5HK7 | pdb_00005hk7

Bacterial sodium channel pore, 2.95 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.236 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation.

Arrigoni, C.Rohaim, A.Shaya, D.Findeisen, F.Stein, R.A.Nurva, S.R.Mishra, S.Mchaourab, H.S.Minor, D.L.

(2016) Cell 164: 922-936

  • DOI: https://doi.org/10.1016/j.cell.2016.02.001
  • Primary Citation Related Structures: 
    5HJ8, 5HK6, 5HK7, 5HKD, 5IWN, 5IWO

  • PubMed Abstract: 

    Voltage-gated ion channels (VGICs) are outfitted with diverse cytoplasmic domains that impact function. To examine how such elements may affect VGIC behavior, we addressed how the bacterial voltage-gated sodium channel (BacNa(V)) C-terminal cytoplasmic domain (CTD) affects function. Our studies show that the BacNa(V) CTD exerts a profound influence on gating through a temperature-dependent unfolding transition in a discrete cytoplasmic domain, the neck domain, proximal to the pore. Structural and functional studies establish that the BacNa(V) CTD comprises a bi-partite four-helix bundle that bears an unusual hydrophilic core whose integrity is central to the unfolding mechanism and that couples directly to the channel activation gate. Together, our findings define a general principle for how the widespread four-helix bundle cytoplasmic domain architecture can control VGIC responses, uncover a mechanism underlying the diverse BacNa(V) voltage dependencies, and demonstrate that a discrete domain can encode the temperature-dependent response of a channel.


  • Organizational Affiliation
    • Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.

Macromolecule Content 

  • Total Structure Weight: 74.35 kDa 
  • Atom Count: 4,667 
  • Modeled Residue Count: 553 
  • Deposited Residue Count: 608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ion transport protein
A, B, C, D
152Alkalilimnicola ehrlichiiMutation(s): 0 
Gene Names: Mlg_0322
Membrane Entity: Yes 
UniProt
Find proteins for Q0ABW0 (Alkalilimnicola ehrlichii (strain ATCC BAA-1101 / DSM 17681 / MLHE-1))
Explore Q0ABW0 
Go to UniProtKB:  Q0ABW0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ABW0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VVA

Query on VVA



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
I [auth B]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
R [auth D]
2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate
C21 H44 N O6 P
KBKQEKNZSDBGFI-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
L [auth B],
Q [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.51α = 90
b = 160.52β = 90
c = 166.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description