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- PDB-5vb2: Crystal structure of the NavAb voltage-gated sodium channel in a ... -

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Basic information

Entry
Database: PDB / ID: 5vb2
TitleCrystal structure of the NavAb voltage-gated sodium channel in a closed conformation
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / 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 potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
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: 3.2 Å
AuthorsLenaeus, M.J. / Catterall, W.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structures of closed and open states of a voltage-gated sodium channel.
Authors: Lenaeus, M.J. / Gamal El-Din, T.M. / Ing, C. / Ramanadane, K. / Pomes, R. / Zheng, N. / Catterall, W.A.
History
DepositionMar 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 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

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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)147,06130
Polymers132,9014
Non-polymers14,16126
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35120 Å2
ΔGint-206 kcal/mol
Surface area48270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.963, 129.853, 196.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ion transport protein


Mass: 33225.219 Da / Num. of mol.: 4 / Mutation: T206F, V213Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5

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Non-polymers , 5 types, 48 molecules

#2: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 6.03 Å3/Da / Density % sol: 79.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate and 100 mM sodium acetate, 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC):CHAPSO bicelles

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→29.627 Å / Num. obs: 53226 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.8
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.811 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY

3rvy


Resolution: 3.2→29.63 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.17
RfactorNum. reflection% reflection
Rfree0.266 1994 3.75 %
Rwork0.233 --
obs0.235 53218 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8179 0 570 22 8771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038962
X-RAY DIFFRACTIONf_angle_d0.70112277
X-RAY DIFFRACTIONf_dihedral_angle_d14.2345005
X-RAY DIFFRACTIONf_chiral_restr0.0441505
X-RAY DIFFRACTIONf_plane_restr0.0031424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.27990.32391370.33063339X-RAY DIFFRACTION92
3.2799-3.36850.27551340.27983549X-RAY DIFFRACTION98
3.3685-3.46750.29781400.2583638X-RAY DIFFRACTION99
3.4675-3.57920.28741440.2453636X-RAY DIFFRACTION100
3.5792-3.70690.24261380.23253676X-RAY DIFFRACTION100
3.7069-3.8550.27641370.21613636X-RAY DIFFRACTION100
3.855-4.03010.22681400.20053638X-RAY DIFFRACTION100
4.0301-4.2420.25461430.20893686X-RAY DIFFRACTION100
4.242-4.50690.21071460.20053662X-RAY DIFFRACTION100
4.5069-4.85350.22851420.19843691X-RAY DIFFRACTION100
4.8535-5.33930.26181470.21493694X-RAY DIFFRACTION100
5.3393-6.1060.34461380.28663712X-RAY DIFFRACTION100
6.106-7.67080.31211490.29033773X-RAY DIFFRACTION100
7.6708-29.62850.26031590.22043894X-RAY DIFFRACTION100
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)
12.3030.25780.71132.691-0.45240.32480.40590.0628-0.1491-0.4125-0.052-0.15731.29030.80770.00010.96660.379-0.13071.19220.01871.006925.9908130.971124.5537
2-0.04220.1922-0.80251.31950.58163.19430.1881-0.1987-0.16890.35560.13-0.01490.43190.40730.0020.5557-0.02350.02510.75220.01890.7912-2.1995151.904937.2144
31.58950.65950.50070.80840.66640.48250.1840.24380.3490.1907-0.14960.062-1.26131.9704-0.00271.3927-0.6193-0.05311.5217-0.1331.109532.7299184.512222.8048
41.3163-0.5440.09320.2971-1.26172.9356-0.0997-0.4810.07870.2730.0587-0.073-0.53370.5576-0.00060.7213-0.025-0.03780.7498-0.04060.801913.8888154.361834.0068
51.5708-0.5487-0.9181.6540.01730.4764-0.1315-0.15060.1347-0.04740.20990.1839-1.9194-0.6632-0.00061.67110.49190.06711.0563-0.14851.1056-19.1636191.035429.2786
60.52510.16441.64320.9706-0.63462.96980.0721-0.25190.05340.4550.0068-0.0914-1.0256-0.20240.00380.8713-0.14540.01340.8005-0.0720.823911.4505170.659535.4186
72.55851.1567-1.56192.7865-0.77351.03260.07340.3461-0.1427-0.07450.15730.22980.5287-1.21660.00010.8779-0.24670.0741.21820.13921.0718-27.6244138.416530.9126
81.22950.1777-0.02790.35710.94982.21960.0853-0.38810.07260.13190.143-0.00690.0983-0.4070.00030.76990.06740.03460.5894-0.07310.8496-4.9712168.103937.0189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1000 THROUGH 1113 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 1114 THROUGH 1265 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 2001 THROUGH 2112 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 2113 THROUGH 2260 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 1002 THROUGH 1113 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 1114 THROUGH 1264 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 1995 THROUGH 2111 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 2112 THROUGH 2262 )

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