4DXW

Crystal structure of NavRh, a voltage-gated sodium channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.052 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel

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.

(2012) Nature 486: 130-134

  • DOI: 10.1038/nature11054

  • PubMed Abstract: 
  • Voltage-gated sodium (Na(v)) channels are essential for the rapid depolarization of nerve and muscle, and are important drug targets. Determination of the structures of Na(v) channels will shed light on ion channel mechanisms and facilitate potential ...

    Voltage-gated sodium (Na(v)) channels are essential for the rapid depolarization of nerve and muscle, and are important drug targets. Determination of the structures of Na(v) channels will shed light on ion channel mechanisms and facilitate potential clinical applications. A family of bacterial Na(v) channels, exemplified by the Na(+)-selective channel of bacteria (NaChBac), provides a useful model system for structure-function analysis. Here we report the crystal structure of Na(v)Rh, a NaChBac orthologue from the marine alphaproteobacterium HIMB114 (Rickettsiales sp. HIMB114; denoted Rh), at 3.05 Å resolution. The channel comprises an asymmetric tetramer. The carbonyl oxygen atoms of Thr 178 and Leu 179 constitute an inner site within the selectivity filter where a hydrated Ca(2+) resides in the crystal structure. The outer mouth of the Na(+) selectivity filter, defined by Ser 181 and Glu 183, is closed, as is the activation gate at the intracellular side of the pore. The voltage sensors adopt a depolarized conformation in which all the gating charges are exposed to the extracellular environment. We propose that Na(v)Rh is in an 'inactivated' conformation. Comparison of Na(v)Rh with Na(v)Ab reveals considerable conformational rearrangements that may underlie the electromechanical coupling mechanism of voltage-gated channels.


    Organizational Affiliation

    State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport protein
A, B, C, D
229alpha proteobacterium HIMB114Mutation(s): 1 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
Voltage-Gated Sodium Channel (NaV)
Find proteins for D0RMU8 (alpha proteobacterium HIMB114)
Go to UniProtKB:  D0RMU8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BNG
Query on BNG

Download SDF File 
Download CCD File 
A, C
B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
PX4
Query on PX4

Download SDF File 
Download CCD File 
B
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.052 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 163.437α = 90.00
b = 163.437β = 90.00
c = 61.071γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXrefinement
SHELXSphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references