Crystal structure of NavRh, a voltage-gated sodium channel

Experimental Data Snapshot

  • Resolution: 3.05 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1038/nature11054
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion transport protein
A, B, C, D
229alpha proteobacterium HIMB114Mutation(s): 1 
Gene Names: HIMB114_0051HIMB114_1443
Membrane Entity: Yes 
Find proteins for D0RMU8 (alpha proteobacterium HIMB114)
Explore D0RMU8 
Go to UniProtKB:  D0RMU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0RMU8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.05 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.437α = 90
b = 163.437β = 90
c = 61.071γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Structure summary