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

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Basic information

Entry
Database: PDB / ID: 6mvv
TitleNavAb voltage-gated sodium channel, I217C/F203A
ComponentsIon transport protein
KeywordsMEMBRANE 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
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
PHOSPHATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLenaeus, M.J. / Catterall, W.A.
CitationJournal: 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
DepositionOct 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: 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 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,66415
Polymers132,1164
Non-polymers4,54811
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18450 Å2
ΔGint-152 kcal/mol
Surface area43100 Å2
MethodPISA
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 number18
Space group name H-MP21221

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Components

#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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.75 Å3/Da / Density % sol: 78.62 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 68271 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 24
Reflection shellResolution: 2.9→3 Å / Num. unique all: 6746 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2005 2.94 %Random selection, 5%
Rwork0.216 ---
obs0.223 68252 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6983 0 209 3 7195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067371
X-RAY DIFFRACTIONf_angle_d0.83410050
X-RAY DIFFRACTIONf_dihedral_angle_d13.8494212
X-RAY DIFFRACTIONf_chiral_restr0.0481211
X-RAY DIFFRACTIONf_plane_restr0.0051179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9006-2.9730.2781430.27234671X-RAY DIFFRACTION97
2.973-3.05330.29611390.26834642X-RAY DIFFRACTION97
3.0533-3.1430.33681390.25544694X-RAY DIFFRACTION97
3.143-3.24430.2551410.25194706X-RAY DIFFRACTION97
3.2443-3.360.23661420.23524658X-RAY DIFFRACTION97
3.36-3.49420.29081410.25864709X-RAY DIFFRACTION97
3.4942-3.65290.23581420.22554683X-RAY DIFFRACTION97
3.6529-3.84490.26721430.22644707X-RAY DIFFRACTION97
3.8449-4.0850.24641380.21634707X-RAY DIFFRACTION97
4.085-4.39910.25841440.21344726X-RAY DIFFRACTION97
4.3991-4.83930.28781460.19464747X-RAY DIFFRACTION97
4.8393-5.53390.27091430.21064764X-RAY DIFFRACTION97
5.5339-6.95090.27361480.22894820X-RAY DIFFRACTION97
6.9509-26.34440.21981550.2024978X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.388-0.802-0.69642.14872.68764.41950.0841-0.27570.31420.41-0.07350.3036-0.2638-0.2091-0.00390.92510.23350.29991.459-0.39470.895699.39962.249536.3004
20.0102-0.0739-0.0470.53530.3410.21720.4113-0.14430.7838-0.3625-0.3830.4965-0.8592-0.9503-0.02590.76480.31030.20291.2434-0.27350.934897.516953.583210.6848
31.5692-1.26-1.13841.80740.3531.22140.0399-0.1482-0.0432-0.1972-0.03440.1033-0.5124-0.11050.03511.1340.20660.38931.1525-0.4451.0034104.135966.360430.0946
42.3538-1.4268-1.09152.23861.95822.23180.1633-0.16280.27430.0258-0.0004-0.0592-0.7099-0.3367-0.14170.8783-0.19630.30711.2017-0.48080.7797112.673458.377929.1023
50.2354-0.1707-0.02370.50780.23750.75380.0521-0.24330.11410.09920.05220.0022-0.04490.06260.10710.5398-0.11370.05260.6193-0.14130.1782138.556941.272218.6063
61.4622-0.2927-0.39492.20110.28251.0378-0.3037-0.8913-0.65920.52440.12570.65620.5257-0.27450.19631.179-0.41340.04391.31050.56031.11699.28313.497234.6738
73.75611.8051-3.46567.3587-4.59384.5186-0.05750.468-1.6321-0.88030.12391.16531.6167-1.3135-0.07811.1579-0.3655-0.27330.75430.1011.2835104.7562.838510.2397
82.13390.0704-2.11191.74670.66434.61670.1511-0.3458-0.35080.13120.18150.5045-0.1073-0.389-0.27931.0092-0.41180.04531.22550.54381.203692.97878.493830.2982
91.30421.10280.51565.3587-2.28971.9070.2486-0.7589-0.11590.45410.05740.66320.2683-0.5923-0.30720.8473-0.12020.21071.20510.51460.917796.055317.353631.5341
107.72211.7195-2.13988.0257-0.01362.71030.39680.1108-0.7909-0.9690.13891.51340.6793-1.2049-0.54250.793-0.3269-0.11341.03150.13290.881196.410816.120517.7321
113.7741-2.35650.6621.4722-0.33956.70450.2727-1.0151-0.9310.46770.33380.78331.0534-1.0128-0.56351.161-0.1826-0.04221.3120.40340.619108.85517.755337.2113
120.647-0.2587-0.13910.43910.26910.51410.0225-0.20870.03340.15110.01490.0443-0.0804-0.05550.14020.5624-0.07030.18540.5854-0.14020.2237117.264244.306417.9812
130.00140.0009-0.00190.0051-0.00060.00250.0291-0.1437-0.0680.1738-0.0167-0.1313-0.05650.14190.00181.0468-0.02180.08151.3015-0.01490.4199123.019731.632950.0499
