7PGG | pdb_00007pgg

NaVAb1p detergent (DM)

• PDB DOI: https://doi.org/10.2210/pdb7PGG/pdb

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.278 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.266 (Depositor), 0.272 (DCC) 
• R-Value Observed: 
  0.267 (Depositor) 

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.

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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: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.73 kDa 
• Atom Count: 2,394 
• Modeled Residue Count: 294 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport protein	A, B	147	Alcanivorax borkumensis	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VVA	C [auth B]	2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate C21 H44 N O6 P KBKQEKNZSDBGFI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.278 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.266 (Depositor), 0.272 (DCC) 
• R-Value Observed: 0.267 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.471	α = 90
b = 157.471	β = 90
c = 106.394	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
Aimless	data scaling
XDS	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Lolicato, M., Arrigoni, C.

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Funding Organization	Location	Grant 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  

• 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