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266  structures 1700  species 0  interactions 25318  sequences 1057  architectures

Family: EF-hand_8 (PF13833)

Summary: EF-hand domain pair

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

EF hand Edit Wikipedia article

The EF hand is a helix-turn-helix structural motif in proteins. It consists of two alpha helices positioned roughly perpendicular to one another and linked by a short loop region (usually about 12 amino acids) that often binds calcium ions. The motif takes its name from traditional nomenclature used in describing the protein parvalbumin, which contains three such motifs and is probably involved in muscle relaxation via its calcium-binding activity. EF hands also appear in each structural domain of the signaling protein calmodulin and in the muscle protein troponin-C.

Sequence specificity

The calcium ion is bound by both protein backbone atoms and by amino acid side chains, specifically those of aspartate and glutamate. The EF hand motif was among the first structural motifs whose sequence requirements were analyzed in detail. Five of the loop residues bind calcium and thus have a strong preference for oxygen-containing side chains, especially aspartate and glutamate. The sixth residue in the loop is necessarily glycine due to the conformational requirements of the backbone. The remaining residues are typically hydrophobic and form a hydrophobic core that binds the stabilizes the two helices.

Another distinct calcium-binding motif composed of alpha helices is the dockerin domain.

External links

References

  • Branden C, Tooze J. (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY.

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 pair 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
(34)
Full
(25318)
Representative proteomes UniProt
(49009)
RP15
(4468)
RP35
(10259)
RP55
(19771)
RP75
(26449)
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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
(34)
Full
(25318)
Representative proteomes UniProt
(49009)
RP15
(4468)
RP35
(10259)
RP55
(19771)
RP75
(26449)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(34)
Full
(25318)
Representative proteomes UniProt
(49009)
RP15
(4468)
RP35
(10259)
RP55
(19771)
RP75
(26449)
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:B4DPI1
Previous IDs: EF_hand_6;
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 34
Number in full: 25318
Average length of the domain: 49.3 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 12.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.0 13.8
Trusted cut-off 28.0 13.8
Noise cut-off 27.9 13.7
Model length: 54
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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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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_8 domain has been found. There are 266 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
A0A044QUS3 View 3D Structure Click here
A0A044U3K9 View 3D Structure Click here
A0A044UJR4 View 3D Structure Click here
A0A044V6Z2 View 3D Structure Click here
A0A044V6Z3 View 3D Structure Click here
A0A077YUZ7 View 3D Structure Click here
A0A077Z2W8 View 3D Structure Click here
A0A077Z339 View 3D Structure Click here
A0A077ZA03 View 3D Structure Click here
A0A077ZFG6 View 3D Structure Click here
A0A0B4J305 View 3D Structure Click here
A0A0B4KHF1 View 3D Structure Click here
A0A0G2K2W5 View 3D Structure Click here
A0A0G2LAC3 View 3D Structure Click here
A0A0K0E762 View 3D Structure Click here
A0A0K0EKR0 View 3D Structure Click here
A0A0K0ETK8 View 3D Structure Click here
A0A0K0JEI4 View 3D Structure Click here
A0A0N4U451 View 3D Structure Click here
A0A0N4UA38 View 3D Structure Click here
A0A0N4UD99 View 3D Structure Click here
A0A0N4UJB9 View 3D Structure Click here
A0A0N7KEZ6 View 3D Structure Click here
A0A0P0VG45 View 3D Structure Click here
A0A0P0VH48 View 3D Structure Click here
A0A0P0W7C9 View 3D Structure Click here
A0A0P0WI02 View 3D Structure Click here
A0A0R0EIV3 View 3D Structure Click here
A0A0R0EXE0 View 3D Structure Click here
A0A0R0FB11 View 3D Structure Click here
A0A0R0G3H9 View 3D Structure Click here
A0A0R0GP97 View 3D Structure Click here
A0A0R0INJ2 View 3D Structure Click here
A0A0R0JLM2 View 3D Structure Click here
A0A0R3REF3 View 3D Structure Click here
A0A0R4IPX8 View 3D Structure Click here
A0A1D6E6R4 View 3D Structure Click here
A0A1D6FBD8 View 3D Structure Click here
A0A1D6FSL1 View 3D Structure Click here
A0A1D6GU50 View 3D Structure Click here