7PG8

NaV_Ae1/Sp1CTD_pore-ANT05 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.306 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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
ANT05 H12 fab fragment, light chain217Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ANT05 H12 fab fragment, heavy chain233Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ion transport protein,Voltage-gated sodium channel143Alkalilimnicola ehrlichii MLHE-1Ruegeria pomeroyi DSS-3
This entity is chimeric
Mutation(s): 0 
Gene Names: Mlg_0322SPO0030
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 F7IVA8 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Explore F7IVA8 
Go to UniProtKB:  F7IVA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ0ABW0F7IVA8
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.306 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.175α = 90
b = 127.175β = 90
c = 445.206γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-06-29
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description