6MWD | pdb_00006mwd

NavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Molecular dissection of multiphase inactivation of the bacterial sodium channel NaVAb.

Gamal El-Din, T.M.Lenaeus, M.J.Ramanadane, K.Zheng, N.Catterall, W.A.

(2019) J Gen Physiol 151: 174-185

  • DOI: https://doi.org/10.1085/jgp.201711884
  • Primary Citation Related Structures: 
    6MWA, 6MWB, 6MWD, 6MWG

  • PubMed Abstract: 

    Homotetrameric bacterial voltage-gated sodium channels share major biophysical features with their more complex eukaryotic counterparts, including a slow-inactivation mechanism that reduces ion-conductance activity during prolonged depolarization through conformational changes in the pore. The bacterial sodium channel Na V Ab activates at very negative membrane potentials and inactivates through a multiphase slow-inactivation mechanism. Early voltage-dependent inactivation during one depolarization is followed by late use-dependent inactivation during repetitive depolarization. Mutations that change the molecular volume of Thr206 in the pore-lining S6 segment can enhance or strongly block early voltage-dependent inactivation, suggesting that this residue serves as a molecular hub controlling the coupling of activation to inactivation. In contrast, truncation of the C-terminal tail enhances the early phase of inactivation yet completely blocks late use-dependent inactivation. Determination of the structure of a C-terminal tail truncation mutant and molecular modeling of conformational changes at Thr206 and the S6 activation gate led to a two-step model of these gating processes. First, bending of the S6 segment, local protein interactions dependent on the size of Thr206, and exchange of hydrogen-bonding partners at the level of Thr206 trigger pore opening followed by the early phase of voltage-dependent inactivation. Thereafter, conformational changes in the C-terminal tail lead to late use-dependent inactivation. These results have important implications for the sequence of conformational changes that lead to multiphase inactivation of Na V Ab and other sodium channels.


  • Organizational Affiliation
    • Department of Pharmacology, University of Washington, Seattle, WA.

Macromolecule Content 

  • Total Structure Weight: 34.49 kDa 
  • Atom Count: 2,116 
  • Modeled Residue Count: 236 
  • Deposited Residue Count: 257 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ion transport proteinA [auth B]257Aliarcobacter butzleri RM4018Mutation(s): 1 
Gene Names: Abu_1752
Membrane Entity: Yes 
UniProt
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018))
Explore A8EVM5 
Go to UniProtKB:  A8EVM5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8EVM5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PX4

Query on PX4



Download:Ideal Coordinates CCD File
B,
C [auth B],
D [auth B],
E [auth B]
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
CPS

Query on CPS



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B],
J [auth B]
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.495α = 90
b = 124.495β = 90
c = 189.669γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description