7PG8 | pdb_00007pg8

NaV_Ae1/Sp1CTD_pore-ANT05 complex

• PDB DOI: https://doi.org/10.2210/pdb7PG8/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Alkalilimnicola ehrlichii MLHE-1, Ruegeria pomeroyi DSS-3
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2021-08-13 Released: 2022-06-08 
• Deposition Author(s): Lolicato, M., Arrigoni, C.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.50 Å
• R-Value Free: 
  0.352 (Depositor), 0.356 (DCC) 
• R-Value Work: 
  0.303 (Depositor), 0.317 (DCC) 
• R-Value Observed: 
  0.306 (Depositor) 

Starting Model: experimental

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

• PubMed: 35655098 
• 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.
Department of Molecular Medicine, University of Pavia, Pavia, Italy.
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
Northeastern Collaborative Access Team, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
Cardiovascular Research Institute, University of California, San Francisco, CA, USA. [e-mail].
Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA. [e-mail].
California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA. [e-mail].
Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, USA. [e-mail].
Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A4B4C4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A8B4 Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - C4 

Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - C4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A4B4C4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A8B4 Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - C4 

Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - C4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 515.69 kDa 
• Atom Count: 22,623 
• Modeled Residue Count: 4,517 
• Deposited Residue Count: 4,744 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANT05 H12 fab fragment, light chain	A [auth P], B [auth M], C [auth V], D [auth S], E [auth G], F [auth D], G [auth J], H [auth A]	217	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANT05 H12 fab fragment, heavy chain	I [auth B], J [auth F], K [auth I], L, M [auth N], N [auth R], O [auth U], P [auth X]	233	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport protein,Voltage-gated sodium channel	Q [auth C], R [auth E], S [auth H], T [auth K], U [auth O], V [auth Q], W [auth T], X [auth W]	143	Alkalilimnicola ehrlichii MLHE-1, Ruegeria pomeroyi DSS-3 This entity is chimeric	Mutation(s): 0  Gene Names: Mlg_0322, SPO0030 Membrane Entity: Yes
UniProt
Find proteins for F7IVA8 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore F7IVA8  Go to UniProtKB:  F7IVA8
Find proteins for Q0ABW0 (Alkalilimnicola ehrlichii (strain ATCC BAA-1101 / DSM 17681 / MLHE-1)) Explore Q0ABW0  Go to UniProtKB:  Q0ABW0
UniProt Groups	Q0ABW0F7IVA8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.50 Å
• R-Value Free:  0.352 (Depositor), 0.356 (DCC) 
• R-Value Work:  0.303 (Depositor), 0.317 (DCC) 
• R-Value Observed: 0.306 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.175	α = 90
b = 127.175	β = 90
c = 445.206	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
XDS	data reduction
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Lolicato, M., Arrigoni, C.

---

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

Revision History  

• 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