142.69691.4361-2.85861.9378-3.68597.02080.0158-0.5856-0.70640.5683-0.079-0.4080.97030.52040.07261.47320.1912-0.36421.43270.42190.8052156.5383-5.623140.6827
151.9355-0.3725-0.5092.9815-0.14764.53450.2448-0.2211-0.3432-0.0968-0.2914-0.41120.98820.52410.02820.70580.2387-0.03621.10550.39660.8364155.33018.070619.5685
162.9085-0.3281-0.91183.0728-0.87423.25290.2408-0.1587-0.5373-0.2441-0.1709-0.2860.61680.10480.02591.2340.3899-0.38561.14640.29620.9519150.8621-3.156226.8712
170.0239-0.0007-0.37930.0494-0.15576.5783-0.0169-0.6155-0.48780.3669-0.01320.00930.75310.31670.03431.15220.1048-0.25761.16410.40240.7938141.73540.194528.6465
187.78642.74662.06135.4395-0.46223.5130.48310.7051-0.6905-1.0543-0.0374-0.09931.61990.2119-0.46581.48370.1119-0.18110.98770.43550.8074143.45891.555815.4128
190.7339-0.89440.57492.0468-0.41864.2442-0.0544-0.2885-0.08920.5240.1057-0.15930.33170.0402-0.05661.00330.0579-0.23941.16940.31910.5394142.269212.194334.8326
200.3434-0.8430.19622.0939-0.59920.6521-0.092-0.5751-0.35670.36590.1010.04170.33880.0993-0.04310.6347-0.1425-0.03480.78080.24120.3773113.917516.246524.398
211.2054-1.15851.71543.287-3.04723.64340.1817-0.2222-0.2343-0.45320.04390.32240.6455-0.3849-0.2230.6107-0.1653-0.11020.57360.0620.2177112.409718.66896.077
221.1145-0.55580.66450.7297-0.20291.18040.1708-0.2305-0.1685-0.06510.07490.10650.3419-0.1588-0.12710.4505-0.0895-0.03970.53160.08370.1454115.60125.353512.4463
230.1105-0.22510.37560.6932-0.44981.6991-0.0572-0.1087-0.01840.312-0.0156-0.0320.13750.1840.10050.606-0.09280.03720.85010.15510.2641116.525926.923727.6584
241.99970.69452.09411.78411.08083.3806-0.4314-0.27670.46550.53110.2545-0.4496-0.49130.48950.24811.1468-0.3304-0.00821.2305-0.54380.9198158.433159.979733.2668
253.28352.4432.98575.2686.69328.5105-0.19250.81051.3699-1.37980.2353-0.5841-1.32780.8355-0.03841.1122-0.37770.14580.8522-0.05260.8521147.863461.64578.5234
260.7778-0.35571.11733.2192-1.84994.06020.0401-0.21710.2618-0.01530.2945-0.4955-0.04230.6784-0.29350.9336-0.38540.12131.3866-0.631.0317162.030655.326326.6091
274.45581.36480.4514.19570.04534.00650.04760.2384-0.1656-0.1260.3027-0.6339-0.08420.6648-0.36690.8066-0.1995-0.15021.2971-0.49260.853160.07846.215423.8481
281.6506-0.68510.82584.0660.60330.6499-0.0325-0.47370.4670.23930.41-0.5245-0.58080.6787-0.38440.8141-0.2232-0.02650.9917-0.31760.5431152.145449.319724.0097
290.4962-0.0801-0.03190.329-0.25410.2140.0116-0.25240.0460.28650.0391-0.12080.06060.16970.01230.63-0.0023-0.16360.69480.04030.1873137.207522.294320.2563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1001 THROUGH 1030 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 1031 THROUGH 1041 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 1042 THROUGH 1073 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 1074 THROUGH 1126 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 1127 THROUGH 1222 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 2002 THROUGH 2030 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 2031 THROUGH 2041 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 2042 THROUGH 2073 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 2074 THROUGH 2088 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 2089 THROUGH 2106 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 2107 THROUGH 2126 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 2127 THROUGH 2214 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 2215 THROUGH 2229 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 1002 THROUGH 1011 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 1012 THROUGH 1041 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 1042 THROUGH 1073 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 1074 THROUGH 1088 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 1089 THROUGH 1106 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 1107 THROUGH 1126 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 1127 THROUGH 1152 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 1153 THROUGH 1162 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 1163 THROUGH 1193 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 1194 THROUGH 1218 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 2001 THROUGH 2030 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 2031 THROUGH 2041 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 2042 THROUGH 2073 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 2074 THROUGH 2095 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 2096 THROUGH 2115 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 2116 THROUGH 2222 )

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