PDB-6mvw: NavAb voltage-gated sodium channel, I217C/F203W

ID or keywords:

Entry

Database: PDB / ID: 6mvw

Title

NavAb voltage-gated sodium channel, I217C/F203W

Components

Ion transport protein

Ion transporter

Keywords

MEMBRANE PROTEIN / Ion channel Voltage-gated Sodium Channel

Function / homology

Function and homology information

monoatomic cation channel activity / identical protein binding /

plasma membrane
Similarity search - Function

Biological species

Arcobacter butzleri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.198 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	6mvw.cif.gz	374 KB	Display	PDBx/mmCIF format
PDB format	pdb6mvw.ent.gz	307.4 KB	Display	PDB format
PDBx/mmJSON format	6mvw.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/6mvw ftp://data.pdbj.org/pub/pdb/validation_reports/mv/6mvw	HTTPS FTP

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Related structure data

Related structure data	6mvvC 6mvxC 6mvyC 3rvyS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6mvv-d 6c1p-d 4mvu-d 4mtf-d 4mtg-d 4mw8-d 3rvy-1 4mvr-d 4mto-d 3rvz-1 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

140 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)	126.220, 126.090, 192.880
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 / Ion transporter Mass: 33144.129 Da / Num. of mol.: 4 / Mutation: I217C, F203W 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 / Dimyristoylphosphatidylcholine Mass: 678.940 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃₆H₇₃NO₈P / Comment: DMPC, phospholipid*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.79 Å³/Da / Density % sol: 78.75 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Ammonium Sulfate, 100 mM Sodium Acetate

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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: 3.198→50 Å / Num. obs: 51427 / % possible obs: 100 % / Redundancy: 7.3 % / R_merge(I) obs: 0.186 / Net I/σ(I): 9.6
Reflection shell	Resolution: 3.198→3.312 Å / Num. unique all: 4990 / CC_1/2: 0.283

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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: 3.198→29.963 Å / Cross valid method: FREE R-VALUE / σ(F): 153.12 / Phase error: 24.1

	R_factor	Num. reflection	% reflection
R_free	0.2459	2002	3.9 %
R_work	0.2124	-	-
obs	0.2175	51426	99.76 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.198→29.963 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6850	0	356	0	7206

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7404
X-RAY DIFFRACTION	f_angle_d	0.544	10086
X-RAY DIFFRACTION	f_dihedral_angle_d	13.146	4179
X-RAY DIFFRACTION	f_chiral_restr	0.04	1192
X-RAY DIFFRACTION	f_plane_restr	0.004	1164

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 (%)
3.1988-3.2787	0.2905	142	0.2624	3409	X-RAY DIFFRACTION	94
3.2787-3.3673	0.2784	138	0.2422	3510	X-RAY DIFFRACTION	96
3.3673-3.4662	0.2643	142	0.2371	3467	X-RAY DIFFRACTION	96
3.4662-3.5779	0.2424	139	0.2269	3496	X-RAY DIFFRACTION	96
3.5779-3.7056	0.2533	145	0.2242	3519	X-RAY DIFFRACTION	96
3.7056-3.8536	0.2361	140	0.2186	3499	X-RAY DIFFRACTION	96
3.8536-4.0286	0.2252	139	0.2035	3492	X-RAY DIFFRACTION	96
4.0286-4.2404	0.2224	145	0.2075	3501	X-RAY DIFFRACTION	96
4.2404-4.5053	0.2955	146	0.2078	3546	X-RAY DIFFRACTION	96
4.5053-4.8518	0.2163	142	0.1908	3527	X-RAY DIFFRACTION	96
4.8518-5.3375	0.2683	144	0.2	3539	X-RAY DIFFRACTION	96
5.3375-6.104	0.2547	145	0.2292	3566	X-RAY DIFFRACTION	96
6.104-7.6685	0.2849	145	0.2313	3610	X-RAY DIFFRACTION	96
7.6685-29.7363	0.2168	150	0.2128	3734	X-RAY DIFFRACTION	96

