8E0E | pdb_00008e0e

nbF3:CaV beta subunit 2a complex

• PDB DOI: https://doi.org/10.2210/pdb8E0E/pdb

• Classification: TRANSPORT PROTEIN/IMMUNE SYSTEM
• Organism(s): Rattus norvegicus, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-09 Released: 2023-01-18 
• Deposition Author(s): Nirwan, N., Minor, D.L.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Selective posttranslational inhibition of Ca V beta 1 -associated voltage-dependent calcium channels with a functionalized nanobody.

Morgenstern, T.J., Nirwan, N., Hernandez-Ochoa, E.O., Bibollet, H., Choudhury, P., Laloudakis, Y.D., Ben Johny, M., Bannister, R.A., Schneider, M.F., Minor Jr., D.L., Colecraft, H.M.

(2022) Nat Commun 13: 7556-7556

• PubMed: 36494348 
• DOI: https://doi.org/10.1038/s41467-022-35025-7
• Primary Citation Related Structures: 
  8DAM, 8E0E


• PubMed Abstract: 
  

  Ca ²⁺ influx through high-voltage-activated calcium channels (HVACCs) controls diverse cellular functions. A critical feature enabling a singular signal, Ca ²⁺ influx, to mediate disparate functions is diversity of HVACC pore-forming α ₁ and auxiliary Ca _V β ₁ -Ca _V β ₄ subunits. Selective Ca _V α ₁ blockers have enabled deciphering their unique physiological roles. By contrast, the capacity to post-translationally inhibit HVACCs based on Ca _V β isoform is non-existent. Conventional gene knockout/shRNA approaches do not adequately address this deficit owing to subunit reshuffling and partially overlapping functions of Ca _V β isoforms. Here, we identify a nanobody (nb.E8) that selectively binds Ca _V β ₁ SH3 domain and inhibits Ca _V β ₁ -associated HVACCs by reducing channel surface density, decreasing open probability, and speeding inactivation. Functionalizing nb.E8 with Nedd4L HECT domain yielded Chisel-1 which eliminated current through Ca _V β ₁ -reconstituted Ca _V 1/Ca _V 2 and native Ca _V 1.1 channels in skeletal muscle, strongly suppressed depolarization-evoked Ca ²⁺ influx and excitation-transcription coupling in hippocampal neurons, but was inert against Ca _V β ₂ -associated Ca _V 1.2 in cardiomyocytes. The results introduce an original method for probing distinctive functions of ion channel auxiliary subunit isoforms, reveal additional dimensions of Ca _V β ₁ signaling in neurons, and describe a genetically-encoded HVACC inhibitor with unique properties.

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Organizational Affiliation: 
• Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA.
Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
Department of Biochemistry and Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA.
Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, USA.
Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].
Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.72 kDa 
• Atom Count: 3,787 
• Modeled Residue Count: 443 
• Deposited Residue Count: 471 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit beta-2	A	349	Rattus norvegicus	Mutation(s): 0  Gene Names: Cacnb2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody nb.F3	B	122	Lama glama	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	D [auth A], G [auth A], H [auth A], J [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL	C [auth A], E [auth A], F [auth A], I [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	L [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.525	α = 90
b = 144.525	β = 90
c = 63.596	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Nirwan, N., Minor, D.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description