2  structures 0  species 0  sequences

Clan: Csr_Rsm_clan (CL00106)


Csr-Rsm protein binding clan

The Csr-Rsm clan contains the sRNA families CsrC, RsmB, RsmX, RsmY, RsmZ and TwoAYGGAY. These families are bound by multiple regulatory proteins called CsrA or RsmA. These bind to hairpins containing the sequence motif 'GGA'. Homology between these families has been established in the published literature [1-9].

This clan contains 9 families and the total number of sequence regions in the clan is 1,877.

Literature references

  1. Liu MY, Gui G, Wei B, Preston JF 3rd, Oakford L, Yuksel U, Giedroc DP, Romeo T, J Biol Chem 1997;272:17502-17510.: The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. 97362239
  2. Cui Y, Chatterjee A, Liu Y, Dumenyo CK, Chatterjee AK, J Bacteriol 1995;177:5108-5115.: Identification of a global repressor gene, rsmA, of Erwinia carotovora subsp. carotovora that controls extracellular enzymes, N-(3-oxohexanoyl)-L-homoserine lactone, and pathogenicity in soft-rotting Erwinia spp. 7665490
  3. Weilbacher T, Suzuki K, Dubey AK, Wang X, Gudapaty S, Morozov I, Baker CS, Georgellis D, Babitzke P, Romeo T, Mol Microbiol 2003;48:657-670.: A novel sRNA component of the carbon storage regulatory system of Escherichia coli. 12694612
  4. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S;, Curr Biol 2001;11:941-950.: Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. 11448770
  5. Aarons S, Abbas A, Adams C, Fenton A, O'Gara F, J Bacteriol 2000;182:3913-3919.: A regulatory RNA (PrrB RNA) modulates expression of secondary metabolite genes in Pseudomonas fluorescens F113. 10869066
  6. Valverde C, Heeb S, Keel C, Haas D, Mol Microbiol 2003;50:1361-1379.: RsmY, a small regulatory RNA, is required in concert with RsmZ for GacA-dependent expression of biocontrol traits in Pseudomonas fluorescens CHA0. 14622422
  7. Moll S, Schneider DJ, Stodghill P, Myers CR, Cartinhour SW, Filiatrault MJ, RNA Biol. 2010;7:508-516.: Construction of an rsmX co-variance model and identification of five rsmX non-coding RNAs in Pseudomonas syringae pv. tomato DC3000. 21060253
  8. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR;, Genome Biol. 2010;11:R31.: Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes. 20230605
  9. Schubert M, Lapouge K, Duss O, Oberstrass FC, Jelesarov I, Haas D, Allain FH, Nat Struct Mol Biol. 2007;14:807-813.: Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. 17704818


This clan contains the following 9 member families:

CsrB CsrC McaS PrrB_RsmZ RsmY TwoAYGGAY rsmX Ysr186_sR026_CsrC RsmW

External database links


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.

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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
RsmW (RF02809) 4 (0.2%) View
Ysr186_sR026_CsrC (RF02767) 3 (0.2%) View
rsmX (RF02144) 96 (5.1%) View
TwoAYGGAY (RF01731) 1,296 (69.0%) View
RsmY (RF00195) 71 (3.8%) View
PrrB_RsmZ (RF00166) 102 (5.4%) View
McaS (RF00115) 13 (0.7%) View
CsrC (RF00084) 38 (2.0%) View
CsrB (RF00018) 254 (13.5%) View