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93  structures 1280  species 0  interactions 6345  sequences 411  architectures

Family: EF-hand_6 (PF13405)

Summary: EF-hand domain

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

This is the Wikipedia entry entitled "EF hand". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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 domain Provide feedback

No Pfam abstract.

Internal 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). Ca2 binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers [ PUBMED:9228939 , PUBMED:8848832 , PUBMED:7553064 , PUBMED:7656053 , PUBMED:10591109 ].

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

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 and the UniProtKB sequence database. More...

View options

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
(544)
Full
(6345)
Representative proteomes UniProt
(13300)
RP15
(1229)
RP35
(2925)
RP55
(5264)
RP75
(6822)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(544)
Full
(6345)
Representative proteomes UniProt
(13300)
RP15
(1229)
RP35
(2925)
RP55
(5264)
RP75
(6822)
Alignment:
Format:
Order:
Sequence:
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Download options

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
(544)
Full
(6345)
Representative proteomes UniProt
(13300)
RP15
(1229)
RP35
(2925)
RP55
(5264)
RP75
(6822)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
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.

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: Jackhmmer:A3PLV3
Previous IDs: EF_hand_4;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 544
Number in full: 6345
Average length of the domain: 32.00 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 9.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 22.9
Trusted cut-off 25.0 22.9
Noise cut-off 24.9 22.8
Model length: 31
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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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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_6 domain has been found. There are 93 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0VYA3 View 3D Structure Click here
A0A0P0Y9X3 View 3D Structure Click here
A0A0R0IE10 View 3D Structure Click here
A0A1D6F2A3 View 3D Structure Click here
A0A1D6HD01 View 3D Structure Click here
A0A1D6IMS2 View 3D Structure Click here
A0A1D6IWH8 View 3D Structure Click here
A0A1D6JD07 View 3D Structure Click here
A0A1D6PB15 View 3D Structure Click here
A0A2R8Q6S0 View 3D Structure Click here
A4I3F5 View 3D Structure Click here
B0BNJ1 View 3D Structure Click here
B3DKC6 View 3D Structure Click here
B4FNQ8 View 3D Structure Click here
B6UH18 View 3D Structure Click here
B8JHU4 View 3D Structure Click here
C0P3C5 View 3D Structure Click here
C0P445 View 3D Structure Click here
C4J3M8 View 3D Structure Click here
C6SYS7 View 3D Structure Click here
C6SYS7 View 3D Structure Click here
E9QJF8 View 3D Structure Click here
F1QUS0 View 3D Structure Click here
F1QYK9 View 3D Structure Click here
F1R647 View 3D Structure Click here
I1J9Y5 View 3D Structure Click here
I1KIJ7 View 3D Structure Click here
I1LA46 View 3D Structure Click here
I1LGL7 View 3D Structure Click here
I1M4C2 View 3D Structure Click here
I1M8Q4 View 3D Structure Click here
I1M9Z0 View 3D Structure Click here
K7MY67 View 3D Structure Click here
K7V294 View 3D Structure Click here
K7V659 View 3D Structure Click here
O14950 View 3D Structure Click here
O95267 View 3D Structure Click here
P04466 View 3D Structure Click here
P18666 View 3D Structure Click here
P19105 View 3D Structure Click here
P19626 View 3D Structure Click here
P22676 View 3D Structure Click here
P24844 View 3D Structure Click here
P30626 View 3D Structure Click here
P40423 View 3D Structure Click here
P54670 View 3D Structure Click here
P91423 View 3D Structure Click here
P97457 View 3D Structure Click here
P97586 View 3D Structure Click here
Q09510 View 3D Structure Click here
Q0DJ94 View 3D Structure Click here
Q10LX4 View 3D Structure Click here
Q21153 View 3D Structure Click here
Q2QP56 View 3D Structure Click here
Q2QY10 View 3D Structure Click here
Q2R1L7 View 3D Structure Click here
Q2RAR8 View 3D Structure Click here
Q38869 View 3D Structure Click here
Q38871 View 3D Structure Click here
Q3THE2 View 3D Structure Click here
Q4CLG1 View 3D Structure Click here
Q4D2E0 View 3D Structure Click here
Q641Z8 View 3D Structure Click here
Q66I73 View 3D Structure Click here
Q6DC93 View 3D Structure Click here
Q6F334 View 3D Structure Click here
Q6H739 View 3D Structure Click here
Q6NVA6 View 3D Structure Click here
Q6P069 View 3D Structure Click here
Q6PHJ8 View 3D Structure Click here
Q6YZJ1 View 3D Structure Click here
Q7T2F7 View 3D Structure Click here
Q7XHW4 View 3D Structure Click here
Q7Z2B8 View 3D Structure Click here
Q84UL5 View 3D Structure Click here
Q8BFY6 View 3D Structure Click here
Q8LHN5 View 3D Structure Click here
Q8VZ50 View 3D Structure Click here
Q8W4L0 View 3D Structure Click here
Q96A32 View 3D Structure Click here
Q96PH1 View 3D Structure Click here
Q9CQ19 View 3D Structure Click here
Q9D9N5 View 3D Structure Click here
Q9FI19 View 3D Structure Click here
Q9SUA6 View 3D Structure Click here
Q9UBV8 View 3D Structure Click here
Q9VG88 View 3D Structure Click here
Q9W200 View 3D Structure Click here