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	0.2026	-0.6171	0.212	2.0613	-0.0711	2.0341	0.1663	-0.0699	-0.1391	0.7314	0.135	0.5561	0.1098	-0.7515	-0.3183	1.542	-0.3783	0.1538	1.4497	0.6621	1.1547	90.51	130.4453	44.7952
2	1.5071	-0.139	0.3829	3.3302	-0.019	0.9102	-0.1862	-0.4376	-0.6221	0.6778	0.2009	0.6351	0.5448	-0.5811	0.1074	0.9511	-0.3711	-0.0517	0.9365	0.4874	1.0906	102.6612	129.5399	29.0363
3	1.3319	0.7217	-0.0983	1.0194	-0.4085	0.2081	0.0548	-0.1603	-0.5272	-0.2459	0.2629	0.2227	0.0688	-0.572	-0.2872	0.9933	-0.3192	-0.0326	1.0371	0.4936	1.2176	96.1862	132.2643	24.2522
4	7.5628	3.2103	0.4486	3.1933	-0.3399	0.1803	0.3243	-0.5138	-0.008	0.6162	-0.2592	0.194	-0.2064	-0.1269	-0.1043	1.0001	-0.0014	0.4189	1.2247	0.4609	0.9133	95.2657	143.8026	32.7062
5	3.751	0.3096	-1.024	3.8965	1.8057	1.2025	-0.0862	0.6211	0.0949	-0.2838	0.16	0.6757	0.3018	-1.1685	-0.5914	0.8241	-0.1594	0.1102	1.2698	0.5514	0.9196	99.0352	140.7684	22.2227
6	0.8139	-0.3619	0.5999	0.4484	0.0012	0.7129	0.1834	-0.5455	0.0886	0.1969	0.067	0.0514	0.1279	-0.1104	0.516	0.6561	-0.0689	0.127	0.7861	-0.1765	0.1865	116.9007	167.2704	21.1246
7	1.2752	-0.4274	0.4857	5.152	-6.1704	8.9216	-0.0406	-0.7547	-0.3153	0.2231	0.0087	-0.2604	0.4294	0.4477	0.0444	0.8637	0.184	-0.1432	1.2202	0.1981	0.6703	156.1971	128.8983	31.3485
8	1.6176	-0.2748	0.536	2.2033	0.5679	0.4171	0.2639	-0.2461	-0.6309	-0.1161	0.512	0.1349	0.487	-0.4561	-0.675	1.061	0.2538	-0.3809	1.1504	0.1977	0.9331	152.5714	126.8774	22.082
9	1.6052	-0.0948	-1.9618	0.2469	0.273	2.5006	-0.0045	-0.2606	-0.2458	0.2797	0.2237	0.1289	0.3249	0.0947	-0.1064	1.0238	0.0462	-0.3351	1.1131	0.5003	0.9209	141.8891	126.1914	29.1218
10	4.4316	0.0064	0.6541	3.2175	-1.6427	1.4213	0.1846	0.4153	-0.2125	-0.5704	0.0184	0.1073	0.8968	0.1282	-0.4492	1.0726	0.0259	-0.1861	1.174	0.5566	0.7971	144.1645	129.6421	20.1647
11	0.1881	-0.4676	0.1184	1.2827	-0.6888	1.2533	0.0902	-0.3549	-0.3384	0.2715	0.0332	0.0458	0.2157	0.0243	-0.2298	0.6137	-0.0892	-0.0371	0.7459	0.2354	0.2614	119.7938	144.4189	20.6899
12	0.3794	0.0583	0.5888	0.2461	0.3657	1.2338	0.0436	0.1232	0.0307	-0.0068	0.0657	0.0632	-0.2196	-0.1941	-0.0656	0.4685	-0.1003	0.0333	0.6824	0.1441	0.2044	108.6192	156.1063	7.6851
13	0.247	-0.2494	0.1962	0.765	-0.1794	1.6157	-0.0411	-0.252	-0.0345	0.4824	0.018	-0.0589	-0.0741	0.3014	0.2154	0.7679	-0.0873	0.0528	0.9482	0.2156	0.2785	116.358	153.4972	27.3499
14	2.8987	0.0834	3.8951	0.9846	0.6557	5.5331	-0.441	-0.0135	0.6873	0.4604	0.087	-0.2261	-0.609	0.4927	0.5045	1.1537	-0.4002	0.0256	1.119	-0.4252	0.8787	154.8023	185.9593	26.742
15	1.7645	1.3833	-0.1137	1.3479	0.1664	0.5759	0.1772	0.2689	0.0181	0.1546	0.2094	-0.1633	0.2493	0.2549	0.1921	0.6608	-0.2519	-0.0079	1.4147	-0.5796	0.9012	161.4094	178.3034	27.9414
16	5.2399	0.2393	1.8654	5.458	-0.4459	0.7158	-0.0799	0.7874	0.0602	-0.2223	0.0798	-0.6769	-0.4189	0.7711	-0.1382	0.6348	-0.2416	-0.1757	1.0413	-0.3041	0.7164	155.1599	174.8793	20.3
17	0.3235	0.1196	0.6589	0.1567	0.3217	1.3991	0.1886	-0.4098	-0.076	0.249	-0.0826	-0.0874	-0.21	-0.0842	-0.2843	0.7045	-0.0509	-0.1211	1.1883	-0.0086	0.3513	143.7292	152.8697	27.8157
