NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|37362670|ref|NP_012556|]
View 

U4/U6-U5 snRNP complex subunit LSM8 [Saccharomyces cerevisiae S288C]

Protein Classification

U6 snRNA-associated Sm-like protein LSm8( domain architecture ID 10109598)

U6 snRNA-associated Sm-like protein LSm8 plays role in pre-mRNA splicing as a component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as a component of the precatalytic spliceosome

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 2-85 9.43e-27

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: 94.51  E-value: 9.43e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37362670   2 SATLKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRI------SKEFICKAQLLRGSEIALVGLIDAENDDSL 75
Cdd:cd01727   1 SSLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVyssdegVEEVPLGLYLLRGDNVAVIGEVDEELDGSI 80

                        90
                ....*....|
gi 37362670  76 APIDEKKVPM 85
Cdd:cd01727  81 DLSKIRAEPL 90
 
Name Accession Description Interval E-value
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 2-85 9.43e-27

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: 94.51  E-value: 9.43e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37362670   2 SATLKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRI------SKEFICKAQLLRGSEIALVGLIDAENDDSL 75
Cdd:cd01727   1 SSLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVyssdegVEEVPLGLYLLRGDNVAVIGEVDEELDGSI 80

                        90
                ....*....|
gi 37362670  76 APIDEKKVPM 85
Cdd:cd01727  81 DLSKIRAEPL 90
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 5-66 7.85e-09

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 47.87  E-value: 7.85e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 37362670      5 LKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRIS---KEFICKAQLLRGSEIALVGL 66
Cdd:smart00651   3 LKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKdgeKKRKLGLVFIRGNNIVYIIL 67
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 5-66 6.72e-07

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: 42.88  E-value: 6.72e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 37362670     5 LKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRISKEFICKA--QLLRGSEIALVGL 66
Cdd:pfam01423   3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLglVLIRGNNIVLISP 66
 
Name Accession Description Interval E-value
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 2-85 9.43e-27

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: 94.51  E-value: 9.43e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37362670   2 SATLKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRI------SKEFICKAQLLRGSEIALVGLIDAENDDSL 75
Cdd:cd01727   1 SSLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVyssdegVEEVPLGLYLLRGDNVAVIGEVDEELDGSI 80

                        90
                ....*....|
gi 37362670  76 APIDEKKVPM 85
Cdd:cd01727  81 DLSKIRAEPL 90
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 5-66 7.85e-09

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 47.87  E-value: 7.85e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 37362670      5 LKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRIS---KEFICKAQLLRGSEIALVGL 66
Cdd:smart00651   3 LKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKdgeKKRKLGLVFIRGNNIVYIIL 67
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 5-66 6.72e-07

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: 42.88  E-value: 6.72e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 37362670     5 LKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRISKEFICKA--QLLRGSEIALVGL 66
Cdd:pfam01423   3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLglVLIRGNNIVLISP 66
LSm1 cd01728
Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring ...
 2-67 7.15e-04

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: 35.18  E-value: 7.15e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 37362670   2 SATLKDYLNKRVVIIKVDGECLIASLNGFDKNTNLFITNVFNRI--SKEF---ICKAQLLRGSEIALVGLI 67
Cdd:cd01728   4 TASLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIivGNQYgdiPRGLFIIRGENVVLLGEI 74
 
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