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- PDB-5hvd: Full length Open-form Sodium Channel NavMs I218C -

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Basic information

Entry
Database: PDB / ID: 5hvd
TitleFull length Open-form Sodium Channel NavMs I218C
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / Integral Membrane Voltage gated sodium channel
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity
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
Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSula, A. / Booker, J.E. / Naylor, C.E. / Wallace, B.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L02625/21 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L006790 United Kingdom
Citation
Journal: Nat Commun / Year: 2017
Title: The complete structure of an activated open sodium channel.
Authors: Sula, A. / Booker, J. / Ng, L.C. / Naylor, C.E. / DeCaen, P.G. / Wallace, B.A.
#1: Journal: Nat Commun / Year: 2013
Title: Role of the C-terminal domain in the structure and function of tetrameric sodium channels.
Authors: Bagneris, C.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4007
Polymers31,2101
Non-polymers1,1906
Water2,000111
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,60028
Polymers124,8394
Non-polymers4,76124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area21990 Å2
ΔGint-197 kcal/mol
Surface area49610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.580, 109.580, 209.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

NA

21A-302-

NA

31A-303-

NA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ion transport protein


Mass: 31209.730 Da / Num. of mol.: 1 / Mutation: I218C
Source method: isolated from a genetically manipulated source
Details: I218C mutation
Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria)
Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_0798 / Plasmid: pet15a / Production host: Escherichia coli (E. coli) / Strain (production host): CD41 / References: UniProt: A0L5S6

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#4: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 4.9 Å3/Da / Density % sol: 75 % / Description: bipyramids
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M NaCl, 0.1 M MES buffer, pH 6.5, 37.8% v/v polyethylene glycol (PEG) 400 and 4% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015 / Details: bi-morph mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 68.83 Å2
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 45.5 % / Rmerge(I) obs: 3.6 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rvy

3rvy


Resolution: 2.6→26.92 Å / Cor.coef. Fo:Fc: 0.9239 / Cor.coef. Fo:Fc free: 0.9131 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.225 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 1047 5.23 %RANDOM
Rwork0.1925 ---
obs0.1936 20032 99.91 %-
Displacement parametersBiso mean: 93.41 Å2
Baniso -1Baniso -2Baniso -3
1--10.4891 Å20 Å20 Å2
2---10.4891 Å20 Å2
3---20.9781 Å2
Refine analyzeLuzzati coordinate error obs: 0.331 Å
Refinement stepCycle: 1 / Resolution: 2.6→26.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 69 111 2156
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012081HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.052814HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d728SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes299HARMONIC5
X-RAY DIFFRACTIONt_it2081HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion17.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion282SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2399SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.74 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2421 145 5.12 %
Rwork0.2109 2688 -
all0.2124 2833 -
obs--99.37 %
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)
14.9539-2.3381-0.02943.961.768.0853-0.0474-0.13880.80050.23430.01920.0673-1.3389-0.80950.0282-0.01210.49880.0848-0.2249-0.1475-0.3146248.885-26.0447239.367
20.8156-0.2526-0.00320.87580.18983.1633-0.0125-0.2670.07220.2262-0.00280.0062-0.47340.1550.0154-0.444-0.0667-0.0127-0.5002-0.0382-0.476278.969-43.2508233.937
33.3199-3.8018-1.42640.5872-0.60333.07910.0764-0.3376-0.1630.33290.0448-0.1504-0.1283-0.1218-0.12120.5214-0.0090.01030.29440.01490.1424272.579-46.0907276.946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|-1 - A|108 }
2X-RAY DIFFRACTION2{ A|109 - A|234 }
3X-RAY DIFFRACTION3{ A|235 - A|261 }

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