PDB-6mvv: NavAb voltage-gated sodium channel, I217C/F203A

ID or keywords:

Entry

Database: PDB / ID: 6mvv

Title

NavAb voltage-gated sodium channel, I217C/F203A

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: 2.9 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mvv.cif.gz	374.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6mvv.ent.gz	307.7 KB	Display	PDB format
PDBx/mmJSON format	6mvv.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/mv/6mvv ftp://data.pdbj.org/pub/pdb/validation_reports/mv/6mvv	HTTPS FTP

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Related structure data

Related structure data	6mvwC 6mvxC 6mvyC 3rvyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6mvw-d 6c1p-d 3rvy-1 6keb-d 4mvu-d 6p6w-d 4mtf-d 5klg-d 4mw8-d 5kls-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 (4) #237 - Sep 2019 Nanodiscs and HDL similarity (1)

Deposited unit

A: Ion transport protein

B: Ion transport protein

C: Ion transport protein

D: Ion transport protein

hetero molecules

137 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)	125.782, 125.969, 192.299
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁22₁

#1: Protein	Ion transport protein Mass: 33028.996 Da / Num. of mol.: 4 / Mutation: F203A, 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-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE Mass: 678.940 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₆H₇₃NO₈P / Comment: DMPC, phospholipid*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / 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: 5.75 Å³/Da / Density % sol: 78.62 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 1.8 M Ammonium Sulfate 100mM Sodium Acetate, pH 5.0

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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: 2.9→50 Å / Num. obs: 68271 / % possible obs: 99.9 % / Redundancy: 7 % / R_merge(I) obs: 0.138 / Net I/σ(I): 24
Reflection shell	Resolution: 2.9→3 Å / Num. unique all: 6746 / CC_1/2: 0.58

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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: 2.9→29.93 Å / Cross valid method: FREE R-VALUE / σ(F): 89.07 / Phase error: 25.69

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.256	2005	2.94 %	Random selection, 5%
R_work	0.216	-	-	-
obs	0.223	68252	99.9 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.9→29.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6983	0	209	3	7195

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7371
X-RAY DIFFRACTION	f_angle_d	0.834	10050
X-RAY DIFFRACTION	f_dihedral_angle_d	13.849	4212
X-RAY DIFFRACTION	f_chiral_restr	0.048	1211
X-RAY DIFFRACTION	f_plane_restr	0.005	1179

