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428  structures 578  species 36  interactions 4693  sequences 327  architectures

Family: EF-hand_1 (PF00036)

Summary: EF hand

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

EF hand Provide feedback

The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.

Literature references

  1. Nakayama S, Moncrief ND, Kretsinger RH; , J Mol Evol 1992;34:416-448.: Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories. PUBMED:1602495 EPMC:1602495

  2. Hogue CW, MacManus JP, Banville D, Szabo AG; , J Biol Chem 1992;267:13340-13347.: Comparison of terbium (III) luminescence enhancement in mutants of EF hand calcium binding proteins. PUBMED:1618836 EPMC:1618836

  3. Bairoch A, Cox JA; , FEBS Lett 1990;269:454-456.: EF-hand motifs in inositol phospholipid-specific phospholipase C. PUBMED:2401372 EPMC:2401372

  4. Finn BE, Forsen S; , Structure 1995;3:7-11.: The evolving model of calmodulin structure, function and activation. PUBMED:7743133 EPMC:7743133


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002048

Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite 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 EF_hand (CL0220), which has the following description:

The EF hand is a calcium binding domain found in a wide variety of proteins [1].

The clan contains the following 22 members:

Caleosin Cbl_N2 DAG_kinase_N Dockerin_1 EF-hand_1 EF-hand_10 EF-hand_11 EF-hand_2 EF-hand_3 EF-hand_4 EF-hand_5 EF-hand_6 EF-hand_7 EF-hand_8 EF-hand_9 EF-hand_like EFhand_Ca_insen IQ IQCJ-SCHIP1 p25-alpha S_100 SPARC_Ca_bdg

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
(571)
Full
(4693)
Representative proteomes UniProt
(9194)
NCBI
(62681)
Meta
(604)
RP15
(1247)
RP35
(2362)
RP55
(3588)
RP75
(4400)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(571)
Full
(4693)
Representative proteomes UniProt
(9194)
NCBI
(62681)
Meta
(604)
RP15
(1247)
RP35
(2362)
RP55
(3588)
RP75
(4400)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(571)
Full
(4693)
Representative proteomes UniProt
(9194)
NCBI
(62681)
Meta
(604)
RP15
(1247)
RP35
(2362)
RP55
(3588)
RP75
(4400)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Prosite
Previous IDs: efhand; EF_hand_1;
Type: Domain
Author: Eddy SR
Number in seed: 571
Number in full: 4693
Average length of the domain: 28.70 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 9.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.4 25.4
Trusted cut-off 25.4 25.4
Noise cut-off 25.3 25.3
Model length: 29
Family (HMM) version: 30
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 36 interactions for this family. More...

FGF KCNQ_channel PI3Ka EF-hand_7 IQ CaATP_NAI EnY2 F-actin_cap_A Death Troponin EF-hand_6 EF-hand_5 CaMBD EF-hand_1 CaMBD Pik1 S_100 Metallophos Pkinase Melittin F-actin_cap_A Synuclein Myosin_head S_100 Sfi1 CH IQ SAC3 EF-hand_8 Ca_chan_IQ EF-hand_5 EF-hand_7 MARCKS ATP_Ca_trans_C EF-hand_8 GFP

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 EF-hand_1 domain has been found. There are 428 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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