NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|755525072|ref|XP_011240458|]
View 

U6 snRNA-associated Sm-like protein LSm1 isoform X1 [Mus musculus]

Protein Classification

U6 snRNA-associated Sm-like protein LSm1( domain architecture ID 10109601)

U6 snRNA-associated Sm-like protein LSm1 is a component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by promoting decapping and leading to accurate 5'-3' mRNA decay

CATH:  2.30.30.100
Gene Ontology:  GO:0006397|GO:0003723|GO:0008380
PubMed:  11259661|18687770

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LSm1 cd01728
Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring ...
 4-77 2.10e-46

Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


:

Pssm-ID: 212475  Cd Length: 74  Bit Score: 143.04  E-value: 2.10e-46
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755525072   4 MPGTASLIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGEI 77
Cdd:cd01728    1 PPGTASLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLLGEI 74
 
Name Accession Description Interval E-value
LSm1 cd01728
Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring ...
 4-77 2.10e-46

Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212475  Cd Length: 74  Bit Score: 143.04  E-value: 2.10e-46
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755525072   4 MPGTASLIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGEI 77
Cdd:cd01728    1 PPGTASLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLLGEI 74
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 10-76 3.18e-16

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. 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. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 66.76  E-value: 3.18e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 755525072   10 LIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKygdIPRGIFVVRGENVVLLGE 76
Cdd:pfam01423   3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEV---RKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 10-76 6.82e-16

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 65.59  E-value: 6.82e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 755525072    10 LIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKygDIPRGIFVVRGENVVLLGE 76
Cdd:smart00651   3 LKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEK--KRKLGLVFIRGNNIVYIIL 67
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
14-73 5.23e-09

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 48.26  E-value: 5.23e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755525072  14 IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERI--HVGKKYGDIprgifVVRGENVVL 73
Cdd:COG1958   13 LGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDdgEVVRKLGTV-----VIRGDNVVF 69
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 14-72 7.20e-04

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 34.98  E-value: 7.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755525072  14 IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERI--HVGKKYGDIprgifVVRGENVV 72
Cdd:PRK00737  13 LNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQdgEVVRKLGKV-----VIRGDNVV 68
 
Name Accession Description Interval E-value
LSm1 cd01728
Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring ...
 4-77 2.10e-46

Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212475  Cd Length: 74  Bit Score: 143.04  E-value: 2.10e-46
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755525072   4 MPGTASLIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGEI 77
Cdd:cd01728    1 PPGTASLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLLGEI 74
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 10-76 3.18e-16

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. 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. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 66.76  E-value: 3.18e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 755525072   10 LIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKygdIPRGIFVVRGENVVLLGE 76
Cdd:pfam01423   3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEV---RKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 10-76 6.82e-16

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 65.59  E-value: 6.82e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 755525072    10 LIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKygDIPRGIFVVRGENVVLLGE 76
Cdd:smart00651   3 LKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEK--KRKLGLVFIRGNNIVYIIL 67
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 8-77 2.00e-13

Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212474  Cd Length: 91  Bit Score: 60.23  E-value: 2.00e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755525072   8 ASLIED-IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERI-HVGKKYGDIPRGIFVVRGENVVLLGEI 77
Cdd:cd01727    1 SSLLEDyLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVySSDEGVEEVPLGLYLLRGDNVAVIGEV 72
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
14-73 5.23e-09

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 48.26  E-value: 5.23e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755525072  14 IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERI--HVGKKYGDIprgifVVRGENVVL 73
Cdd:COG1958   13 LGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDdgEVVRKLGTV-----VIRGDNVVF 69
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 14-74 9.32e-09

Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure.


Pssm-ID: 212466  Cd Length: 70  Bit Score: 47.51  E-value: 9.32e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755525072  14 IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKygdIPRGIFVVRGENVVLL 74
Cdd:cd01719    9 MDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEK---TPIGMVVIRGNSIIMI 66
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 14-71 2.70e-07

Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212473  Cd Length: 68  Bit Score: 43.66  E-value: 2.70e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755525072  14 IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERI--HVGKKYGDIprgifVVRGENV 71
Cdd:cd01726   10 IGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVdgQLVAKYGDA-----FIRGNNV 64
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 10-73 1.87e-06

archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic 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). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain.


Pssm-ID: 212478  Cd Length: 69  Bit Score: 41.79  E-value: 1.87e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755525072  10 LIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVErihVGKKYGDIPRGIFVVRGENVVL 73
Cdd:cd01731    6 LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEE---IIEGESVRKLGTVLVRGDNVVF 66
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 14-74 2.53e-06

Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.


Pssm-ID: 212462 [Multi-domain]  Cd Length: 63  Bit Score: 41.08  E-value: 2.53e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755525072  14 IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKygdIPRGIFVVRGENVVLL 74
Cdd:cd00600    5 IGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKV---RVLGLVLIRGSNIVSI 62
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 20-72 7.21e-05

Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212464  Cd Length: 80  Bit Score: 37.92  E-value: 7.21e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755525072  20 VLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKYGD------IPR--GIFVVRGENVV 72
Cdd:cd01717   15 VTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKkgeereEKRvlGLVLLRGENVV 75
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 14-80 8.83e-05

Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212476  Cd Length: 89  Bit Score: 37.95  E-value: 8.83e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755525072  14 IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERI---HVGKKYGDIPR--GIFVVRGENVVLlgeIAPV 80
Cdd:cd01729   11 VDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLrdpEDPYKLTDETRslGLVVCRGTSVVL---ISPV 79
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 14-72 7.20e-04

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 34.98  E-value: 7.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755525072  14 IDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERI--HVGKKYGDIprgifVVRGENVV 72
Cdd:PRK00737  13 LNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQdgEVVRKLGKV-----VIRGDNVV 68
LSMD1 cd06168
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 22-49 6.44e-03

LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes.


Pssm-ID: 212486  Cd Length: 73  Bit Score: 32.53  E-value: 6.44e-03
                         10        20
                 ....*....|....*....|....*...
gi 755525072  22 LRDGRTLIGFLRSIDQFANLVLHQTVER 49
Cdd:cd06168   16 LTDGRVLVGTFVCTDKDGNIILSNAEEY 43
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH