
X-RAY DIFFRACTION	f_chiral_restr	0.044	1132
X-RAY DIFFRACTION	f_plane_restr	0.005	1103

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.4578-3.5442	0.2691	137	0.2525	2650	X-RAY DIFFRACTION	93
3.5442-3.6398	0.26	139	0.236	2641	X-RAY DIFFRACTION	94
3.6398-3.7467	0.2821	137	0.241	2660	X-RAY DIFFRACTION	94
3.7467-3.8673	0.2315	139	0.2337	2656	X-RAY DIFFRACTION	94
3.8673-4.0052	0.2221	143	0.2162	2679	X-RAY DIFFRACTION	94
4.0052-4.165	0.2341	143	0.2219	2683	X-RAY DIFFRACTION	94
4.165-4.354	0.2706	142	0.2279	2659	X-RAY DIFFRACTION	94
4.354-4.5826	0.2666	143	0.2168	2666	X-RAY DIFFRACTION	94
4.5826-4.8684	0.2499	142	0.2173	2723	X-RAY DIFFRACTION	95
4.8684-5.2421	0.2487	145	0.2202	2744	X-RAY DIFFRACTION	95
5.2421-5.7656	0.2318	145	0.2486	2708	X-RAY DIFFRACTION	95
5.7656-6.5907	0.338	141	0.2761	2748	X-RAY DIFFRACTION	95
6.5907-8.2691	0.2813	143	0.2438	2765	X-RAY DIFFRACTION	95
8.2691-28.3113	0.2696	156	0.2369	2848	X-RAY DIFFRACTION	95