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 (%)
2.9006-2.973	0.278	143	0.2723	4671	X-RAY DIFFRACTION	97
2.973-3.0533	0.2961	139	0.2683	4642	X-RAY DIFFRACTION	97
3.0533-3.143	0.3368	139	0.2554	4694	X-RAY DIFFRACTION	97
3.143-3.2443	0.255	141	0.2519	4706	X-RAY DIFFRACTION	97
3.2443-3.36	0.2366	142	0.2352	4658	X-RAY DIFFRACTION	97
3.36-3.4942	0.2908	141	0.2586	4709	X-RAY DIFFRACTION	97
3.4942-3.6529	0.2358	142	0.2255	4683	X-RAY DIFFRACTION	97
3.6529-3.8449	0.2672	143	0.2264	4707	X-RAY DIFFRACTION	97
3.8449-4.085	0.2464	138	0.2163	4707	X-RAY DIFFRACTION	97
4.085-4.3991	0.2584	144	0.2134	4726	X-RAY DIFFRACTION	97
4.3991-4.8393	0.2878	146	0.1946	4747	X-RAY DIFFRACTION	97
4.8393-5.5339	0.2709	143	0.2106	4764	X-RAY DIFFRACTION	97
5.5339-6.9509	0.2736	148	0.2289	4820	X-RAY DIFFRACTION	97
6.9509-26.3444	0.2198	155	0.202	4978	X-RAY DIFFRACTION	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	0.388	-0.802	-0.6964	2.1487	2.6876	4.4195	0.0841	-0.2757	0.3142	0.41	-0.0735	0.3036	-0.2638	-0.2091	-0.0039	0.9251	0.2335	0.2999	1.459	-0.3947	0.8956	99.399	62.2495	36.3004
2	0.0102	-0.0739	-0.047	0.5353	0.341	0.2172	0.4113	-0.1443	0.7838	-0.3625	-0.383	0.4965	-0.8592	-0.9503	-0.0259	0.7648	0.3103	0.2029	1.2434	-0.2735	0.9348	97.5169	53.5832	10.6848
3	1.5692	-1.26	-1.1384	1.8074	0.353	1.2214	0.0399	-0.1482	-0.0432	-0.1972	-0.0344	0.1033	-0.5124	-0.1105	0.0351	1.134	0.2066	0.3893	1.1525	-0.445	1.0034	104.1359	66.3604	30.0946
4	2.3538	-1.4268	-1.0915	2.2386	1.9582	2.2318	0.1633	-0.1628	0.2743	0.0258	-0.0004	-0.0592	-0.7099	-0.3367	-0.1417	0.8783	-0.1963	0.3071	1.2017	-0.4808	0.7797	112.6734	58.3779	29.1023
5	0.2354	-0.1707	-0.0237	0.5078	0.2375	0.7538	0.0521	-0.2433	0.1141	0.0992	0.0522	0.0022	-0.0449	0.0626	0.1071	0.5398	-0.1137	0.0526	0.6193	-0.1413	0.1782	138.5569	41.2722	18.6063
6	1.4622	-0.2927	-0.3949	2.2011	0.2825	1.0378	-0.3037	-0.8913	-0.6592	0.5244	0.1257	0.6562	0.5257	-0.2745	0.1963	1.179	-0.4134	0.0439	1.3105	0.5603	1.116	99.2831	3.4972	34.6738
7	3.7561	1.8051	-3.4656	7.3587	-4.5938	4.5186	-0.0575	0.468	-1.6321	-0.8803	0.1239	1.1653	1.6167	-1.3135	-0.0781	1.1579	-0.3655	-0.2733	0.7543	0.101	1.2835	104.756	2.8385	10.2397
8	2.1339	0.0704	-2.1119	1.7467	0.6643	4.6167	0.1511	-0.3458	-0.3508	0.1312	0.1815	0.5045	-0.1073	-0.389	-0.2793	1.0092	-0.4118	0.0453	1.2255	0.5438	1.2036	92.9787	8.4938	30.2982
9	1.3042	1.1028	0.5156	5.3587	-2.2897	1.907	0.2486	-0.7589	-0.1159	0.4541	0.0574	0.6632	0.2683	-0.5923	-0.3072	0.8473	-0.1202	0.2107	1.2051	0.5146	0.9177	96.0553	17.3536	31.5341
10	7.7221	1.7195	-2.1398	8.0257	-0.0136	2.7103	0.3968	0.1108	-0.7909	-0.969	0.1389	1.5134	0.6793	-1.2049	-0.5425	0.793	-0.3269	-0.1134	1.0315	0.1329	0.8811	96.4108	16.1205	17.7321
11	3.7741	-2.3565	0.662	1.4722	-0.3395	6.7045	0.2727	-1.0151	-0.931	0.4677	0.3338	0.7833	1.0534	-1.0128	-0.5635	1.161	-0.1826	-0.0422	1.312	0.4034	0.619	108.855	17.7553	37.2113
12	0.647	-0.2587	-0.1391	0.4391	0.2691	0.5141	0.0225	-0.2087	0.0334	0.1511	0.0149	0.0443	-0.0804	-0.0555	0.1402	0.5624	-0.0703	0.1854	0.5854	-0.1402	0.2237	117.2642	44.3064	17.9812
13	0.0014	0.0009	-0.0019	0.0051	-0.0006	0.0025	0.0291	-0.1437	-0.068	0.1738	-0.0167	-0.1313	-0.0565	0.1419	0.0018	1.0468	-0.0218	0.0815	1.3015	-0.0149	0.4199	123.0197	31.6329	50.0499
14	2.6969	1.4361	-2.8586	1.9378	-3.6859	7.0208	0.0158	-0.5856	-0.7064	0.5683	-0.079	-0.408	0.9703	0.5204	0.0726	1.4732	0.1912	-0.3642	1.4327	0.4219	0.8052	156.5383	-5.6231	40.6827
15	1.9355	-0.3725	-0.509	2.9815	-0.1476	4.5345	0.2448	-0.2211	-0.3432	-0.0968	-0.2914	-0.4112	0.9882	0.5241	0.0282	0.7058	0.2387	-0.0362	1.1055	0.3966	0.8364	155.3301	8.0706	19.5685
16	2.9085	-0.3281	-0.9118	3.0728	-0.8742	3.2529	0.2408	-0.1587	-0.5373	-0.2441	-0.1709	-0.286	0.6168	0.1048	0.0259	1.234	0.3899	-0.3856	1.1464	0.2962	0.9519	150.8621	-3.1562	26.8712
17	0.0239	-0.0007	-0.3793	0.0494	-0.1557	6.5783	-0.0169	-0.6155	-0.4878	0.3669	-0.0132	0.0093	0.7531	0.3167	0.0343	1.1522	0.1048	-0.2576	1.1641	0.4024	0.7938	141.7354	0.1945	28.6465
18	7.7864	2.7466	2.0613	5.4395	-0.4622	3.513	0.4831	0.7051	-0.6905	-1.0543	-0.0374	-0.0993	1.6199	0.2119	-0.4658	1.4837	0.1119	-0.1811	0.9877	0.4355	0.8074	143.4589	1.5558	15.4128
19	0.7339	-0.8944	0.5749	2.0468	-0.4186	4.2442	-0.0544	-0.2885	-0.0892	0.524	0.1057	-0.1593	0.3317	0.0402	-0.0566	1.0033	0.0579	-0.2394	1.1694	0.3191	0.5394	142.2692	12.1943	34.8326
20	0.3434	-0.843	0.1962	2.0939	-0.5992	0.6521	-0.092	-0.5751	-0.3567	0.3659	0.101	0.0417	0.3388	0.0993	-0.0431	0.6347	-0.1425	-0.0348	0.7808	0.2412	0.3773	113.9175	16.2465	24.398
21	1.2054	-1.1585	1.7154	3.287	-3.0472	3.6434	0.1817	-0.2222	-0.2343	-0.4532	0.0439	0.3224	0.6455	-0.3849	-0.223	0.6107	-0.1653	-0.1102	0.5736	0.062	0.2177	112.4097	18.6689	6.077
22	1.1145	-0.5558	0.6645	0.7297	-0.2029	1.1804	0.1708	-0.2305	-0.1685	-0.0651	0.0749	0.1065	0.3419	-0.1588	-0.1271	0.4505	-0.0895	-0.0397	0.5316	0.0837	0.1454	115.601	25.3535	12.4463
23	0.1105	-0.2251	0.3756	0.6932	-0.4498	1.6991	-0.0572	-0.1087	-0.0184	0.312	-0.0156	-0.032	0.1375	0.184	0.1005	0.606	-0.0928	0.0372	0.8501	0.1551	0.2641	116.5259	26.9237	27.6584
24	1.9997	0.6945	2.0941	1.7841	1.0808	3.3806	-0.4314	-0.2767	0.4655	0.5311	0.2545	-0.4496	-0.4913	0.4895	0.2481	1.1468	-0.3304	-0.0082	1.2305	-0.5438	0.9198	158.4331	59.9797	33.2668
25	3.2835	2.443	2.9857	5.268	6.6932	8.5105	-0.1925	0.8105	1.3699	-1.3798	0.2353	-0.5841	-1.3278	0.8355	-0.0384	1.1122	-0.3777	0.1458	0.8522	-0.0526	0.8521	147.8634	61.6457	8.5234
26	0.7778	-0.3557	1.1173	3.2192	-1.8499	4.0602	0.0401	-0.2171	0.2618	-0.0153	0.2945	-0.4955	-0.0423	0.6784	-0.2935	0.9336	-0.3854	0.1213	1.3866	-0.63	1.0317	162.0306	55.3263	26.6091
27	4.4558	1.3648	0.451	4.1957	0.0453	4.0065	0.0476	0.2384	-0.1656	-0.126	0.3027	-0.6339	-0.0842	0.6648	-0.3669	0.8066	-0.1995	-0.1502	1.2971	-0.4926	0.853	160.078	46.2154	23.8481
28	1.6506	-0.6851	0.8258	4.066	0.6033	0.6499	-0.0325	-0.4737	0.467	0.2393	0.41	-0.5245	-0.5808	0.6787	-0.3844	0.8141	-0.2232	-0.0265	0.9917	-0.3176	0.5431	152.1454	49.3197	24.0097
29	0.4962	-0.0801	-0.0319	0.329	-0.2541	0.214	0.0116	-0.2524	0.046	0.2865	0.0391	-0.1208	0.0606	0.1697	0.0123	0.63	-0.0023	-0.1636	0.6948	0.0403	0.1873	137.2075	22.2943	20.2563

