2  structures 39  species 325  sequences

Family: Hammerhead_3 (RF00008)

Description: Hammerhead ribozyme (type III)



This family is a member of clan (CL00010), which contains the following 5 members:

Hammerhead_1 Hammerhead_3 Hammerhead_HH10 Hammerhead_HH9 Hammerhead_II

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Hammerhead ribozyme. More...

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



There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.


Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Alignment format:


Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

Secondary structure

This section shows a variety of different secondary structure representations for this family. More...

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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...

Tree controls


The tree shows the occurrence of this RNA across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

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


For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the Hammerhead_3 family has been found.

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Motif matches

There are 1 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Motif Accession Motif Description Number of Hits Fraction of Hits Sum of Bits Image
7 RM00008 GNRA tetraloop 8 0.098 81.7 Match Image


This section shows the database cross-references that we have for this Rfam family.

Literature references

  1. Pley HW, Flaherty KM, McKay DB Nature 1994;372:68-74. Three-dimensional structure of a hammerhead ribozyme. PUBMED:7969422

  2. Murray JB, Terwey DP, Maloney L, Karpeisky A, Usman N, Beigelman L, Scott WG Cell 1998;92:665-673. The structural basis of hammerhead ribozyme self-cleavage. PUBMED:9506521

  3. Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R Genome Res 2000;10:1011-1019. Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank. PUBMED:10899150

  4. Chi YI, Martick M, Lares M, Kim R, Scott WG, Kim SH PLoS Biol. 2008;6:e234. Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PUBMED:18834200

  5. Mir A, Chen J, Robinson K, Lendy E, Goodman J, Neau D, Golden BL Biochemistry. 2015;54:6369-6381. Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction. PUBMED:26398724

  6. Mir A, Golden BL Biochemistry. 2016;55:633-636. Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue. PUBMED:26551631

External database links

Curation and family details

This section shows the detailed information about the Rfam family. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.


Seed source Bateman A
Structure source Published; PMID:7969422
Type Gene; ribozyme;
Author Bateman AORCID logo, Ontiveros-Palacios NORCID logo
Alignment details
Alignment Number of
full 240
seed 85

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB
Gathering cutoff 41.8
Trusted cutoff 41.8
Noise cutoff 41.7
Covariance model Download