7PGG

NaVAb1p detergent (DM)

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Alcanivorax borkumensis
  • Expression System: Escherichia coli
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTM

  • Deposited: 2021-08-13 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: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
A, B
147Alcanivorax borkumensisMutation(s): 0 
Gene Names: ABO_1668
Membrane Entity: Yes 
UniProt
Find proteins for Q0VNY2 (Alcanivorax borkumensis (strain ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2))
Explore Q0VNY2 
Go to UniProtKB:  Q0VNY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0VNY2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VVA
Query on VVA

Download Ideal Coordinates CCD File 
C [auth B]2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate
C21 H44 N O6 P
KBKQEKNZSDBGFI-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.471α = 90
b = 157.471β = 90
c = 106.394γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
Aimlessdata scaling
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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