PROSITE documentation PDOC01005
CRM domain profile


The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterized members of the family (CRS1, CAF1, CAF2 and YhbY). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multidomain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [1,2].

The CRM domain is a compact α/β domain consisting of a four-stranded β sheet and three α helices with an α-β-α-β-α-β-β topology (see <PDB:1LN4>). The β sheet face is basic, consistent with a role in RNA binding. Proximal to the basic β sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand β1 and helix α2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue [3].

Some proteins known to contain a CRM domain are listed below:

  • Maize CRS1, CAF1 and CAF2 proteins. They contain multiple copies of the domain and are required for the splicing of group II introns in chloroplasts.
  • Escherichia coli protein yhbY. It is bound tightly and specifically to pre- 50S ribosomal subunits, suggesting that it facilitates ribosome maturation.

The profile we developed covers the entire CRM domain.


The CRM domain has also been called CRS1-YhbY domain [2].

Last update:

February 2007 / Pattern removed, profile added and text revised.


Technical section

PROSITE method (with tools and information) covered by this documentation:

CRM, PS51295; CRM domain profile  (MATRIX)


1AuthorsOstheimer G.J. Williams-Carrier R. Belcher S. Osborne E. Gierke J. Barkan A.
TitleGroup II intron splicing factors derived by diversification of an ancient RNA-binding domain.
SourceEMBO J. 22:3919-3929(2003).
PubMed ID12881426

2AuthorsBarkan A. Klipcan L. Ostersetzer O. Kawamura T. Asakura Y. Watkins K.P.
TitleThe CRM domain: an RNA binding module derived from an ancient ribosome-associated protein.
SourceRNA 13:55-64(2007).
PubMed ID17105995

3AuthorsOstheimer G.J. Barkan A. Matthews B.W.
TitleCrystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins.
SourceStructure 10:1593-1601(2002).
PubMed ID12429100

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