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- PDB-4dxw: Crystal structure of NavRh, a voltage-gated sodium channel -

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Basic information

Entry
Database: PDB / ID: 4dxw
TitleCrystal structure of NavRh, a voltage-gated sodium channel
ComponentsIon transport proteinIon transporter
KeywordsTRANSPORT PROTEIN / tetrameric / voltage-gated sodium channel / sodium selective / voltage-gated ion channel
Function / homology
Function and homology information


monoatomic cation channel activity / membrane => GO:0016020 / calcium ion binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channels. Chain C / Polycystic kidney disease type 2 protein / 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 ...Voltage-gated potassium channels. Chain C / Polycystic kidney disease type 2 protein / 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
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesalpha proteobacterium HIMB114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.052 Å
AuthorsZhang, X. / Ren, W.L. / Yan, C.Y. / Wang, J.W. / Yan, N.
CitationJournal: Nature / Year: 2012
Title: Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel
Authors: Zhang, X. / Ren, W.L. / DeCaen, P. / Yan, C.Y. / Tao, X. / Tang, L. / Wang, J.J. / Hasegawa, K. / Kumasaka, T. / He, J.H. / Wang, J.W. / Clapham, D.E. / Yan, N.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)107,98711
Polymers106,0024
Non-polymers1,9857
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18000 Å2
ΔGint-148 kcal/mol
Surface area39710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.437, 163.437, 61.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
Ion transport protein / Ion transporter / NavRh


Mass: 26500.607 Da / Num. of mol.: 4 / Mutation: S208G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) alpha proteobacterium HIMB114 (bacteria)
Gene: HIMB114_0051, HIMB114_1443 / Production host: Escherichia coli (E. coli) / References: UniProt: D0RMU8
#2: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.85 Å3/Da / Density % sol: 68.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG 8000 (v/v), 100mM HEPES-NaOH, pH 7.0, 100mM CaCl2, 10% Glycerol, 20% 1,4-Butandiol, VAPOR DIFFUSION, HANGING DROP, temperature 291KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 31124 / Num. obs: 31031 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.05→3.16 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.052→45.329 Å / Occupancy max: 1 / Occupancy min: 0.67 / FOM work R set: 0.7241 / SU ML: 0.49 / σ(F): 1.34 / Phase error: 33.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1429 4.61 %THIN SHELL
Rwork0.2372 ---
all0.2389 31124 --
obs0.2389 31018 99.64 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.73 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso max: 237.88 Å2 / Biso mean: 95.8998 Å2 / Biso min: 39.04 Å2
Baniso -1Baniso -2Baniso -3
1-3.1301 Å20 Å2-0 Å2
2--3.1301 Å20 Å2
3----6.2647 Å2
Refinement stepCycle: LAST / Resolution: 3.052→45.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 121 6 6914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117068
X-RAY DIFFRACTIONf_angle_d1.4529621
X-RAY DIFFRACTIONf_dihedral_angle_d21.7632558
X-RAY DIFFRACTIONf_chiral_restr0.0931216
X-RAY DIFFRACTIONf_plane_restr0.0061107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0525-3.1616000.3105301999
3.1616-3.2881000.27513077100
3.2881-3.43770.33294040.24462690100
3.4377-3.6189000.25393098100
3.6189-3.84550.293870.2352699100
3.8455-4.1422000.22943099100
4.1422-4.55870.30912760.21932818100
4.5587-5.2175000.21513120100
5.2175-6.57040.39672150.28722937100
6.5704-45.33420.15861470.2178303298
Refinement TLS params.Method: refined / Origin x: 44.7968 Å / Origin y: -38.6596 Å / Origin z: 14.9821 Å
111213212223313233
T0.3993 Å2-0.0014 Å20.0763 Å2-0.3241 Å20.0539 Å2--0.3763 Å2
L1.3106 °20.1362 °2-0.0358 °2-1.7756 °2-0.1166 °2--2.61 °2
S-0.1058 Å °-0.0673 Å °0.0269 Å °0.2134 Å °-0.0382 Å °-0.0358 Å °0.011 Å °0.0283 Å °0.0953 Å °
Refinement TLS groupSelection details: all

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