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3  structures 175  species 0  interactions 674  sequences 39  architectures

Family: VGCC_alpha2 (PF08473)

Summary: Neuronal voltage-dependent calcium channel alpha 2acd

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Neuronal voltage-dependent calcium channel alpha 2acd Provide feedback

This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits. It is also found in other calcium channel alpha-2 delta subunits to the C-terminus of a Cache domain (PF02743).

Literature references

  1. Brust PF, Simerson S, McCue AF, Deal CR, Schoonmaker S, Williams ME, Velicelebi G, Johnson EC, Harpold MM, Ellis SB; , Neuropharmacology 1993;32:1089-1102.: Human neuronal voltage-dependent calcium channels: studies on subunit structure and role in channel assembly. PUBMED:8107964 EPMC:8107964


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013680

Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins [PUBMED:14657414]. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits.

Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels.

This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits. It is also found in other calcium channel alpha-2/delta subunits to the N terminus of a Cache domain (INTERPRO).

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Cache (CL0165), which has the following description:

The Cache domain an extracellular domain that is thought to have a role in small-molecule recognition in a wide range of proteins, including the animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors [1].

The clan contains the following 24 members:

2CSK_N Cache_3-Cache_2 CHASE CHASE4 CHASE7 CHASE8 dCache_1 dCache_2 dCache_3 Diacid_rec DUF2222 DUF4153 DUF4173 GAPES1 LuxQ-periplasm PhoQ_Sensor sCache_2 sCache_3_2 sCache_3_3 sCache_like SMP_2 Stimulus_sens_1 VGCC_alpha2 YkuI_C

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(16)
Full
(674)
Representative proteomes UniProt
(1178)
NCBI
(3220)
Meta
(0)
RP15
(137)
RP35
(261)
RP55
(469)
RP75
(588)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(16)
Full
(674)
Representative proteomes UniProt
(1178)
NCBI
(3220)
Meta
(0)
RP15
(137)
RP35
(261)
RP55
(469)
RP75
(588)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(16)
Full
(674)
Representative proteomes UniProt
(1178)
NCBI
(3220)
Meta
(0)
RP15
(137)
RP35
(261)
RP55
(469)
RP75
(588)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_4072 (release 18.0)
Previous IDs: none
Type: Family
Author: Wuster A
Number in seed: 16
Number in full: 674
Average length of the domain: 340.10 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 37.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.9 20.8
Noise cut-off 20.1 20.7
Model length: 434
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the VGCC_alpha2 domain has been found. There are 3 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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