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	1.1094	-1.3809	0.5888	2.6087	0.7187	3.6552	-0.1121	-0.4934	-0.397	-0.0728	0.2896	0.2618	0.6891	-0.5223	-0.0572	1.5524	0.0257	-0.1485	1.1589	0.9721	1.5133	0.105	-83.2501	-21.6382
2	0.1635	0.5412	-0.0323	1.7887	-0.1038	0.223	-0.1171	-0.2932	-0.5301	0.1985	0.3171	0.2732	0.3117	0.0424	0.2387	1.5293	-0.2189	-0.2427	1.8083	1.2564	1.9906	-11.7395	-82.4212	-19.5466
3	4.8665	0.0639	-0.1662	2.7857	-2.0416	2.7289	0.0538	-0.5548	-0.6381	0.612	-0.0224	-0.2899	0.1847	-0.1184	-0.0393	1.065	-0.2802	-0.3655	1.2953	1.0525	2.1549	-8.0489	-75.5218	-24.7681
4	2.1813	-0.5174	0.0099	0.592	0.6716	1.3806	0.3334	-1.159	-0.2534	-0.0525	0.0369	0.0562	0.4367	0.0002	-0.0134	0.6306	-0.121	0.0998	1.2128	0.1014	-0.0538	-15.6912	-47.1439	-30.2392
5	0.94	-0.7163	-0.525	1.3409	0.9301	1.0281	-0.1492	-0.4361	-0.0811	0.4345	-0.136	0.0106	0.3954	0.4762	0.1583	0.7288	-0.3689	0.2194	1.3237	-0.0979	0.0685	-12.6645	-41.0818	-20.8415
6	3.6309	0.675	-0.9859	0.8829	0.4752	2.1209	-0.0045	-2.5109	-0.253	2.0703	0.5676	-1.7946	0.5977	1.2214	-0.6697	1.743	-0.3416	-0.8737	2.5629	-0.037	1.4105	44.0755	-52.489	-2.4414
7	3.5722	0.1398	2.2182	0.0062	0.0887	1.377	-0.1957	-1.2697	0.6275	1.6683	0.2634	-1.3835	-0.7813	1.6442	0.058	1.1549	-0.2674	-0.7202	1.7201	-0.1668	1.1338	36.0919	-42.0666	-17.0814
8	3.5409	-2.7848	-4.5676	2.212	3.6357	5.9765	0.1409	0.0124	-0.1333	0.1683	0.1847	0.0484	0.4764	0.1401	-0.2801	1.1506	-0.3202	0.0862	1.8593	-0.0551	1.0327	35.1427	-39.8284	-37.7103
9	5.2747	-1.8762	2.6104	3.2865	-0.0468	2.7279	0.301	-0.5206	0.6524	0.287	-0.0873	-0.9301	0.22	0.7461	-0.1287	0.6622	-0.0514	-0.2375	1.7976	-0.4634	1.2105	41.192	-50.1167	-21.5241
10	0.5709	1	1.6736	1.7549	2.8645	5.55	0.1875	0.1849	-0.3029	-0.6412	-0.0331	0.9409	-0.1438	-1.4408	-0.2512	2.3107	-0.0257	-1.0126	3.0075	-0.0782	1.2509	33.6264	-61.1129	-5.4405
11	0.2662	0.1575	-0.706	0.6899	1.1681	6.1336	0.0491	-1.1849	-0.3886	0.741	0.1297	-0.1829	0.2561	0.2156	-0.2352	1.3766	-0.0063	-0.8121	1.9526	0.1457	0.9213	30.7846	-57.1396	-17.0576
12	2.9987	-0.7707	-0.4578	6.0148	1.3536	0.4549	-0.3853	-0.7958	0.1208	0.8871	0.0739	-0.5711	1.219	0.8438	-0.0764	1.1133	-0.0201	-0.3029	1.299	-0.0904	0.6089	29.8649	-51.852	-23.9505
13	6.5234	5.4395	3.5463	4.8237	2.9392	1.931	0.3027	-1.5303	-0.7009	0.8139	0.0074	0.0626	-0.5284	-0.5321	0.0482	0.7672	-0.0788	-0.4756	1.6689	0.4743	0.8137	6.3996	-60.2105	-18.7193
14	9.5286	-1.9175	-1.0249	5.7636	-3.9255	5.496	0.0401	1.6759	-0.7141	-2.4109	0.1998	-0.0296	1.204	0.0773	-0.2877	1.4304	0.2153	-0.0073	0.7961	-0.0289	0.2288	-0.4908	-63.9383	-42.0534
15	2.1078	0.0156	-0.2519	1.861	0.0949	2.5563	0.3088	-0.5939	-0.4206	-0.1605	0.2141	-0.222	-0.1067	0.1155	0.1807	0.5606	-0.1496	-0.1242	0.8083	0.3448	0.4815	-4.9221	-56.9457	-30.6784
16	8.6971	-4.6201	-0.8104	2.5071	0.494	8.1933	1.154	-2.863	3.1882	2.8665	-0.6236	-0.5413	-2.4796	1.6638	-0.4347	2.4806	0.1808	0.3373	2.6002	-0.5152	1.5238	3.6455	0.8113	-5.2223
17	0.0615	0.1329	0.0061	0.302	0.0286	0.0006	-0.158	-0.0836	0.2792	-0.3025	0.1608	0.1896	-0.5661	0.1525	0.4142	1.8644	-0.3241	0.5527	1.3481	-1.1982	2.222	3.2582	-7.504	-21.7177
18	1.6116	0.3713	0.6308	1.6697	-0.0982	2.1218	0.2267	-0.5232	0.7983	0.4208	0.0325	0.0879	-0.4082	0.2687	0.0875	0.6697	-0.1998	-0.0844	1.1547	-0.3356	0.2586	12.265	-37.0839	-28.4244
19	1.1287	0.7088	0.5248	0.9095	0.1968	0.2831	0.058	-0.3968	0.1843	0.315	-0.2345	0.0893	0.086	-0.1867	0.0594	0.8258	-0.0791	-0.2705	1.2526	-0.0009	0.2499	9.7992	-49.3994	-20.6265
20	2.2187	-0.521	1.1661	1.4122	-0.1703	1.3969	0.4658	-0.6614	0.1793	0.8843	-0.0428	0.8747	-0.1018	-1.1753	-0.4865	1.5661	-0.3111	0.503	2.3811	0.5486	1.1348	-48.1364	-38.1558	-7.0311
21	5.8876	-0.2342	-1.3333	7.2792	-0.4104	1.2362	0.0577	-0.7002	0.2348	-0.0612	0.0508	1.0525	0.3317	-1.0037	0.0131	0.5396	-0.1443	0.1044	1.7436	0.0739	0.7967	-38.0625	-48.1858	-28.5606
22	4.5795	1.0001	-1.5772	4.8091	1.7821	3.8695	0.2058	-0.3268	0.5191	0.3559	-0.0249	0.4367	-0.1449	0.2813	-0.4645	0.7477	0.0421	0.3707	2.4657	0.1781	0.6423	-42.6575	-36.7079	-21.8195
23	6.7145	-0.0591	-3.94	4.2549	-1.4267	2.8143	0.3779	-1.2881	0.6056	0.7471	0.1545	0.3027	-0.6801	0.1077	-0.5554	0.8451	0.0718	0.486	2.164	-0.0431	0.9293	-34.0124	-32.3349	-20.1037
24	3.0605	1.1039	-1.5474	1.4509	-0.2717	2.2106	-0.1587	-0.3911	0.1006	0.4458	0.3122	0.2967	0.336	-0.638	-0.1564	0.9486	-0.1681	0.3636	1.6193	0.0742	0.335	-27.817	-38.9888	-19.6535
25	0.1296	-0.1209	-0.113	0.2072	0.2438	0.2967	-0.1122	-0.3935	0.1001	0.2095	-0.2502	0.3635	0.0459	-0.4317	-0.2929	1.2711	-0.0688	0.6311	1.4924	-0.8083	1.0373	-3.1091	-23.5707	-24.5015
26	3.0548	0.4051	-0.2523	3.087	-0.2661	2.0713	0.4497	-0.0929	0.9366	0.0096	0.0068	0.02	-0.6081	-0.1395	-0.2351	0.8521	-0.1021	0.0778	0.7595	-0.3887	0.4969	1.8614	-30.8669	-37.8618
27	2.8125	-0.5488	1.4121	2.786	2.0039	2.6478	0.1159	-0.9499	0.3579	0.3405	0.0077	-0.2739	-0.2153	0.4453	-0.1727	0.8209	-0.2523	0.164	1.464	-0.6126	0.7803	2.8134	-33.9266	-20.3107

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1003 through 1041 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1042 through 1096 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1097 through 1112 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1113 through 1193 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1194 through 1220 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2002 through 2011 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2012 through 2029 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2030 through 2041 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2042 through 2065 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2066 through 2074 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 2075 through 2088 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 2089 through 2113 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 2114 through 2151 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 2152 through 2162 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 2163 through 2217 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1002 through 1011 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1012 through 1088 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1089 through 1193 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 1194 through 1219 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2002 through 2011 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 2012 through 2041 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 2042 through 2073 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 2074 through 2088 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 2089 through 2127 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 2128 through 2151 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 2152 through 2193 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 2194 through 2218 )

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About Yorodumi

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi