8DAM | pdb_00008dam

nbF3:nbE8:CaV beta subunit 1b complex

• PDB DOI: https://doi.org/10.2210/pdb8DAM/pdb

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


• Deposited: 2022-06-13 Released: 2022-12-21 
• 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: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (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 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.62 kDa 
• Atom Count: 4,486 
• Modeled Residue Count: 541 
• Deposited Residue Count: 623 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit beta-1	A	370	Mus musculus	Mutation(s): 0  Gene Names: Cacnb1, Cacnlb1
UniProt
Find proteins for Q8R3Z5 (Mus musculus) Explore Q8R3Z5  Go to UniProtKB:  Q8R3Z5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody F3	B	123	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody E8	C	130	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	D [auth A], F [auth B], G [auth C], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.358	α = 90
b = 81.072	β = 90
c = 93.332	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-21 
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: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-30
  Changes: Structure summary