SMART: Sm domain annotation

Sm snRNP Sm proteins

SMART accession number:	SM00651
Description:	small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Interpro abstract (IPR001163):	This domain is found in Lsm (like-Sm) proteins, which have a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [ (PUBMED:10801455) (PUBMED:12438310) ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) [ (PUBMED:15130578) ]. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker [ (PUBMED:7744013) ]. Other snRNPs, such as U7 snRNP, can contain different Lsm proteins. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus, suggesting a more general role for Lsm proteins. Archaeal Lsm proteins have been shown to bind to small RNAs and are probably involved in many cellular processes [ (PUBMED:20826804) ]. Archaeal Lsm proteins are likely to represent the ancestral Lsm domain [ (PUBMED:11399068) ].
Family alignment:	View or

There are 20551 Sm domains in 20519 proteins in SMART's nrdb database.

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Evolution (species in which this domain is found)
Taxonomic distribution of proteins containing Sm domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Sm domain is also avaliable.

Click on the protein counts, or double click on taxonomic names to display all proteins containing Sm domain in the selected taxonomic class.
Cellular role (predicted cellular role)
Binding / catalysis: protein binding
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Kambach C et al.
- Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.
- Cell. 1999; 96: 375-87
- Display abstract
- The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F, and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs (snRNAs). These proteins share a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Crystal structures of two Sm protein complexes, D3B and D1D2, show that these proteins have a common fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta sheet, and the D1D2 and D3B dimers superpose closely in their core regions, including the dimer interfaces. The crystal structures suggest that the seven Sm proteins could form a closed ring and the snRNAs may be bound in the positively charged central hole.
- Hermann H et al.
- snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions.
- EMBO J. 1995; 14: 2076-88
- Display abstract
- The spliceosomal small nuclear ribonucleoproteins (snRNPs) U1, U2, U4/U6 and U5 share eight proteins B', B, D1, D2, D3, E, F and G which form the structural core of the snRNPs. This class of common proteins plays an essential role in the biogenesis of the snRNPs. In addition, these proteins represent the major targets for the so-called anti-Sm auto-antibodies which are diagnostic for systemic lupus erythematosus (SLE). We have characterized the proteins F and G from HeLa cells by cDNA cloning, and, thus, all human Sm protein sequences are now available for comparison. Similar to the D, B/B' and E proteins, the F and G proteins do not possess any of the known RNA binding motifs, suggesting that other types of RNA-protein interactions occur in the snRNP core. Strikingly, the eight human Sm proteins possess mutual homology in two regions, 32 and 14 amino acids long, that we term Sm motifs 1 and 2. The Sm motifs are evolutionarily highly conserved in all of the putative homologues of the human Sm proteins identified in the data base. These results suggest that the Sm proteins may have arisen from a single common ancestor. Several hypothetical proteins, mainly of plant origin, that clearly contain the conserved Sm motifs but exhibit only comparatively low overall homology to one of the human Sm proteins, were identified in the data base. This suggests that the Sm motifs may also be shared by non-spliceosomal proteins. Further, we provide experimental evidence that the Sm motifs are involved, at least in part, in Sm protein-protein interactions. Specifically, we show by co-immunoprecipitation analyses of in vitro translated B' and D3 that the Sm motifs are essential for complex formation between B' and D3. Our finding that the Sm proteins share conserved sequence motifs may help to explain the frequent occurrence in patient sera of anti-Sm antibodies that cross-react with multiple Sm proteins and may ultimately further our understanding of how the snRNPs act as auto-antigens and immunogens in SLE.
Structure (3D structures containing this domain)

3D Structures of Sm domains in PDB

PDB code	Main view	Title
1b34		CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CORE DOMAIN
1d3b		CRYSTAL STRUCTURE OF THE D3B SUBCOMPLEX OF THE HUMAN CORE SNRNP DOMAIN AT 2.0A RESOLUTION
1h64		Crystal structure of the Sm-related protein of P. abyssi : the biological unit is a heptamer
1i4k		CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS AT 2.5A RESOLUTION
1i5l		CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA
1i81		CRYSTAL STRUCTURE OF A HEPTAMERIC LSM PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
1i8f		THE CRYSTAL STRUCTURE OF A HEPTAMERIC ARCHAEAL SM PROTEIN: IMPLICATIONS FOR THE EUKARYOTIC SNRNP CORE
1jbm		Heptameric crystal structure of Mth649, an Sm-like archaeal protein from Methanobacterium thermautotrophicum
1jri		The Crystal Structure of an Sm-like Archaeal Protein with Two Heptamers in the Asymmetric Unit.
1ljo		CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION
1lnx		Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)
1loj		Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)
1m5q		Crystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum
1m8v		Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer
1mgq		CRYSTAL STRUCTURE OF A HEPTAMERIC SM-LIKE PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
1n9r		Crystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122
1n9s		Crystal structure of yeast SmF in spacegroup P43212
1th7		Crystal Structure of an Archaeal Sm Protein from Sulfolobus solfataricus
3bw1		Crystal structure of homomeric yeast Lsm3 exhibiting novel octameric ring organisation
3cw1		Crystal Structure of Human Spliceosomal U1 snRNP
3jb9		3JB9
3jcm		3JCM
3jcr		3JCR
3pgg		Crystal structure of cryptosporidium parvum u6 snrna-associated sm-like protein lsm5
3pgw		Crystal structure of human U1 snRNP
3s6n		Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1/D2/F/E/G from Human
3swn		Structure of the LSm657 Complex: An Assembly Intermediate of the LSm1 7 and LSm2 8 Rings
4c8q		Crystal structure of the yeast Lsm1-7-Pat1 complex
4c92		Crystal structure of the yeast Lsm1-7 complex
4emg		Crystal structure of SpLsm3
4emh		Crystal structure of SpLsm4
4emk		Crystal structure of SpLsm5/6/7
4f7u		Macromolecular Machine 6
4m75		Crystal structure of Lsm1-7 complex
4m77		Crystal structure of Lsm2-8 complex, space group I212121
4m78		Crystal structure of Lsm2-8 complex, space group P21
4m7a		Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA
4m7d		Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU
4n0a		Crystal structure of Lsm2-3-Pat1C complex from Saccharomyces cerevisiae
4pjo		4PJO
4v98		4V98
4wzj		4WZJ
4xq3		4XQ3
5gam		5GAM
5gan		5GAN
5gao		5GAO
5gm6		5GM6
5gmk		5GMK
5lj3		5LJ3
5lj5		5LJ5
5lqw		5LQW

Links (links to other resources describing this domain)
PFAM Sm
INTERPRO IPR001163

PFAM	Sm
INTERPRO	IPR001163

Sm

Taxonomic distribution of proteins containing Sm domain.

3D Structures of Sm domains in PDB