7PGH

NaVAe1/Sp1CTDp (DDM)

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Alkalilimnicola ehrlichii MLHE-1, Ruegeria pomeroyi
  • Expression System: Escherichia coli
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTM

  • Deposited: 2021-08-14 Released: 2022-06-15 
  • Deposition Author(s): Lolicato, M., Arrigoni, C.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.318 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Quaternary structure independent folding of voltage-gated ion channel pore domain subunits.

Arrigoni, C.Lolicato, M.Shaya, D.Rohaim, A.Findeisen, F.Fong, L.K.Colleran, C.M.Dominik, P.Kim, S.S.Schuermann, J.P.DeGrado, W.F.Grabe, M.Kossiakoff, A.A.Minor Jr., D.L.

(2022) Nat Struct Mol Biol 29: 537-548

  • DOI: https://doi.org/10.1038/s41594-022-00775-x
  • Primary Citation of Related Structures:  
    7PG8, 7PGB, 7PGF, 7PGG, 7PGH, 7PGI

  • PubMed Abstract: 

    Every voltage-gated ion channel (VGIC) has a pore domain (PD) made from four subunits, each comprising an antiparallel transmembrane helix pair bridged by a loop. The extent to which PD subunit structure requires quaternary interactions is unclear. Here, we present crystal structures of a set of bacterial voltage-gated sodium channel (BacNa V ) 'pore only' proteins that reveal a surprising collection of non-canonical quaternary arrangements in which the PD tertiary structure is maintained. This context-independent structural robustness, supported by molecular dynamics simulations, indicates that VGIC-PD tertiary structure is independent of quaternary interactions. This fold occurs throughout the VGIC superfamily and in diverse transmembrane and soluble proteins. Strikingly, characterization of PD subunit-binding Fabs indicates that non-canonical quaternary PD conformations can occur in full-length VGICs. Together, our data demonstrate that the VGIC-PD is an autonomously folded unit. This property has implications for VGIC biogenesis, understanding functional states, de novo channel design, and VGIC structural origins.


  • Organizational Affiliation

    Cardiovascular Research Institute, University of California, San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion transport protein,Voltage-gated sodium channel subunit143Alkalilimnicola ehrlichii MLHE-1Ruegeria pomeroyi
This entity is chimeric
Mutation(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
Find proteins for Q6TMY8 (Ruegeria pomeroyi)
Explore Q6TMY8 
Go to UniProtKB:  Q6TMY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ0ABW0Q6TMY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
12P
Query on 12P

Download Ideal Coordinates CCD File 
AA [auth H],
S [auth C],
T [auth C]
DODECAETHYLENE GLYCOL
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
PE4
Query on PE4

Download Ideal Coordinates CCD File 
I [auth F]
J [auth F]
K [auth F]
L [auth F]
N [auth A]
I [auth F],
J [auth F],
K [auth F],
L [auth F],
N [auth A],
O [auth A],
P [auth A],
W [auth G],
Y [auth H]
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
U [auth D],
Z [auth H]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
D12
Query on D12

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth B],
V [auth G],
X [auth H]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
OCT
Query on OCT

Download Ideal Coordinates CCD File 
R [auth C]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth F]
B [auth A]
C [auth B]
D [auth C]
E [auth D]
A [auth F],
B [auth A],
C [auth B],
D [auth C],
E [auth D],
F [auth E],
G,
H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.318 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.465α = 90
b = 134.696β = 90
c = 155.545γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States--
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary