7PGH | pdb_00007pgh

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 (Depositor), 0.347 (DCC) 
  • R-Value Work: 
    0.318 (Depositor), 0.324 (DCC) 
  • R-Value Observed: 
    0.318 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7PGH

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 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.

Macromolecule Content 

  • Total Structure Weight: 136.95 kDa 
  • Atom Count: 8,697 
  • Modeled Residue Count: 1,043 
  • Deposited Residue Count: 1,144 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.347 (DCC) 
  • R-Value Work:  0.318 (Depositor), 0.324 (DCC) 
  • R-Value Observed: 0.318 (Depositor) 
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



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