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- PDB-3zjz: Open-form NavMS Sodium Channel Pore (with C-terminal Domain) -

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Basic information

Entry
Database: PDB / ID: 3zjz
TitleOpen-form NavMS Sodium Channel Pore (with C-terminal Domain)
ComponentsION TRANSPORT PROTEIN
KeywordsTRANSPORT PROTEIN / SELECTIVITY FILTER / MEMBRANE PROTEIN
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ion transport protein
Similarity search - Component
Biological speciesMAGNETOCOCCUS MARINUS MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsBagneris, C. / Naylor, C.E. / Wallace, B.A.
Citation
Journal: Nat.Commun. / Year: 2013
Title: Role of the C-Terminal Domain in the Structure and Function of Tetrameric Sodium Channels.
Authors: Bagneris, C. / Decaen, P.G. / Hall, B.A. / Naylor, C.E. / Clapham, D.E. / Kay, C.W.M. / Wallace, B.A.
#1: Journal: Nat.Commun. / Year: 2012
Title: Structure of a Bacterial Voltage-Gated Sodium Channel Pore Reveals Mechanisms of Opening and Closing.
Authors: Mccusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.A.
History
DepositionJan 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)70,61916
Polymers67,3464
Non-polymers3,27312
Water2,738152
1
A: ION TRANSPORT PROTEIN
B: ION TRANSPORT PROTEIN
hetero molecules

A: ION TRANSPORT PROTEIN
B: ION TRANSPORT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,18818
Polymers67,3464
Non-polymers3,84214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area10590 Å2
ΔGint-166.9 kcal/mol
Surface area15920 Å2
MethodPISA
2
C: ION TRANSPORT PROTEIN
D: ION TRANSPORT PROTEIN
hetero molecules

C: ION TRANSPORT PROTEIN
D: ION TRANSPORT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,04914
Polymers67,3464
Non-polymers2,70310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8510 Å2
ΔGint-94.2 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.150, 334.380, 80.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1401-

NA

21C-1400-

NA

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.00221, -0.00167, -1), (-0.00138, 1, -0.00167), (1, 0.00139, 0.00221)-20.08971, -0.00958, 60.19363
2given(0.98956, 0.00587, 0.14403), (0.00667, -0.99996, -0.00507), (0.144, 0.00598, -0.98956)-2.87084, -163.81683, 46.11888
3given(0.14291, 0.00531, -0.98972), (0.00698, -0.99997, -0.00436), (-0.98971, -0.00628, -0.14294)-14.09059, -163.83861, -17.21008

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Components

#1: Protein
ION TRANSPORT PROTEIN / NAVMS


Mass: 16836.502 Da / Num. of mol.: 4 / Fragment: PORE AND CTD, RESIDUES 130-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MAGNETOCOCCUS MARINUS MC-1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0L5S6
#2: Chemical
ChemComp-2CV / HEGA-10


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


Mass: 546.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT CONSISTS OF PORE AND C-TERMINAL DOMAIN ONLY

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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: 7.6 Å3/Da / Density % sol: 84 % / Description: NONE
Crystal growpH: 8 / Details: 0.1 M NA3CITRATE, 0.1 M TRIS, PH 8.0, 34% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 23873 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 54.83 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.9
Reflection shellResolution: 2.92→3.1 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F4L

4f4l


Resolution: 2.92→45.77 Å / Cor.coef. Fo:Fc: 0.8438 / Cor.coef. Fo:Fc free: 0.6991 / SU R Cruickshank DPI: 0.408 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.413 / SU Rfree Blow DPI: 0.307 / SU Rfree Cruickshank DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1238 5.19 %RANDOM
Rwork0.2572 ---
obs0.2588 23860 99.47 %-
Displacement parametersBiso mean: 52.91 Å2
Baniso -1Baniso -2Baniso -3
1-7.3775 Å20 Å20 Å2
2---19.4132 Å20 Å2
3---12.0357 Å2
Refine analyzeLuzzati coordinate error obs: 0.411 Å
Refinement stepCycle: LAST / Resolution: 2.92→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 157 152 3184
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013197HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14429HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1026SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes444HARMONIC5
X-RAY DIFFRACTIONt_it3197HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion19.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion416SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4038SEMIHARMONIC4
LS refinement shellResolution: 2.92→3.05 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2363 146 5.23 %
Rwork0.2196 2646 -
all0.2204 2792 -
obs--99.47 %
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)
11.84720.77961.16340.6286-2.2343.0429-0.0060.09350.3190.10020.0873-0.0018-0.29160.009-0.0812-0.33590.00570.04140.17070.0288-0.0862-27.9259-63.935411.0455
23.0243.4494-0.62762.33291.1131.2966-0.0116-0.04480.3123-0.02660.1140.0759-0.37740.1715-0.1025-0.20250.0017-0.08220.18420.0068-0.2605-31.1906-63.85732.3111
30.818-0.94940.03562.0894-1.45761.5162-0.002-0.0409-0.2660.05850.0196-0.08360.2851-0.0167-0.0176-0.2441-0.0169-0.04420.19710.0359-0.1004-29.4655-99.830330.9193
44.1685-2.97321.70861.49851.01612.0612-0.0122-0.0797-0.32570.03550.0492-0.11760.22230.0199-0.037-0.21780.01850.14680.1534-0.0223-0.3315-29.3208-99.76119.3821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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