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1001 THROUGH 1030 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 1031 THROUGH 1041 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 1042 THROUGH 1073 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 1074 THROUGH 1126 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 1127 THROUGH 1222 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 2002 THROUGH 2030 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 2031 THROUGH 2041 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 2042 THROUGH 2073 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 2074 THROUGH 2088 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 2089 THROUGH 2106 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 2107 THROUGH 2126 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 2127 THROUGH 2214 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 2215 THROUGH 2229 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 1002 THROUGH 1011 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 1012 THROUGH 1041 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 1042 THROUGH 1073 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 1074 THROUGH 1088 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 1089 THROUGH 1106 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 1107 THROUGH 1126 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 1127 THROUGH 1152 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 1153 THROUGH 1162 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 1163 THROUGH 1193 )
23	X-RAY DIFFRACTION	23	CHAIN 'C' AND (RESID 1194 THROUGH 1218 )
24	X-RAY DIFFRACTION	24	CHAIN 'D' AND (RESID 2001 THROUGH 2030 )
25	X-RAY DIFFRACTION	25	CHAIN 'D' AND (RESID 2031 THROUGH 2041 )
26	X-RAY DIFFRACTION	26	CHAIN 'D' AND (RESID 2042 THROUGH 2073 )
27	X-RAY DIFFRACTION	27	CHAIN 'D' AND (RESID 2074 THROUGH 2095 )
28	X-RAY DIFFRACTION	28	CHAIN 'D' AND (RESID 2096 THROUGH 2115 )
29	X-RAY DIFFRACTION	29	CHAIN 'D' AND (RESID 2116 THROUGH 2222 )

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-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

-
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