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- PDB-4cbc: Open-form NavMS Sodium Channel Pore (with C-terminal Domain) afte... -

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Basic information

Entry
Database: PDB / ID: 4cbc
TitleOpen-form NavMS Sodium Channel Pore (with C-terminal Domain) after thallium soak
ComponentsION TRANSPORT PROTEIN
KeywordsTRANSPORT PROTEIN / SODIUM CHANNEL / 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: 2.664 Å
AuthorsBagneris, C. / Naylor, C.E. / Wallace, B.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Prokaryotic Navms Channel as a Structural and Functional Model for Eukaryotic Sodium Channel Antagonism.
Authors: Bagneris, C. / Decaen, P.G. / Naylor, C.E. / Pryde, D.C. / Nobeli, I. / Clapham, D.E. / 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. / Decaen, P.G. / Hall, B.A. / Naylor, C.E. / Clapham, D.E. / Kay, C.W.M. / Wallace, B.A.
#2: 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
DepositionOct 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Dec 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)69,76116
Polymers67,3464
Non-polymers2,41512
Water1,58588
1
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)69,00214
Polymers67,3464
Non-polymers1,65610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area7400 Å2
ΔGint-107.3 kcal/mol
Surface area16720 Å2
MethodPISA
2
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)70,52018
Polymers67,3464
Non-polymers3,17414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area7640 Å2
ΔGint-113.5 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.901, 331.704, 79.933
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-1301-

NA

21A-1302-

NA

31C-1301-

NA

41C-1302-

NA

51C-1303-

NA

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.00188, 0.0008, -1), (0.00155, 1, 0.00081), (1, -0.00155, 0.00187)-19.87411, 0.0233, 59.80415
2given(0.9885, 0.02297, 0.14949), (0.02313, -0.99973, 0.00066), (0.14946, 0.0028, -0.98876)-1.86051, -162.2475, 45.89515
3given(0.15026, 0.00207, -0.98864), (0.01885, -0.99982, 0.00077), (-0.98847, -0.01875, -0.15027)-14.07262, -162.36835, -17.81792

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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) / Plasmid: PET15B / 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.: 6 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3

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Sample preparation

CrystalDensity Matthews: 7.5 Å3/Da / Density % sol: 83.5 % / 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97572
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97572 Å / Relative weight: 1
ReflectionResolution: 2.67→45.47 Å / Num. obs: 30860 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 11.7
Reflection shellResolution: 2.67→2.79 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.7 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BHA

4bha
PDB Unreleased entry


Resolution: 2.664→45.469 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 34.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2994 1576 5.1 %
Rwork0.276 --
obs0.2772 30784 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.17 Å2
Refinement stepCycle: LAST / Resolution: 2.664→45.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 125 88 3125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053113
X-RAY DIFFRACTIONf_angle_d0.9334236
X-RAY DIFFRACTIONf_dihedral_angle_d13.1591061
X-RAY DIFFRACTIONf_chiral_restr0.063506
X-RAY DIFFRACTIONf_plane_restr0.005504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6635-2.74950.34721340.3072521X-RAY DIFFRACTION95
2.7495-2.84770.36121330.29332602X-RAY DIFFRACTION100
2.8477-2.96170.29181370.28262637X-RAY DIFFRACTION100
2.9617-3.09650.26451430.26062627X-RAY DIFFRACTION100
3.0965-3.25970.28231450.26912621X-RAY DIFFRACTION100
3.2597-3.46390.28151340.26472691X-RAY DIFFRACTION100
3.4639-3.73120.33451530.252610X-RAY DIFFRACTION100
3.7312-4.10650.25981340.25292680X-RAY DIFFRACTION100
4.1065-4.70020.29761420.26012722X-RAY DIFFRACTION100
4.7002-5.91970.28051680.27972679X-RAY DIFFRACTION100
5.9197-45.47520.32521530.32172818X-RAY DIFFRACTION99
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)
14.32680.65660.23622.71690.06664.90160.0279-0.0970.69050.04360.17320.2304-0.4585-0.1385-0.09750.3190.00970.03850.51830.02830.4028-27.7254-63.21611.6843
25.2596-0.246-0.46892.93070.73264.6013-0.16550.23480.5419-0.08110.1938-0.0793-0.678-0.04440.00490.4303-0.044-0.03280.53790.01710.3333-31.6827-63.233232.2469
33.9268-0.62180.04312.9934-0.054.45350.0840.0247-0.47710.2360.11540.19060.4571-0.284-0.16490.345-0.0281-0.03130.53190.03380.3636-29.2565-99.846430.1683
44.8682-0.38220.394.13810.89044.0521-0.2076-0.1965-0.37020.10750.0919-0.23450.44750.15550.07830.3420.05460.04480.5611-0.00280.2939-29.809-99.82879.2931
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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