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Conserved domains on  [gi|1061385089|ref|NP_001317766|]
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snRNP core protein D1 [Caenorhabditis elegans]

Protein Classification

LSm family protein( domain architecture ID 249)

LSm family protein such as eukaryotic LSm (Sm-like proteins) and bacterial LSm-related Hfq proteins, that have an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, and are involved in processes associated with RNA processing and gene expression regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_like super family cl00259
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 1-59 1.36e-31

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.


The actual alignment was detected with superfamily member cd01724:

Pssm-ID: 469694  Cd Length: 92  Bit Score: 106.16  E-value: 1.36e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1061385089  1 MGVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYIILPDPLALDTLLIDDEPRKK 59
Cdd:cd01724   29 TGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNNIRYIILPDSLNLDTLLVDDTPKAK 87
 
Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 1-59 1.36e-31

Sm protein D1; 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 D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 106.16  E-value: 1.36e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1061385089  1 MGVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYIILPDPLALDTLLIDDEPRKK 59
Cdd:cd01724   29 TGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNNIRYIILPDSLNLDTLLVDDTPKAK 87
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 2-41 2.24e-08

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: 46.35  E-value: 2.24e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 1061385089  2 GVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYIIL 41
Cdd:pfam01423 27 GFDQFMNLVLDDVEETIKDGEVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 2-41 3.72e-07

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 43.25  E-value: 3.72e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1061385089   2 GVDVAMNTHLRAVSMTVKN-KEPVKLDTLSIRGNNIRYIIL 41
Cdd:smart00651 27 GFDQFMNLVLEDVEETVKDgEKKRKLGLVFIRGNNIVYIIL 67
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
2-39 4.15e-03

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 32.85  E-value: 4.15e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1061385089  2 GVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYI 39
Cdd:COG1958   33 GYDQHMNLVLEDAEEIDDGEVVRKLGTVVIRGDNVVFI 70
 
Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 1-59 1.36e-31

Sm protein D1; 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 D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 106.16  E-value: 1.36e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1061385089  1 MGVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYIILPDPLALDTLLIDDEPRKK 59
Cdd:cd01724   29 TGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNNIRYIILPDSLNLDTLLVDDTPKAK 87
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 2-41 2.24e-08

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: 46.35  E-value: 2.24e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 1061385089  2 GVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYIIL 41
Cdd:pfam01423 27 GFDQFMNLVLDDVEETIKDGEVRKLGLVLIRGNNIVLISP 66
Sm_D3 cd01721
Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 7-43 6.49e-08

Sm protein D3; 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 D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits.


Pssm-ID: 212468  Cd Length: 70  Bit Score: 45.20  E-value: 6.49e-08
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 1061385089  7 MNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYIILPD 43
Cdd:cd01721   34 MNCQLKDVTVTARDGKVSKLEQVYIRGSQIRFIILPD 70
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 2-41 3.72e-07

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 43.25  E-value: 3.72e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1061385089   2 GVDVAMNTHLRAVSMTVKN-KEPVKLDTLSIRGNNIRYIIL 41
Cdd:smart00651 27 GFDQFMNLVLEDVEETVKDgEKKRKLGLVFIRGNNIVYIIL 67
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 2-40 1.84e-05

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: 38.77  E-value: 1.84e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1061385089  2 GVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYII 40
Cdd:cd00600   25 AFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIVSIR 63
LSm4 cd01723
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 3-43 1.37e-04

Like-Sm protein 4; 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. 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: 212470 [Multi-domain]  Cd Length: 76  Bit Score: 36.78  E-value: 1.37e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1061385089  3 VDVAMNTHLRAVSMTVKNKEP-VKLDTLSIRGNNIRYIILPD 43
Cdd:cd01723   31 CDNWMNIHLKNVICTSKDGDRfWKMPECYIRGNTIKYLRLPD 72
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
2-39 4.15e-03

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 32.85  E-value: 4.15e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1061385089  2 GVDVAMNTHLRAVSMTVKNKEPVKLDTLSIRGNNIRYI 39
Cdd:COG1958   33 GYDQHMNLVLEDAEEIDDGEVVRKLGTVVIRGDNVVFI 70
 
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.
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