2  structures 0  species 0  sequences

Clan: Hammerhead (CL00010)


Hammerhead clan

The Hammerhead clan contains the RNA families Hammerhead_3 and Hammerhead_1. Homology between these families has been established in the published literature [1,2].

This clan contains 5 families and the total number of sequence regions in the clan is 191,361.

Literature references

  1. Hertel KJ, Pardi A, Uhlenbeck OC, Koizumi M, Ohtsuka E, Uesugi S, Cedergren R, Eckstein F, Gerlach WL, Hodgson R, Nucleic Acids Res. 1992;20:3252.: Numbering system for the hammerhead. 1620624
  2. Ruffner DE, Stormo GD, Uhlenbeck OC, Biochemistry. 1990;29:10695-702.: Sequence requirements of the hammerhead RNA self-cleavage reaction. 1703005


This clan contains the following 5 member families:

Hammerhead_3 Hammerhead_1 Hammerhead_HH9 Hammerhead_II Hammerhead_HH10


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 mapping between the Rfam families in this clan, the corresponding EMBL entries, and the region of the three-dimensional structures that are available for that sequence.

Loading structure mapping...

Secondary structures

This tool allows you to view the secondary structure images of two clan members side-by-side. Choose the family structures using the two drop-down menus below.


The table below shows the number of occurrences of each family throughout the sequence database. In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this family. The rightmost column provides a link to the alignments tab for each family.

Rfam family Num. regions Alignment
Hammerhead_HH10 (RF02277) 33 (0.0%) View
Hammerhead_II (RF02276) 203 (0.1%) View
Hammerhead_HH9 (RF02275) 235 (0.1%) View
Hammerhead_1 (RF00163) 190,650 (99.6%) View
Hammerhead_3 (RF00008) 240 (0.1%) View