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7  structures 83  species 0  interactions 334  sequences 9  architectures

Family: CaMBD (PF02888)

Summary: Calmodulin binding domain

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Calmodulin binding domain Edit Wikipedia article

CaMBD
PDB 1kkd EBI.jpg
solution structure of the calmodulin binding domain (cambd) of small conductanceCa2+-activated potassium channels (sk2)
Identifiers
Symbol CaMBD
Pfam PF02888
InterPro IPR004178
SCOP 1kkd
SUPERFAMILY 1kkd

In molecular biology, calmodulin binding domain (CaMBD) is a protein domain found in small-conductance calcium-activated potassium channels (SK channels). These channels are independent of voltage and gated solely by intracellular Ca2+. They are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM).[1] CaM binds to the SK channel through the CaMBD, which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known.[1] This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.

References[edit]

  1. ^ a b Schumacher MA, Rivard AF, Bachinger HP, Adelman JP (April 2001). "Structure of the gating domain of a Ca2+-activated K+ channel complexed with Ca2+/calmodulin". Nature 410 (6832): 1120–4. doi:10.1038/35074145. PMID 11323678. 

This article incorporates text from the public domain Pfam and InterPro IPR004178

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Calmodulin binding domain Provide feedback

Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM) [1]. CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known [1]. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.

Literature references

  1. Schumacher MA, Rivard AF, Bachinger HP, Adelman JP; , Nature 2001;410:1120-1124.: Structure of the gating domain of a Ca2+-activated K+ channel complexed with Ca2+/calmodulin. PUBMED:11323678 EPMC:11323678


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004178

Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM) [PUBMED:11323678]. CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known [PUBMED:11323678]. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.

Gene Ontology

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Domain organisation

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Alignments

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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.

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Full
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Representative proteomes NCBI
(297)
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RP35
(45)
RP55
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RP75
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  Seed
(5)
Full
(334)
Representative proteomes NCBI
(297)
Meta
(0)
RP15
(31)
RP35
(45)
RP55
(98)
RP75
(163)
Alignment:
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  Seed
(5)
Full
(334)
Representative proteomes NCBI
(297)
Meta
(0)
RP15
(31)
RP35
(45)
RP55
(98)
RP75
(163)
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Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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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: Psi-blast P70604/413-489
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 5
Number in full: 334
Average length of the domain: 74.40 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 13.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 28.8 28.1
Noise cut-off 23.7 22.9
Model length: 77
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 CaMBD domain has been found. There are 7 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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