18	1.3608	-0.0531	1.1921	0.9075	-0.34	1.5047	0.1203	-0.112	-0.2048	0.1874	-0.0253	-0.0528	0.0791	-0.0206	-0.1392	0.4871	0.0231	-0.184	0.5961	0.1527	0.2496	133.9789	146.4697	15.9008
19	0.1905	0.3563	0.5953	2.5553	2.147	2.4247	0.3633	-0.0771	0.6529	0.0745	-0.2517	0.4661	-0.3593	-0.2913	0.1472	0.8841	0.1882	0.2267	1.4869	-0.2719	0.6644	98.9436	185.6894	28.8146
20	0.3946	-0.5925	0.0524	1.0439	0.1044	0.2116	-0.1067	-0.1875	-0.1038	0.0268	0.0128	0.2503	-0.0507	0.0143	0.7665	0.9568	0.1933	0.4115	1.0685	-0.4088	0.9585	107.0317	191.3973	30.38
21	0.4495	-0.0148	-0.2669	4.1234	0.0194	0.2658	0.0842	1.0361	0.4915	-1.4428	-0.0108	0.1898	-0.5498	-0.318	-0.0808	0.8888	-0.0784	-0.0268	1.1713	-0.3677	0.9303	111.7447	189.9484	15.0957
22	0.1715	-0.082	0.1479	0.1631	0.028	0.1949	-0.1533	-0.3072	0.0427	0.2817	0.0106	0.1414	-0.0967	-0.1336	-0.2389	0.7645	-0.128	0.1335	1.0025	-0.3291	0.4082	127.2702	175.8436	28.603
23	2.4513	-2.2847	-2.1325	3.5382	3.1263	3.3021	0.4976	0.192	0.3249	-0.7717	0.0409	-0.2233	-1.0018	0.2912	-0.2575	0.6808	-0.0478	-0.0056	0.4553	-0.0931	0.1996	140.1712	171.6035	4.509
24	0.0622	-0.0345	0.1152	0.3367	0.0858	0.2863	0.0215	-0.193	0.0793	0.0021	0.0278	0.0147	0.1776	0.019	0.0254	0.4947	-0.0683	-0.0056	0.8457	-0.2109	0.1823	138.2618	163.6846	17.5342

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1002 through 1011 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1012 through 1031 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1032 through 1070 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1071 through 1088 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1089 through 1113 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1114 through 1218 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2001 through 2031 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2032 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 2113 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 2114 through 2183 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 2184 through 2193 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 2194 through 2218 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1001 through 1041 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1042 through 1088 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1089 through 1113 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1114 through 1152 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1153 through 1218 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 2001 through 2041 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2042 through 2088 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 2089 through 2102 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 2103 through 2152 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 2153 through 2162 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 2163 through 2217 )

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