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- PDB-3rvy: Crystal structure of the NavAb voltage-gated sodium channel (Ile2... -

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Basic information

Entry
Database: PDB / ID: 3rvy
TitleCrystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.7 A)
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / tetrameric ion channel / voltage-gated sodium-selective ion channel / membrane
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
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPayandeh, J. / Scheuer, T. / Zheng, N. / Catterall, W.A.
CitationJournal: Nature / Year: 2011
Title: The crystal structure of a voltage-gated sodium channel.
Authors: Payandeh, J. / Scheuer, T. / Zheng, N. / Catterall, W.A.
History
DepositionMay 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,00012
Polymers66,2102
Non-polymers6,78910
Water362
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)145,99924
Polymers132,4204
Non-polymers13,57920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area18820 Å2
ΔGint-160 kcal/mol
Surface area44270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.594, 125.483, 192.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ion transport protein


Mass: 33105.094 Da / Num. of mol.: 2 / Mutation: I217C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Strain: RM4018 / Gene: Abu_1752 / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 5.72 Å3/Da / Density % sol: 78.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: CHAPSO:DMPC bicelles, 2 M ammonium sulphate, 0.1 M Na-citrate pH 4.75, 28% glucose, 0.01 M YCl3, nicotinic acid (sat.), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99994 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2010
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 42048 / Num. obs: 36497 / % possible obs: 86.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.12
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.69 / % possible all: 55.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: Built using SAD data sets from Hg and SeMet crystals
RfactorNum. reflectionSelection details
Rfree0.273 1816 random
Rwork0.266 --
all0.273 42048 -
obs0.266 36494 -
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 95 2 3717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009438
X-RAY DIFFRACTIONc_angle_deg1.18869
LS refinement shellResolution: 2.7→2.73 Å
RfactorNum. reflection
Rfree0.3915 20
Rwork0.3924 -
obs-454

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